{"filter":{"age_category":"elderly"},"n_projects":402,"projects":[{"accession":"PRJEB11419","age_categories":{"adolescent":93,"adult":4213,"child":99,"elderly":790,"infant":79,"neonate":1,"unknown":2078},"countries":{"AE":2,"AT":3,"AU":25,"BE":9,"BR":3,"CA":45,"CH":3,"CN":2,"CR":1,"CZ":1,"DE":15,"ES":481,"FM":1,"FR":10,"GB":864,"GE":1,"HK":2,"HR":2,"IE":6,"IT":5,"JE":1,"JP":528,"LV":2,"MD":1,"MN":2,"MX":547,"MY":1,"NL":4,"NO":5,"NZ":1,"PH":86,"PR":1,"RS":3,"SE":1,"TH":6,"US":3501,"ZA":2},"first_public_year":"2015","gbp_per_sample_median":0.12,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":419,"cardiometabolic_other":110,"crohns_disease":7,"gi_infection_or_diarrhoea":26,"healthy_control":241,"ibd_unspecified":46,"ibs":560,"kidney_disease":41,"liver_disease":40,"neurological_psychiatric":379,"other_cancer":218,"other_disease":925,"pregnancy_postpartum":1,"type2_diabetes":91,"ulcerative_colitis":14},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":7353,"papers":[{"doi":"10.1016/j.csbj.2020.08.028","pmcid":"PMC7516180","pmid":"33005310","title":"Multi-population cohort meta-analysis of human intestinal microbiota in early life reveals the existence of infant community state types (ICSTs)."},{"doi":"10.3389/fmolb.2022.949563","pmcid":"PMC9403272","pmid":"36032669","title":"Genomic reconstruction of short-chain fatty acid production by the human gut microbiota."},{"doi":"10.12938/bmfh.2023-043","pmcid":"PMC10767325","pmid":"38188664","title":"Heterogeneity of gut microbiome compositions in the third decade of life in Japanese women: insights from a comparative analysis."},{"doi":"10.1128/msystems.00929-24","pmcid":"PMC11494892","pmid":"39287373","title":"Exploring the vitamin biosynthesis landscape of the human gut microbiota."},{"doi":"10.1128/msystems.00031-18","pmcid":"PMC5954204","pmid":"29795809","title":"American Gut: an Open Platform for Citizen Science Microbiome Research."}],"sample_intervention_arms":{},"sex":{"female":3603,"male":2157},"title":"American Gut Project","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB11419","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB11419_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB11419.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB11419.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB11419.csv.gz"}},{"accession":"PRJNA1347413","age_categories":{"elderly":4711},"countries":{"US":4711},"first_public_year":"2025","gbp_per_sample_median":2.98,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":4711,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Metagenomic data from the ASPREE-XT study","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1347413","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1347413_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1347413.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1347413.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1347413.csv.gz"}},{"accession":"PRJEB108450","age_categories":{"adolescent":291,"adult":2038,"child":1362,"elderly":16,"infant":27,"neonate":3,"unknown":365},"countries":{"CA":3738,"US":364},"first_public_year":"2026","gbp_per_sample_median":2.49,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":4102,"papers":[],"sample_intervention_arms":{},"sex":{"female":1930,"male":1701},"title":"Exploring Fecal Microbiome in the CHILD COVID-19 sub-project","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB108450","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB108450_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB108450.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB108450.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB108450.csv.gz"}},{"accession":"PRJEB32762","age_categories":{"adult":3419,"elderly":342,"infant":1,"neonate":3},"countries":{"AR":1126,"ES":119,"GB":732,"US":1764},"first_public_year":"2019","gbp_per_sample_median":0.18,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"allergy_or_atopy":180,"healthy_control":1157,"neurological_psychiatric":1779,"other_disease":4,"type2_diabetes":16},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":3765,"papers":[{"doi":"10.1177/1352458520924594","pmcid":"PMC7968892","pmid":"33115343","title":"Household paired design reduces variance and increases power in multi-city gut microbiome study in multiple sclerosis."},{"doi":"10.1016/j.cell.2022.08.021","pmcid":"PMC10143502","pmid":"36113426","title":"Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course."},{"doi":"10.1128/spectrum.02183-24","pmcid":"PMC11974365","pmid":"39998261","title":"Reevaluation of the gastrointestinal methanogenic archaeome in multiple sclerosis and its association with treatment."},{"doi":"10.1038/s41564-025-02225-y","pmcid":"PMC13244660","pmid":"41507585","title":"Gut microbial ethanol metabolism contributes to auto-brewery syndrome in an observational cohort."},{"doi":"10.1128/msystems.00416-26","pmcid":"PMC13483414","pmid":"42484622","title":"Integrative multicohort analysis reveals consistent sex differences in gut microbiota of multiple sclerosis patients."}],"sample_intervention_arms":{},"sex":{"female":1820,"male":1647},"title":"iMSMS Baranzini data","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB32762","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB32762_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB32762.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB32762.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB32762.csv.gz"}},{"accession":"PRJEB46788","age_categories":{"adolescent":46,"adult":1720,"elderly":13,"infant":252,"neonate":18,"unknown":701},"countries":{"DE":472,"GA":659,"KR":92,"VN":685,"ZA":173},"first_public_year":"2022","gbp_per_sample_median":0.31,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":1763},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":2750,"papers":[{"doi":"10.1128/msystems.01294-23","pmcid":"PMC11019788","pmid":"38441032","title":"Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation."},{"doi":"10.1128/msystems.00929-24","pmcid":"PMC11494892","pmid":"39287373","title":"Exploring the vitamin biosynthesis landscape of the human gut microbiota."},{"doi":"10.1080/19490976.2025.2587966","pmcid":"PMC12688249","pmid":"41358671","title":"Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa."}],"sample_intervention_arms":{},"sex":{"female":868,"male":36},"title":"Codiversification of gut microbiota with humans","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB46788","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB46788_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB46788.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB46788.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB46788.csv.gz"}},{"accession":"PRJEB110772","age_categories":{"elderly":2398},"countries":{"SE":2398},"first_public_year":"2026","gbp_per_sample_median":7.48,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":2398,"papers":[{"doi":"10.1038/s41467-026-75176-5","pmcid":"PMC13346421","pmid":"42420265","title":"Gut microbiota associates with frailty in older women."}],"sample_intervention_arms":{},"sex":{"female":2398},"title":"Gut microbiota associates with frailty in older women","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB110772","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB110772_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB110772.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB110772.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB110772.csv.gz"}},{"accession":"PRJEB45799","age_categories":{"adolescent":222,"adult":1441,"child":481,"elderly":11,"infant":200,"neonate":18,"unknown":21},"countries":{"AR":26,"CN":27,"CO":24,"GW":340,"IT":48,"US":1260},"first_public_year":"2022","gbp_per_sample_median":8.77,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":424,"preterm_nicu":47},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":2394,"papers":[{"doi":"10.1038/s41586-022-05620-1","pmcid":"PMC9892008","pmid":"36653448","title":"The person-to-person transmission landscape of the gut and oral microbiomes."},{"doi":"10.1128/msystems.00305-26","pmcid":"PMC13288982","pmid":"42171373","title":"Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis."}],"sample_intervention_arms":{},"sex":{"female":1229,"male":1152},"title":"The person-to-person transmission landscape of the gut and oral microbiomes","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB45799","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB45799_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB45799.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB45799.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB45799.csv.gz"}},{"accession":"PRJNA398089","age_categories":{"adolescent":650,"adult":742,"child":315,"elderly":61,"unknown":273},"countries":{"US":2041},"first_public_year":"2017","gbp_per_sample_median":1.46,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":1,"healthy_control":544,"ibd_or_gi_disease":1496},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":2041,"papers":[{"doi":"10.3389/fmolb.2022.949563","pmcid":"PMC9403272","pmid":"36032669","title":"Genomic reconstruction of short-chain fatty acid production by the human gut microbiota."},{"doi":"10.1038/s41564-023-01549-x","pmcid":"PMC10769871","pmid":"38172624","title":"BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen."},{"doi":"10.1128/msystems.00305-26","pmcid":"PMC13288982","pmid":"42171373","title":"Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis."},{"doi":"10.1101/2024.02.02.578701","pmcid":null,"pmid":null,"title":"Metagenomic estimation of dietary intake from human stool"}],"sample_intervention_arms":{},"sex":{"female":989,"male":1052},"title":"Longitudinal Multi’omics of the Human Microbiome in Inflammatory Bowel Disease","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA398089","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA398089_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA398089.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA398089.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA398089.csv.gz"}},{"accession":"PRJNA1157371","age_categories":{"elderly":1820},"countries":{"BF":384,"GH":235,"KE":239,"ZA":962},"first_public_year":"2025","gbp_per_sample_median":4.56,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":1820,"papers":[{"doi":"10.1128/msystems.01800-25","pmcid":"PMC13483426","pmid":"42517623","title":"Participant engagement and feedback in microbiome projects: a case of AWI-Gen 2."}],"sample_intervention_arms":{},"sex":{},"title":"AWI-Gen 2 Microbiome Project","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1157371","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1157371_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1157371.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1157371.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1157371.csv.gz"}},{"accession":"PRJNA1195215","age_categories":{"adult":38,"elderly":4,"unknown":1668},"countries":{"KR":1710},"first_public_year":"2025","gbp_per_sample_median":6.11,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":895,"healthy_control":489},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":1710,"papers":[{"doi":"10.1128/msystems.00954-25","pmcid":"PMC12710354","pmid":"41196050","title":"Metagenome-assembled genomes reveal microbial signatures and metabolic pathways linked to coronary artery disease."},{"doi":"10.1128/spectrum.00971-25","pmcid":"PMC13055376","pmid":"41778788","title":"Gut microbial community structure, metabolic signature, and resistome in dyslipidemia: implications for cardiovascular disease management."}],"sample_intervention_arms":{},"sex":{"female":453,"male":931},"title":"Human gut metagenome","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1195215","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1195215_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1195215.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1195215.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1195215.csv.gz"}},{"accession":"PRJNA1235197","age_categories":{"adult":936,"elderly":707,"unknown":8},"countries":{"US":1651},"first_public_year":"2025","gbp_per_sample_median":3.14,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":68,"healthy_control":287,"other_cancer":1294,"other_disease":2},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":1651,"papers":[{"doi":"10.1016/j.cell.2026.09.009","pmcid":null,"pmid":"42810338","title":"Microbiome signatures linked to cancer and treatment adverse events in a real-world cohort."}],"sample_intervention_arms":{},"sex":{"female":905,"male":746},"title":"Microbiome signatures linked to cancer and treatment adverse events in a real-world cohort","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1235197","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1235197_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1235197.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1235197.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1235197.csv.gz"}},{"accession":"PRJEB28097","age_categories":{"adult":1602,"elderly":11},"countries":{},"first_public_year":"2018","gbp_per_sample_median":1.18,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"healthy_control":1613},"intervention_design":"randomized_controlled_trial","intervention_detail":"11-strain probiotic vs placebo; post-antibiotic probiotic vs autologous FMT","interventions":["antibiotic","fmt","probiotic"],"n_samples":1613,"papers":[{"doi":"10.1186/s40168-021-01015-y","pmcid":"PMC7931531","pmid":"33658077","title":"Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing."},{"doi":"10.1128/mbio.03456-22","pmcid":"PMC9972980","pmid":"36719226","title":"Strains Colonizing Different Intestinal Sites within an Individual Are Derived from a Single Founder Population."},{"doi":"10.1038/s41564-021-00920-0","pmcid":"PMC8318886","pmid":"34226711","title":"Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner."},{"doi":"10.1038/s42003-021-02724-8","pmcid":"PMC8523657","pmid":"34663913","title":"Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota."},{"doi":"10.3390/life11111246","pmcid":"PMC8620312","pmid":"34833122","title":"Lacticaseibacillus paracasei: Occurrence in the Human Gut Microbiota and K-Mer-Based Assessment of Intraspecies Diversity."}],"sample_intervention_arms":{"antibiotic":555,"bowel_preparation":20,"fmt":60,"no_intervention":579,"placebo":47,"probiotic":240},"sex":{"female":687,"male":926},"title":"(1) Personalized microbiome and host features resist gut mucosal colonization by empiric probiotics (2) Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB28097","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB28097_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB28097.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB28097.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB28097.csv.gz"}},{"accession":"PRJEB83236","age_categories":{"adult":283,"child":83,"elderly":10,"infant":578,"neonate":655},"countries":{"BD":1609},"first_public_year":"2025","gbp_per_sample_median":0.4,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":1609,"papers":[{"doi":"10.1128/msphere.00314-25","pmcid":"PMC12570478","pmid":"40951971","title":"Abundance of &lt;i&gt;Bifidobacterium&lt;/i&gt; species in the infant gut microbiota and associations with maternal-infant characteristics in Dhaka, Bangladesh."},{"doi":"10.1128/msphere.00314-25","pmcid":"PMC12570478","pmid":"40951971","title":"Abundance of &lt;i&gt;Bifidobacterium&lt;/i&gt; species in the infant gut microbiota and associations with maternal-infant characteristics in Dhaka, Bangladesh."},{"doi":"10.1016/j.chom.2025.11.002","pmcid":"PMC12875530","pmid":"41308639","title":"Environmental and maternal imprints on infant gut metabolic development."}],"sample_intervention_arms":{},"sex":{"female":1180,"male":429},"title":"SEPSIS Human Microbiome Study","trial_population_condition":"pregnancy_postpartum","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB83236","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB83236_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB83236.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB83236.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB83236.csv.gz"}},{"accession":"PRJNA699281","age_categories":{"elderly":1569},"countries":{"US":1569},"first_public_year":"2022","gbp_per_sample_median":1.24,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":1569,"papers":[{"doi":"10.1038/s43587-022-00287-9","pmcid":"PMC9667708","pmid":"36398033","title":"Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults."}],"sample_intervention_arms":{},"sex":{},"title":"The microbiome of aging: instability, heterogeneity, and pathogenicity reservoirs in the skin, oral, and gut microbiome of older adults","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA699281","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA699281_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA699281.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA699281.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA699281.csv.gz"}},{"accession":"PRJNA643353","age_categories":{"adult":1156,"elderly":36},"countries":{"CN":1192},"first_public_year":"2021","gbp_per_sample_median":10.73,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"type2_diabetes":1192},"intervention_design":"randomized_controlled_trial","intervention_detail":"Berberine and/or probiotics vs placebo, with gentamycin run-in pretreatment","interventions":["antibiotic","drug_therapy","probiotic"],"n_samples":1192,"papers":[{"doi":"10.1038/s41467-020-18414-8","pmcid":"PMC7538905","pmid":"33024120","title":"Gut microbiome-related effects of berberine and probiotics on type 2 diabetes (the PREMOTE study)."},{"doi":"10.1080/19490976.2021.2003176","pmcid":"PMC8726654","pmid":"34923903","title":"Combined berberine and probiotic treatment as an effective regimen for improving postprandial hyperlipidemia in type 2 diabetes patients: a double blinded placebo controlled randomized study."},{"doi":"10.1038/s41564-021-00920-0","pmcid":"PMC8318886","pmid":"34226711","title":"Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner."},{"doi":"10.1002/imt2.179","pmcid":"PMC11170963","pmid":"38882498","title":"Deciphering unique and shared interactions between the human gut microbiota and oral antidiabetic drugs."},{"doi":"10.1016/j.heliyon.2024.e37986","pmcid":"PMC11438002","pmid":"39347390","title":"Clinical significance of the genetically variable landscape of the gut microbiome in patients with gestational diabetes mellitus patients."}],"sample_intervention_arms":{"antibiotic":403,"drug_therapy":85,"no_intervention":405,"other_intervention":104,"placebo":97,"probiotic":98},"sex":{"female":146,"male":216},"title":"The gut microbiome related effect of Berberine and probiotics in treating Type 2 Diabetes","trial_population_condition":"type2_diabetes","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA643353","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA643353_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA643353.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA643353.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA643353.csv.gz"}},{"accession":"PRJNA1305379","age_categories":{"adult":509,"elderly":655},"countries":{"IT":1164},"first_public_year":"2026","gbp_per_sample_median":7.19,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":1164,"papers":[{"doi":"10.1038/s41416-026-03495-x","pmcid":null,"pmid":"42286232","title":"Fecal immunochemical tests from population-based colorectal cancer screening programs support prospective microbiome cohorts."}],"sample_intervention_arms":{},"sex":{"female":534,"male":630},"title":"Fecal immunochemical tests from population-based colorectal cancer screening programs support prospective microbiome cohorts","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1305379","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1305379_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1305379.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1305379.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1305379.csv.gz"}},{"accession":"PRJNA1450325","age_categories":{"adolescent":7,"adult":1050,"elderly":67},"countries":{"GH":427,"NG":697},"first_public_year":"2026","gbp_per_sample_median":9.43,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":417,"other_disease":65},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":1124,"papers":[],"sample_intervention_arms":{},"sex":{"female":566,"male":317},"title":"Metagenomes of fermented foods and gut microbiome from non Western populations","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1450325","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1450325_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1450325.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1450325.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1450325.csv.gz"}},{"accession":"PRJNA1370810","age_categories":{"elderly":1032},"countries":{"IE":1032},"first_public_year":"2026","gbp_per_sample_median":8.85,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"healthy_control":1032},"intervention_design":"single_arm_before_after","intervention_detail":"Colon-targeted (delayed-release) vitamin B2/riboflavin supplement","interventions":["dietary_supplement"],"n_samples":1032,"papers":[{"doi":"10.64898/2026.04.01.26349391","pmcid":null,"pmid":null,"title":"Colon-delivered vitamin B2 as a functional modulator of the human gut microbiome"}],"sample_intervention_arms":{"dietary_supplement":516,"placebo":172},"sex":{},"title":"Colon-delivered vitamin B2 as a functional modulator of the human gut microbiome","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1370810","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1370810_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1370810.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1370810.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1370810.csv.gz"}},{"accession":"PRJNA987980","age_categories":{"adult":322,"elderly":240,"unknown":467},"countries":{"AT":467,"DE":129,"FR":433},"first_public_year":"2024","gbp_per_sample_median":2.99,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":115,"healthy_control":186,"other_cancer":261},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":1029,"papers":[{"doi":"10.1099/mgen.0.001330","pmcid":"PMC11728698","pmid":"39804694","title":"Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines."}],"sample_intervention_arms":{},"sex":{"female":223,"male":339},"title":"Microbiome Pipeline Benchmarking","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA987980","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA987980_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA987980.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA987980.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA987980.csv.gz"}},{"accession":"PRJEB38742","age_categories":{"adult":260,"elderly":185,"unknown":573},"countries":{"DE":269,"DK":294,"FR":455},"first_public_year":"2020","gbp_per_sample_median":2.95,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":603,"healthy_control":1,"obesity":157,"type2_diabetes":213},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":1018,"papers":[{"doi":"10.1038/s41467-020-19589-w","pmcid":"PMC7676231","pmid":"33208748","title":"Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology."},{"doi":"10.1136/gutjnl-2021-325753","pmcid":"PMC9664128","pmid":"35017197","title":"Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism."},{"doi":"10.1038/s41591-022-01688-4","pmcid":"PMC8863577","pmid":"35177860","title":"Microbiome and metabolome features of the cardiometabolic disease spectrum."},{"doi":"10.1038/s41467-023-39824-4","pmcid":"PMC10511707","pmid":"37730687","title":"Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide."},{"doi":"10.1038/s41591-024-03067-7","pmcid":"PMC11620793","pmid":"38918632","title":"Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes."}],"sample_intervention_arms":{},"sex":{"female":99,"male":368},"title":"Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology","trial_population_condition":"type2_diabetes","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB38742","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB38742_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB38742.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB38742.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB38742.csv.gz"}},{"accession":"PRJNA698223","age_categories":{"adult":989,"elderly":4},"countries":{"PE":384},"first_public_year":"2022","gbp_per_sample_median":1.36,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"gi_infection_or_diarrhoea":138,"healthy_control":191,"other_disease":107},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":993,"papers":[{"doi":"10.1038/s41467-022-34862-w","pmcid":"PMC9722912","pmid":"36470885","title":"Impact of international travel and diarrhea on gut microbiome and resistome dynamics."}],"sample_intervention_arms":{},"sex":{"female":446,"male":264},"title":"TD Cusco travelers study","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA698223","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA698223_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA698223.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA698223.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA698223.csv.gz"}},{"accession":"PRJEB11532","age_categories":{"adult":939,"elderly":30},"countries":{"IL":900},"first_public_year":"2015","gbp_per_sample_median":2.74,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":900},"intervention_design":"randomized_controlled_trial","intervention_detail":"Personalized diet intervention based on predicted glycemic response algorithm","interventions":["diet_intervention"],"n_samples":969,"papers":[{"doi":"10.1016/j.cell.2015.11.001","pmcid":null,"pmid":"26590418","title":"Personalized Nutrition by Prediction of Glycemic Responses."},{"doi":"10.7717/peerj.4303","pmcid":"PMC5807925","pmid":"29441232","title":"Detection of stable community structures within gut microbiota co-occurrence networks from different human populations."},{"doi":"10.1038/s41588-020-00763-1","pmcid":"PMC8515199","pmid":"33462485","title":"Large-scale association analyses identify host factors influencing human gut microbiome composition."},{"doi":"10.1038/s41591-022-01686-6","pmcid":"PMC12365913","pmid":"35177859","title":"Metabolomic and microbiome profiling reveals personalized risk factors for coronary artery disease."},{"doi":"10.1371/journal.pone.0265756","pmcid":"PMC8947124","pmid":"35324954","title":"An atlas of robust microbiome associations with phenotypic traits based on large-scale cohorts from two continents."}],"sample_intervention_arms":{},"sex":{"female":547,"male":353},"title":"Towards personalized nutrition by prediction of glycemic responses","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB11532","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB11532_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB11532.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB11532.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB11532.csv.gz"}},{"accession":"PRJNA993675","age_categories":{"adult":898,"elderly":62},"countries":{"US":960},"first_public_year":"2024","gbp_per_sample_median":2.7,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":471,"healthy_control":160,"ibd_unspecified":15,"ulcerative_colitis":314},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":960,"papers":[{"doi":"10.1016/j.chom.2024.05.022","pmcid":"PMC11239293","pmid":"38917808","title":"Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases."}],"sample_intervention_arms":{},"sex":{"female":540,"male":420},"title":"Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA993675","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA993675_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA993675.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA993675.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA993675.csv.gz"}},{"accession":"PRJEB64515","age_categories":{"adolescent":6,"adult":351,"child":1,"elderly":292,"unknown":296},"countries":{"PL":946},"first_public_year":"2023","gbp_per_sample_median":0.09,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":6,"other_cancer":64,"other_disease":206,"other_infection":574,"type1_diabetes":1,"type2_diabetes":95},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":946,"papers":[{"doi":"10.3389/fmicb.2024.1342749","pmcid":"PMC11219902","pmid":"38962119","title":"Gut microbiome dynamics and predictive value in hospitalized COVID-19 patients: a comparative analysis of shallow and deep shotgun sequencing."},{"doi":"10.1093/gigascience/giaf015","pmcid":"PMC11927397","pmid":"40117176","title":"Healthy microbiome-moving towards functional interpretation."}],"sample_intervention_arms":{},"sex":{"female":238,"male":412},"title":"Gut Microbiome Dynamics and Predictive Value in Hospitalized COVID-19 Patients: A Comparative Analysis of Shallow and Deep Shotgun Sequencing","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB64515","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB64515_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB64515.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB64515.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB64515.csv.gz"}},{"accession":"PRJNA1167328","age_categories":{"adult":651,"elderly":293},"countries":{"US":944},"first_public_year":"2026","gbp_per_sample_median":2.56,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_infection":480},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":944,"papers":[{"doi":"10.1080/19490976.2026.2718581","pmcid":"PMC13502034","pmid":"42615987","title":"Gut microbiome signatures during acute infection are associated with long COVID."}],"sample_intervention_arms":{},"sex":{"female":587,"male":357},"title":"Gut Microbiome Signatures Predict Long COVID","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1167328","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1167328_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1167328.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1167328.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1167328.csv.gz"}},{"accession":"PRJEB104496","age_categories":{"elderly":942},"countries":{"ES":942},"first_public_year":"2026","gbp_per_sample_median":2.53,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":942,"papers":[{"doi":"10.1080/19490976.2026.2701446","pmcid":"PMC13378717","pmid":"42458961","title":"Ecological restructuring of the nonbacterial fecal microbiome in obesity across human cohorts."}],"sample_intervention_arms":{},"sex":{},"title":"The Ageing Imageomics Study","trial_population_condition":"obesity","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB104496","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB104496_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB104496.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB104496.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB104496.csv.gz"}},{"accession":"PRJNA850529","age_categories":{"adolescent":61,"adult":829,"elderly":33},"countries":{"PL":923},"first_public_year":"2023","gbp_per_sample_median":2.34,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"allergy_or_atopy":129,"autoimmune_inflammatory":40,"cardiometabolic_other":66,"ibd_unspecified":4,"ibs":21,"kidney_disease":3,"liver_disease":1,"pregnancy_postpartum":6},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":923,"papers":[{"doi":"10.1128/msystems.00986-22","pmcid":"PMC10134842","pmid":"36786595","title":"Host Factors Associated with Gut Mycobiome Structure."},{"doi":"10.1158/2326-6066.cir-23-0592","pmcid":"PMC10985481","pmid":"38315788","title":"Gut Mycobiota Dysbiosis Is Associated with Melanoma and Response to Anti-PD-1 Therapy."}],"sample_intervention_arms":{},"sex":{"female":438,"male":484},"title":"Host factors associated with gut mycobiome structure","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA850529","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA850529_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA850529.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA850529.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA850529.csv.gz"}},{"accession":"PRJNA1237248","age_categories":{"adult":397,"elderly":500},"countries":{"US":897},"first_public_year":"2025","gbp_per_sample_median":6.15,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":435,"colorectal_cancer":14,"healthy_control":448},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":897,"papers":[{"doi":"10.1038/s41591-025-03693-9","pmcid":"PMC12283368","pmid":"40461820","title":"Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer."}],"sample_intervention_arms":{},"sex":{"female":897},"title":"MicroN Study Prescient data","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1237248","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1237248_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1237248.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1237248.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1237248.csv.gz"}},{"accession":"PRJEB115441","age_categories":{"adult":782,"elderly":98},"countries":{"SG":880},"first_public_year":"2026","gbp_per_sample_median":2.53,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":880,"papers":[{"doi":"10.64898/2026.08.12.26358109","pmcid":null,"pmid":null,"title":"Population-scale analysis reveals limited and non-generalizable associations between the gut microbiome and obesity in Asian adults"}],"sample_intervention_arms":{},"sex":{"female":541,"male":329},"title":"Shotgun gut metagenomes for multi-ethnic Asian adults to investigate obesity, diet, and microbiome relationships (HELIOS Singapore cohort)","trial_population_condition":"obesity","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB115441","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB115441_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB115441.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB115441.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB115441.csv.gz"}},{"accession":"PRJEB114255","age_categories":{"adolescent":3,"adult":785,"elderly":56},"countries":{"FR":844},"first_public_year":"2026","gbp_per_sample_median":16.43,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":500,"healthy_control":98,"ulcerative_colitis":246},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":844,"papers":[{"doi":"10.1080/19490976.2026.2690688","pmcid":"PMC13290079","pmid":"42324633","title":"Inhibition of Aryl hydrocarbon receptor Interleukin-22 signaling and worsening of intestinal inflammation by &lt;i&gt;Sutterella&lt;/i&gt; species."}],"sample_intervention_arms":{},"sex":{"female":466,"male":374},"title":"IBD Parisian Gut Microbiome Cohorte","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB114255","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB114255_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB114255.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB114255.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB114255.csv.gz"}},{"accession":"PRJNA957107","age_categories":{"adult":575,"elderly":151},"countries":{"GB":726},"first_public_year":"2024","gbp_per_sample_median":8.04,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":726},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":726,"papers":[{"doi":"10.1093/rheumatology/keae045","pmcid":"PMC11637416","pmid":"38291926","title":"Treatment response in rheumatoid arthritis is predicted by the microbiome: a large observational study in UK DMARD-naive patients."}],"sample_intervention_arms":{},"sex":{"female":534,"male":188},"title":"Imrabiome - Rheumatoid project","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA957107","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA957107_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA957107.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA957107.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA957107.csv.gz"}},{"accession":"PRJNA834801","age_categories":{"adult":256,"elderly":469},"countries":{"US":725},"first_public_year":"2022","gbp_per_sample_median":6.64,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":2,"crohns_disease":1,"healthy_control":194,"neurological_psychiatric":488},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":725,"papers":[{"doi":"10.1038/s41467-022-34667-x","pmcid":"PMC9663292","pmid":"36376318","title":"Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms."},{"doi":"10.1038/s41531-025-01040-w","pmcid":"PMC12219260","pmid":"40593920","title":"Enrichment of gut-derived metabolites in a Parkinson's disease subtype with REM sleep behavior disorder."},{"doi":"10.1038/s41467-025-63473-4","pmcid":"PMC12413466","pmid":"40913049","title":"Gut microbial production of imidazole propionate drives Parkinson's pathologies."},{"doi":"10.1016/j.isci.2025.114261","pmcid":"PMC12757628","pmid":"41488771","title":"Genome-wide identification of tissue-specific fitness genes in murine models of &lt;i&gt;Staphylococcus aureus&lt;/i&gt; infection."},{"doi":"10.1038/s41467-024-48309-x","pmcid":"PMC11099085","pmid":"38755164","title":"Gut microbiota produces biofilm-associated amyloids with potential for neurodegeneration."}],"sample_intervention_arms":{},"sex":{"female":345,"male":380},"title":"Characterizing dysbiosis of the Parkinson's disease gut microbiome using shotgun metagenomics","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA834801","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA834801_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA834801.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA834801.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA834801.csv.gz"}},{"accession":"PRJNA797994","age_categories":{"adolescent":51,"adult":400,"child":174,"elderly":25},"countries":{"MY":650},"first_public_year":"2022","gbp_per_sample_median":3.01,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":true,"health_conditions":{"healthy_control":352,"other_infection":298},"intervention_design":"single_arm_before_after","intervention_detail":"Albendazole anthelmintic treatment (deworming), longitudinal pre/post sampling","interventions":["drug_therapy"],"n_samples":650,"papers":[{"doi":"10.1016/j.celrep.2022.111725","pmcid":"PMC9790084","pmid":"36450245","title":"Clostridia isolated from helminth-colonized humans promote the life cycle of Trichuris species."},{"doi":"10.1186/s40168-022-01385-x","pmcid":"PMC9727879","pmid":"36476263","title":"Gut microbiome of helminth-infected indigenous Malaysians is context dependent."},{"doi":"10.1038/s41467-025-61687-0","pmcid":"PMC12246136","pmid":"40640199","title":"Global diversity of soil-transmitted helminths reveals population-biased genetic variation that impacts diagnostic targets."},{"doi":"10.1038/s41467-026-71521-w","pmcid":"PMC13079874","pmid":"41980943","title":"Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery."}],"sample_intervention_arms":{"drug_therapy":243,"no_intervention":407},"sex":{"female":387,"male":263},"title":"Gut Microbiome of Helminth Infected Indigenous Malaysians Is Context Dependent","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA797994","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA797994_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA797994.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA797994.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA797994.csv.gz"}},{"accession":"PRJDB4176","age_categories":{"adult":375,"elderly":270},"countries":{"JP":645},"first_public_year":"2019","gbp_per_sample_median":6.49,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":72,"colorectal_cancer":258,"healthy_control":247,"other_cancer":40},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":645,"papers":[{"doi":"10.1186/s12866-021-02153-x","pmcid":"PMC8011136","pmid":"33789570","title":"Bacterial community structure alterations within the colorectal cancer gut microbiome."},{"doi":"10.7717/peerj.21488","pmcid":"PMC13378470","pmid":"42491728","title":"Clinical strains isolated from early-stage colorectal cancer patients promote tumorigenesis."},{"doi":"10.1038/s41588-026-02692-x","pmcid":"PMC13553305","pmid":"42576026","title":"Prevalence and chronology of colibactin-associated mutational processes and their microbiome spectra in Japanese colorectal cancer."},{"doi":"10.1186/s12864-020-6749-z","pmcid":"PMC7216530","pmid":"32393180","title":"Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment."},{"doi":"10.1038/s41598-021-82449-0","pmcid":"PMC7854710","pmid":"33531651","title":"Bacterial associations in the healthy human gut microbiome across populations."}],"sample_intervention_arms":{},"sex":{"female":263,"male":360},"title":"metagenomic data from human fecal samples","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB4176","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB4176_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB4176.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB4176.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB4176.csv.gz"}},{"accession":"PRJNA1086951","age_categories":{"elderly":638},"countries":{"US":638},"first_public_year":"2025","gbp_per_sample_median":2.45,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"healthy_control":325,"intervention_cohort":313},"intervention_design":"randomized_controlled_trial","intervention_detail":"MIND diet vs control diet with caloric restriction, up to 3 years","interventions":["diet_intervention"],"n_samples":638,"papers":[{"doi":"10.1002/trc2.70239","pmcid":"PMC13060763","pmid":"41958469","title":"Weight loss and metabolic improvements dominate the microbiome response in the MIND diet intervention: a randomized controlled trial."}],"sample_intervention_arms":{"diet_intervention":312,"no_intervention":326},"sex":{"female":444,"male":194},"title":"MIND Study - Fecal Metagenomics","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1086951","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1086951_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1086951.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1086951.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1086951.csv.gz"}},{"accession":"PRJNA688274","age_categories":{"adult":572,"elderly":42},"countries":{"NL":614},"first_public_year":"2021","gbp_per_sample_median":1.18,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":610,"other_disease":4},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":614,"papers":[{"doi":"10.1186/s13073-021-00893-z","pmcid":"PMC8182900","pmid":"34092249","title":"Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers."},{"doi":"10.1080/19490976.2022.2060676","pmcid":"PMC8993065","pmid":"35388735","title":"Enterobacteriaceae and Bacteroidaceae provide resistance to travel-associated intestinal colonization by multi-drug resistant Escherichia coli."}],"sample_intervention_arms":{},"sex":{"female":218,"male":162},"title":"Netherland Travelers","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA688274","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA688274_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA688274.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA688274.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA688274.csv.gz"}},{"accession":"PRJNA832909","age_categories":{"adult":228,"elderly":332},"countries":{"JP":278},"first_public_year":"2022","gbp_per_sample_median":1.16,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":470,"other_cancer":90},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":560,"papers":[{"doi":"10.1053/j.gastro.2022.03.054","pmcid":null,"pmid":"35398347","title":"Metagenomic Identification of Microbial Signatures Predicting Pancreatic Cancer From a Multinational Study."},{"doi":"10.17305/bb.2023.9934","pmcid":"PMC11293218","pmid":"38153528","title":"Oral microbiome-driven virulence factors: A novel approach to pancreatic cancer diagnosis."},{"doi":"10.1371/journal.pone.0302361","pmcid":"PMC11060577","pmid":"38687802","title":"Leveraging genomic signatures of oral microbiome-associated antibiotic resistance genes for diagnosing pancreatic cancer."},{"doi":"10.1101/2024.10.02.616338","pmcid":null,"pmid":null,"title":"Genderized Gut and Oral Microbiome Shifts: Uncovering Sex-Specific Dysbiosis in Pancreatic Cancer"},{"doi":"10.1038/s41467-024-54797-8","pmcid":"PMC11603027","pmid":"39604394","title":"Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn's disease."}],"sample_intervention_arms":{},"sex":{"female":252,"male":308},"title":"Metagenomics of the fecal and salivary microbiome of pancreatic cancer patients","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA832909","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA832909_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA832909.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA832909.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA832909.csv.gz"}},{"accession":"PRJNA557323","age_categories":{"adult":97,"elderly":3,"unknown":456},"countries":{"HK":556},"first_public_year":"2020","gbp_per_sample_median":7.56,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":556,"papers":[{"doi":"10.1136/gutjnl-2019-319635","pmcid":"PMC7569397","pmid":"32051205","title":"Southern Chinese populations harbour non-nucleatum Fusobacteria possessing homologues of the colorectal cancer-associated FadA virulence factor."},{"doi":"10.1099/mgen.0.001202","pmcid":"PMC10926697","pmid":"38381034","title":"ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data."},{"doi":"10.1002/advs.202508389","pmcid":"PMC13067863","pmid":"41755800","title":"Highly Resolved Community Sewage Metagenomics Unveiling Landscape and Transmission Patterns of Antibiotic Resistome in Hong Kong Populations."},{"doi":"10.1099/jgv.0.002254","pmcid":"PMC13155725","pmid":"42101460","title":"Benchmarks for taxonomic classification of jingmenviruses and closely related viruses using newly identified genomic sequences."},{"doi":"10.1038/s41467-022-30957-6","pmcid":"PMC9184491","pmid":"35680952","title":"Profiling Fusobacterium infection at high taxonomic resolution reveals lineage-specific correlations in colorectal cancer."}],"sample_intervention_arms":{},"sex":{"female":43,"male":57},"title":"Human gut metagenomes from Hong Kong populations","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA557323","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA557323_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA557323.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA557323.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA557323.csv.gz"}},{"accession":"PRJEB6997","age_categories":{"adult":525,"elderly":5},"countries":{"CN":530},"first_public_year":"2015","gbp_per_sample_median":5.72,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":302,"healthy_control":195},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":530,"papers":[{"doi":"10.1073/pnas.2023202118","pmcid":"PMC8201803","pmid":"34083435","title":"A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases."},{"doi":"10.1128/spectrum.00348-22","pmcid":"PMC9603985","pmid":"36040159","title":"Dysbiotic Oral and Gut Viromes in Untreated and Treated Rheumatoid Arthritis Patients."},{"doi":"10.1038/s41598-023-36833-7","pmcid":"PMC10276029","pmid":"37328529","title":"CXCL10 as a shared specific marker in rheumatoid arthritis and inflammatory bowel disease and a clue involved in the mechanism of intestinal flora in rheumatoid arthritis."},{"doi":"10.1038/s41522-023-00414-3","pmcid":"PMC10318035","pmid":"37400465","title":"A catalog of bacterial reference genomes from cultivated human oral bacteria."},{"doi":"10.1186/s12934-023-02255-3","pmcid":"PMC10704812","pmid":"38066544","title":"Prediction of BMI traits in the Chinese population based on the gut metagenome."}],"sample_intervention_arms":{},"sex":{"female":383,"male":111},"title":"Gut and Oral Microbiome Dysbiosis in Rheumatoid Arthritis","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB6997","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB6997_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB6997.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB6997.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB6997.csv.gz"}},{"accession":"PRJNA1046438","age_categories":{"adolescent":2,"adult":388,"elderly":80,"unknown":49},"countries":{"IT":519},"first_public_year":"2024","gbp_per_sample_median":2.03,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":519,"papers":[{"doi":"10.1002/smi.70152","pmcid":"PMC12911220","pmid":"41700653","title":"Severity of Depressive Symptoms by Perceived Stress and Gut Microbiota Composition: A Sex-Stratified Bayesian Approach in a Non-Clinical Sample."},{"doi":"10.1128/msystems.01294-23","pmcid":"PMC11019788","pmid":"38441032","title":"Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation."},{"doi":"10.1128/msystems.00929-24","pmcid":"PMC11494892","pmid":"39287373","title":"Exploring the vitamin biosynthesis landscape of the human gut microbiota."},{"doi":"10.1128/msystems.01294-23","pmcid":"PMC11019788","pmid":"38441032","title":"Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation."},{"doi":"10.1016/j.isci.2026.116578","pmcid":"PMC13378389","pmid":"42491748","title":"Fecal calprotectin and gut microbiome in a cohort without intestinal pathologies from northern Italy."}],"sample_intervention_arms":{},"sex":{"female":312,"male":204},"title":"Profiling the gut microbiota throughout human lifespan","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1046438","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1046438_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1046438.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1046438.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1046438.csv.gz"}},{"accession":"PRJNA1023797","age_categories":{"adult":242,"elderly":257},"countries":{"FR":499},"first_public_year":"2024","gbp_per_sample_median":3.17,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":499},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":499,"papers":[{"doi":"10.1038/s41522-025-00827-2","pmcid":"PMC12475161","pmid":"41006325","title":"Intestinal fungal signatures and their impact on immune checkpoint inhibitor efficacy: a multi-cohort meta-analysis."},{"doi":"10.1186/s40168-025-02273-w","pmcid":"PMC12781464","pmid":"41345980","title":"Deciphering the personalized functional redundancy hierarchy in the gut microbiome."},{"doi":"10.1002/advs.202520095","pmcid":"PMC13334858","pmid":"41972457","title":"A Microbial Lipid-ATP Synthase Axis Fuels NK Cell Antitumor Activity."}],"sample_intervention_arms":{},"sex":{},"title":"Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome.","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1023797","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1023797_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1023797.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1023797.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1023797.csv.gz"}},{"accession":"PRJNA529586","age_categories":{"elderly":490},"countries":{"US":490},"first_public_year":"2020","gbp_per_sample_median":0.38,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":490,"papers":[{"doi":"10.1080/19490976.2021.1897209","pmcid":"PMC8007149","pmid":"33764826","title":"The high prevalence of Clostridioides difficile among nursing home elders associates with a dysbiotic microbiome."},{"doi":"10.1109/access.2025.3599857","pmcid":"PMC12483529","pmid":"41036149","title":"ADAM-1: An AI Reasoning and Bioinformatics Model for Alzheimer's Disease Detection and Microbiome-Clinical Data Integration."}],"sample_intervention_arms":{},"sex":{},"title":"Alzheimers Disease microbiome in elders","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA529586","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA529586_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA529586.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA529586.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA529586.csv.gz"}},{"accession":"PRJNA217052","age_categories":{"adolescent":13,"adult":132,"child":5,"elderly":11,"unknown":323},"countries":{"FJ":484},"first_public_year":"2015","gbp_per_sample_median":0.99,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":307},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":484,"papers":[{"doi":"10.1038/nbt.3329","pmcid":"PMC4720164","pmid":"26368049","title":"Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning."},{"doi":"10.1038/nature18927","pmcid":"PMC4983458","pmid":"27409808","title":"Mobile genes in the human microbiome are structured from global to individual scales."},{"doi":"10.1038/nmeth.3955","pmcid":"PMC5007149","pmid":"27479330","title":"Virtual microfluidics for digital quantification and single-cell sequencing."},{"doi":"10.1038/s41564-019-0409-6","pmcid":"PMC7450247","pmid":"30911128","title":"Transmission of human-associated microbiota along family and social networks."},{"doi":"10.3389/fgene.2021.644516","pmcid":"PMC8062976","pmid":"33897763","title":"G2S: A New Deep Learning Tool for Predicting Stool Microbiome Structure From Oral Microbiome Data."}],"sample_intervention_arms":{},"sex":{"female":110,"male":57},"title":"Fiji COMP","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA217052","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA217052_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA217052.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA217052.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA217052.csv.gz"}},{"accession":"PRJNA1125469","age_categories":{"adult":462,"elderly":17},"countries":{"US":479},"first_public_year":"2025","gbp_per_sample_median":2.95,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":160,"neurological_psychiatric":319},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":479,"papers":[{"doi":"10.1038/s41591-025-03788-3","pmcid":"PMC12416096","pmid":"40715814","title":"AI-driven multi-omics modeling of myalgic encephalomyelitis/chronic fatigue syndrome."}],"sample_intervention_arms":{},"sex":{"female":328,"male":151},"title":"Longitudinal Gut Metagenomics profiling of ME/CFS","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1125469","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1125469_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1125469.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1125469.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1125469.csv.gz"}},{"accession":"PRJEB113070","age_categories":{"adult":165,"elderly":267},"countries":{"SG":432},"first_public_year":"2026","gbp_per_sample_median":4.02,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":432,"papers":[],"sample_intervention_arms":{},"sex":{"female":221,"male":211},"title":"Longitudinal metagenomics analysis of CPE carriers","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB113070","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB113070_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB113070.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB113070.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB113070.csv.gz"}},{"accession":"PRJNA804384","age_categories":{"adolescent":8,"adult":386,"elderly":38},"countries":{},"first_public_year":"2022","gbp_per_sample_median":3.48,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":312,"ulcerative_colitis":120},"intervention_design":"single_arm_before_after","intervention_detail":"Biological therapy (one of four agents) for IBD, pre/post samples","interventions":["drug_therapy"],"n_samples":432,"papers":[{"doi":"10.1093/ecco-jcc/jjad061","pmcid":"PMC10588789","pmid":"37052201","title":"Community Types of the Human Gut Virome are Associated with Endoscopic Outcome in Ulcerative Colitis."}],"sample_intervention_arms":{"drug_therapy":432},"sex":{"female":255,"male":177},"title":"Inflammatory bowel disease patients undergoing biological therapy","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA804384","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA804384_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA804384.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA804384.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA804384.csv.gz"}},{"accession":"PRJNA642308","age_categories":{"adolescent":13,"adult":368,"elderly":28},"countries":{"US":409},"first_public_year":"2021","gbp_per_sample_median":0.25,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ibd_unspecified":409},"intervention_design":"single_arm_before_after","intervention_detail":"IBD Anti-Inflammatory Diet (IBD-AID), pre-post single-arm trial","interventions":["diet_intervention"],"n_samples":409,"papers":[{"doi":"10.1080/19490976.2022.2046244","pmcid":"PMC8942410","pmid":"35311458","title":"Dietary manipulation of the gut microbiome in inflammatory bowel disease patients: Pilot study."},{"doi":"10.1186/s40168-023-01604-z","pmcid":"PMC10408196","pmid":"37553697","title":"Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions."}],"sample_intervention_arms":{},"sex":{"female":226,"male":183},"title":"Gut microbiome of subjects with inflammatory bowel disease undergoing diet intervention","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA642308","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA642308_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA642308.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA642308.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA642308.csv.gz"}},{"accession":"PRJEB1220","age_categories":{"adult":380,"elderly":16},"countries":{"DK":177,"ES":219},"first_public_year":"2014","gbp_per_sample_median":3.76,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":248,"ibd_unspecified":148},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":396,"papers":[{"doi":"10.1038/nbt.2939","pmcid":null,"pmid":"24997787","title":"Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes."},{"doi":"10.1371/journal.pone.0133492","pmcid":"PMC4510569","pmid":"26197475","title":"Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data."},{"doi":"10.1371/journal.pcbi.1004573","pmcid":"PMC4643905","pmid":"26565399","title":"Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes."},{"doi":"10.1093/gigascience/giab005","pmcid":"PMC7931821","pmid":"33543271","title":"MB-GAN: Microbiome Simulation via Generative Adversarial Network."},{"doi":"10.1016/j.csbj.2022.07.010","pmcid":"PMC9293737","pmid":"35891785","title":"FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling."}],"sample_intervention_arms":{},"sex":{"female":188,"male":139},"title":"A method for identifying metagenomic species and variable genetic elements by exhaustive co-abundance binning","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB1220","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB1220_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB1220.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB1220.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB1220.csv.gz"}},{"accession":"PRJNA1116523","age_categories":{"adult":231,"elderly":156},"countries":{"PL":387},"first_public_year":"2024","gbp_per_sample_median":3.72,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":121,"other_cancer":150,"other_disease":116},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":387,"papers":[{"doi":"10.3390/ijms25158026","pmcid":"PMC11311272","pmid":"39125593","title":"Microbial and Metabolic Gut Profiling across Seven Malignancies Identifies Fecal Faecalibacillus intestinalis and Formic Acid as Commonly Altered in Cancer Patients."}],"sample_intervention_arms":{},"sex":{"female":138,"male":117},"title":"Microbial and metabolic gut profiling across seven malignancies identifies fecal Faecalibacillus intestinalis and formic acid as commonly altered in cancer patients","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1116523","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1116523_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1116523.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1116523.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1116523.csv.gz"}},{"accession":"PRJEB21528","age_categories":{"adult":281,"elderly":104},"countries":{"CN":385},"first_public_year":"2017","gbp_per_sample_median":5.39,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":214,"healthy_control":171},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":385,"papers":[{"doi":"10.1038/s41467-017-00900-1","pmcid":"PMC5635030","pmid":"29018189","title":"The gut microbiome in atherosclerotic cardiovascular disease."},{"doi":"10.3390/genes11080946","pmcid":"PMC7465921","pmid":"32824429","title":"Assembling Reads Improves Taxonomic Classification of Species."},{"doi":"10.3390/e23020187","pmcid":"PMC7913240","pmid":"33540903","title":"Information Theoretic Metagenome Assembly Allows the Discovery of Disease Biomarkers in Human Microbiome."},{"doi":"10.1016/j.chom.2022.11.015","pmcid":"PMC9839529","pmid":"36549300","title":"Two distinct gut microbial pathways contribute to meta-organismal production of phenylacetylglutamine with links to cardiovascular disease."},{"doi":"10.1016/j.isci.2023.106960","pmcid":"PMC10291474","pmid":"37378328","title":"A consortium of three-bacteria isolated from human feces inhibits formation of atherosclerotic deposits and lowers lipid levels in a mouse model."}],"sample_intervention_arms":{},"sex":{"female":154,"male":226},"title":"Here we performed a metagenome-wide association study (MWAS) on stools from 218 individuals with atherosclerotic cardiovascular disease (ACVD) and 187 healthy controls.","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB21528","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB21528_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB21528.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB21528.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB21528.csv.gz"}},{"accession":"PRJNA530339","age_categories":{"adult":301,"elderly":84},"countries":{"CN":385},"first_public_year":"2020","gbp_per_sample_median":6.69,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":385,"papers":[{"doi":"10.46471/gigabyte.12","pmcid":"PMC9631969","pmid":"36824343","title":"Linking gut microbiome to bone mineral density: a shotgun metagenomic dataset from 361 elderly women."},{"doi":"10.1038/s41467-026-71521-w","pmcid":"PMC13079874","pmid":"41980943","title":"Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery."}],"sample_intervention_arms":{},"sex":{"female":385},"title":"Shotgun Metagenomics of 361 post-menopause women reveals gut microbiome change along with the bone loss","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA530339","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA530339_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA530339.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA530339.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA530339.csv.gz"}},{"accession":"PRJEB38909","age_categories":{"adult":254,"elderly":70,"infant":60},"countries":{"US":384},"first_public_year":"2024","gbp_per_sample_median":1.92,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":384,"papers":[{"doi":"10.1128/msystems.00465-20","pmcid":"PMC7527136","pmid":"32994287","title":"Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome."},{"doi":"10.1128/msystems.00528-20","pmcid":"PMC7567581","pmid":"33051377","title":"Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV."},{"doi":"10.1016/j.jpain.2021.08.006","pmcid":"PMC9854399","pmid":"34530155","title":"Reduced Gut Microbiome Diversity in People With HIV Who Have Distal Neuropathic Pain."},{"doi":"10.3390/v13101891","pmcid":"PMC8537977","pmid":"34696320","title":"Markers of Gut Barrier Function and Microbial Translocation Associate with Lower Gut Microbial Diversity in People with HIV."},{"doi":"10.3389/fcimb.2023.1119875","pmcid":"PMC10277638","pmid":"37342245","title":"Alterations of the gut microbiota associated with the occurrence and progression of viral hepatitis."}],"sample_intervention_arms":{},"sex":{},"title":"Depression in HIV and HCV Co-Infected Individuals is Associated with Systematic Differences in the Gut Microbiome and Metabolome","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB38909","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB38909_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB38909.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB38909.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB38909.csv.gz"}},{"accession":"PRJEB91718","age_categories":{"adult":365,"elderly":18},"countries":{"PL":383},"first_public_year":"2025","gbp_per_sample_median":10.05,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":1,"healthy_control":141,"other_cancer":24,"other_disease":73,"other_infection":97,"type2_diabetes":47},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":383,"papers":[{"doi":"10.3389/fmicb.2024.1342749","pmcid":"PMC11219902","pmid":"38962119","title":"Gut microbiome dynamics and predictive value in hospitalized COVID-19 patients: a comparative analysis of shallow and deep shotgun sequencing."}],"sample_intervention_arms":{},"sex":{"female":95,"male":147},"title":"COVID-19 Microbiome - deep samples","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB91718","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB91718_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB91718.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB91718.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB91718.csv.gz"}},{"accession":"PRJNA728374","age_categories":{"adult":312,"elderly":66},"countries":{"SG":378},"first_public_year":"2022","gbp_per_sample_median":1.24,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":378},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":378,"papers":[{"doi":"10.1038/s41522-022-00287-y","pmcid":"PMC9001705","pmid":"35411007","title":"Gut microbiome responses to dietary intervention with hypocholesterolemic vegetable oils."},{"doi":"10.1038/s41522-022-00342-8","pmcid":"PMC9547895","pmid":"36209276","title":"The hallmarks of dietary intervention-resilient gut microbiome."}],"sample_intervention_arms":{"diet_intervention":378},"sex":{"female":195,"male":183},"title":"Gut microbiome responses to dietary intervention with hypocholesterolemic vegetable oils.","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA728374","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA728374_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA728374.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA728374.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA728374.csv.gz"}},{"accession":"PRJNA422434","age_categories":{"adolescent":2,"adult":328,"elderly":40},"countries":{"CN":370},"first_public_year":"2012","gbp_per_sample_median":3.35,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":183,"type2_diabetes":183},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":370,"papers":[{"doi":"10.1038/nature11450","pmcid":null,"pmid":"23023125","title":"A metagenome-wide association study of gut microbiota in type 2 diabetes."},{"doi":"10.1073/pnas.2023202118","pmcid":"PMC8201803","pmid":"34083435","title":"A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases."},{"doi":"10.3389/fimmu.2017.01430","pmcid":"PMC5671494","pmid":"29163505","title":"IL17eScan: A Tool for the Identification of Peptides Inducing IL-17 Response."},{"doi":"10.1186/s12864-020-07357-5","pmcid":"PMC7814594","pmid":"33468056","title":"Prediction and analysis of metagenomic operons via MetaRon: a pipeline for prediction of Metagenome and whole-genome opeRons."},{"doi":"10.1101/gr.276306.121","pmcid":"PMC9248880","pmid":"35545448","title":"Rapid evolution and strain turnover in the infant gut microbiome."}],"sample_intervention_arms":{},"sex":{"female":145,"male":194},"title":"A metagenome-wide association study of gut microbiota in type 2 diabetes.","trial_population_condition":"type2_diabetes","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA422434","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA422434_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA422434.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA422434.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA422434.csv.gz"}},{"accession":"PRJEB54704","age_categories":{"adult":174,"elderly":177},"countries":{"DE":229,"US":122},"first_public_year":"2023","gbp_per_sample_median":0.07,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":351},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":351,"papers":[{"doi":"10.1038/s41591-023-02234-6","pmcid":"PMC10121864","pmid":"36914893","title":"A non-antibiotic-disrupted gut microbiome is associated with clinical responses to CD19-CAR-T cell cancer immunotherapy."},{"doi":"10.1182/blood.2024025366","pmcid":"PMC12782970","pmid":"39441941","title":"Antibiotic-induced loss of gut microbiome metabolic output correlates with clinical responses to CAR T-cell therapy."},{"doi":"10.3390/microorganisms13112595","pmcid":"PMC12654497","pmid":"41304278","title":"Multi-Kingdom Gut Microbiome Interaction Characteristics Predict Immune Checkpoint Inhibitor Efficacy Across Pan-Cancer Cohorts."}],"sample_intervention_arms":{},"sex":{"female":97,"male":254},"title":"Gut microbiome associations with clinical outcomes of CD19-targeted CAR-T cell immunotherapy","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB54704","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB54704_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB54704.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB54704.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB54704.csv.gz"}},{"accession":"PRJNA589866","age_categories":{"adult":135,"elderly":214},"countries":{"BG":107,"HU":32,"PL":36,"RO":87,"RS":81,"US":6},"first_public_year":"2020","gbp_per_sample_median":7.45,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{},"intervention_design":"randomized_controlled_trial","intervention_detail":"Ribaxamase (oral beta-lactamase) vs placebo with IV ceftriaxone","interventions":["antibiotic","drug_therapy"],"n_samples":349,"papers":[{"doi":"10.2147/idr.s260258","pmcid":"PMC7383106","pmid":"32801790","title":"Ribaxamase, an Orally Administered β-Lactamase, Diminishes Changes to Acquired Antimicrobial Resistance of the Gut Resistome in Patients Treated with Ceftriaxone."}],"sample_intervention_arms":{"drug_therapy":129,"no_intervention":119,"placebo":101},"sex":{"female":139,"male":207},"title":"human gut metagenome Metagenome","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA589866","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA589866_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA589866.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA589866.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA589866.csv.gz"}},{"accession":"PRJNA613947","age_categories":{"adult":78,"elderly":254,"unknown":16},"countries":{"CN":348},"first_public_year":"2020","gbp_per_sample_median":6.33,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":95,"healthy_control":221,"type2_diabetes":11},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":348,"papers":[{"doi":"10.1038/s41586-022-05620-1","pmcid":"PMC9892008","pmid":"36653448","title":"The person-to-person transmission landscape of the gut and oral microbiomes."},{"doi":"10.1371/journal.pcbi.1013883","pmcid":"PMC12810900","pmid":"41525322","title":"Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study."},{"doi":"10.3390/microorganisms11102560","pmcid":"PMC10609127","pmid":"37894218","title":"A Pipeline for Constructing Reference Genomes for Large Cohort-Specific Metagenome Compression."},{"doi":"10.1080/19490976.2024.2393756","pmcid":"PMC11364081","pmid":"39197040","title":"Consistent signatures in the human gut microbiome of longevous populations."},{"doi":"10.1080/19490976.2024.2426623","pmcid":"PMC11559365","pmid":"39529240","title":"Biosynthetic potential of the gut microbiome in longevous populations."}],"sample_intervention_arms":{},"sex":{"female":178,"male":169},"title":"human gut metagenome Metagenome","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA613947","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA613947_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA613947.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA613947.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA613947.csv.gz"}},{"accession":"PRJNA734860","age_categories":{"adult":269,"elderly":72},"countries":{"US":341},"first_public_year":"2023","gbp_per_sample_median":2.83,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"type2_diabetes":125},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":341,"papers":[{"doi":"10.1002/hep.32197","pmcid":"PMC8930512","pmid":"34633706","title":"Gut microbiome features associated with liver fibrosis in Hispanics, a population at high risk for fatty liver disease."},{"doi":"10.1128/msystems.00033-22","pmcid":"PMC9238400","pmid":"35477306","title":"Gut Microbiome Alterations Associated with Diabetes in Mexican Americans in South Texas."},{"doi":"10.1128/msystems.00434-24","pmcid":"PMC11406975","pmid":"39166873","title":"Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes."},{"doi":"10.1080/19490976.2024.2399260","pmcid":"PMC11382720","pmid":"39239875","title":"Protection against fibrosis by a bacterial consortium in metabolic dysfunction-associated steatohepatitis and the role of amino acid metabolism."},{"doi":"10.1002/hep4.1490","pmcid":"PMC7109342","pmid":"32258950","title":"Bile Acid Changes Associated With Liver Fibrosis and Steatosis in the Mexican-American Population of South Texas"}],"sample_intervention_arms":{},"sex":{"female":238,"male":103},"title":"Stool microbiome of Hispanics in the Cameron County Hispanic Cohort","trial_population_condition":"liver_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA734860","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA734860_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA734860.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA734860.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA734860.csv.gz"}},{"accession":"PRJNA751792","age_categories":{"adult":163,"elderly":175},"countries":{"FR":338},"first_public_year":"2021","gbp_per_sample_median":3.25,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"neurological_psychiatric":161,"other_cancer":177},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":338,"papers":[{"doi":"10.1038/s41591-021-01655-5","pmcid":"PMC9330544","pmid":"35115705","title":"Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer."},{"doi":"10.1186/s12967-026-07900-0","pmcid":"PMC13041121","pmid":"41749306","title":"Distinct gut virome profiles are associated with response to anti-PD-1 therapy in non-small cell lung cancer."},{"doi":"10.20517/mrr.2025.117","pmcid":"PMC13091084","pmid":"42007374","title":"A responder-informed gut microbial consortium enhances anti-PD-1 efficacy in a mouse cancer model."},{"doi":"10.1038/s41467-023-42997-7","pmcid":"PMC10654443","pmid":"37973916","title":"Gut microbial structural variation associates with immune checkpoint inhibitor response."},{"doi":"10.20517/mrr.2024.09","pmcid":"PMC11480726","pmid":"39421249","title":"Pangenomic analysis identifies correlations between &lt;i&gt;Akkermansia&lt;/i&gt; species and subspecies and human health outcomes."}],"sample_intervention_arms":{},"sex":{"female":112,"male":226},"title":"Intestinal Akkermansia muciniphila predicts clinical response to PD1 blockade in advanced non-small cell lung cancer patients","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA751792","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA751792_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA751792.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA751792.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA751792.csv.gz"}},{"accession":"PRJNA675598","age_categories":{"adult":44,"elderly":286},"countries":{"JP":330},"first_public_year":"2021","gbp_per_sample_median":1.75,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":328},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":330,"papers":[{"doi":"10.1038/s41586-021-03832-5","pmcid":null,"pmid":"34325466","title":"Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians."},{"doi":"10.1111/acel.14028","pmcid":"PMC10726799","pmid":"38015106","title":"Age-dependent changes in the gut microbiota and serum metabolome correlate with renal function and human aging."},{"doi":"10.1093/bib/bbae419","pmcid":"PMC11367760","pmid":"39222063","title":"Enteropathway: the metabolic pathway database for the human gut microbiota."},{"doi":"10.1002/imt2.70001","pmcid":"PMC11865343","pmid":"40027489","title":"EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research."},{"doi":"10.1080/19490976.2024.2393756","pmcid":"PMC11364081","pmid":"39197040","title":"Consistent signatures in the human gut microbiome of longevous populations."}],"sample_intervention_arms":{},"sex":{"female":226,"male":104},"title":"Identification of unique bile acid metabolizing bacteria from the microbiome of centenarians","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA675598","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA675598_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA675598.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA675598.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA675598.csv.gz"}},{"accession":"PRJNA1056456","age_categories":{"adult":316,"elderly":11},"countries":{"CN":327},"first_public_year":"2024","gbp_per_sample_median":6.65,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ibs":327},"intervention_design":"non_randomized_controlled","intervention_detail":"Selective microbiota transplantation (SMT) vs fecal microbiota transplantation (FMT)","interventions":["fmt","other_intervention"],"n_samples":327,"papers":[],"sample_intervention_arms":{"fmt":176,"other_intervention":151},"sex":{"female":103,"male":219},"title":"Homo sapiens Metagenome","trial_population_condition":"ibs","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1056456","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1056456_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1056456.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1056456.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1056456.csv.gz"}},{"accession":"PRJNA685797","age_categories":{"adult":318,"elderly":5},"countries":{"NL":323},"first_public_year":"2021","gbp_per_sample_median":4.03,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":323},"intervention_design":"single_arm_before_after","intervention_detail":"BCG vaccination with pre/post blood and stool sampling","interventions":["vaccine"],"n_samples":323,"papers":[{"doi":"10.1186/s13059-021-02482-0","pmcid":"PMC8456614","pmid":"34551799","title":"The influence of the gut microbiome on BCG-induced trained immunity."},{"doi":"10.1016/j.ebiom.2026.106404","pmcid":"PMC13427514","pmid":"42492179","title":"Investigating the role of baseline gut Akkermansia muciniphila and its co-metabolite palmitoleic acid in BCG vaccine efficacy: a preclinical study."}],"sample_intervention_arms":{},"sex":{"female":181,"male":139},"title":"The Influence of the gut microbiome on BCG-induced trained immunity","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA685797","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA685797_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA685797.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA685797.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA685797.csv.gz"}},{"accession":"PRJNA686265","age_categories":{"adult":319,"elderly":1},"countries":{"TZ":320},"first_public_year":"2021","gbp_per_sample_median":5.09,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":320},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":320,"papers":[{"doi":"10.1038/s41467-021-25213-2","pmcid":"PMC8357928","pmid":"34381036","title":"Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations."},{"doi":"10.1038/s41586-023-06893-w","pmcid":"PMC10808065","pmid":"38172637","title":"Host genetic regulation of human gut microbial structural variation."}],"sample_intervention_arms":{},"sex":{"female":163,"male":157},"title":"Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA686265","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA686265_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA686265.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA686265.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA686265.csv.gz"}},{"accession":"PRJNA707487","age_categories":{"adult":311,"elderly":9},"countries":{"US":320},"first_public_year":"2021","gbp_per_sample_median":1.75,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"observational_with_procedure","intervention_detail":"Hematopoietic cell transplantation, stool sampled around procedure","interventions":["other_intervention"],"n_samples":320,"papers":[{"doi":"10.1038/s41467-022-28048-7","pmcid":"PMC8803835","pmid":"35102136","title":"Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults."},{"doi":"10.1016/j.chom.2025.07.004","pmcid":"PMC12358190","pmid":"40730160","title":"The prototypic crAssphage is a linear phage-plasmid."}],"sample_intervention_arms":{},"sex":{},"title":"Metagenomic sequencing of stool samples from human hematopoietic cell transplantation patients","trial_population_condition":"transplant_or_immunocompromised","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA707487","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA707487_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA707487.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA707487.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA707487.csv.gz"}},{"accession":"PRJNA1177009","age_categories":{"adult":131,"elderly":186},"countries":{"US":317},"first_public_year":"2024","gbp_per_sample_median":3.82,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"healthy_control":317},"intervention_design":"randomized_controlled_trial","intervention_detail":"2'-fucosyllactose (HMO) two doses vs placebo, 6 weeks","interventions":["prebiotic_or_fibre"],"n_samples":317,"papers":[{"doi":"10.1016/j.xcrm.2025.102256","pmcid":"PMC12432366","pmid":"40738103","title":"A human milk oligosaccharide alters the microbiome, circulating hormones, and metabolites in a randomized controlled trial of older adults."}],"sample_intervention_arms":{"placebo":111,"prebiotic_or_fibre":206},"sex":{"female":176,"male":141},"title":"A human milk oligosaccharide alters the microbiome, circulating hormones, cytokines and metabolites in a randomized controlled trial of older individuals","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1177009","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1177009_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1177009.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1177009.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1177009.csv.gz"}},{"accession":"PRJNA993161","age_categories":{"adult":262,"elderly":54},"countries":{"US":316},"first_public_year":"2023","gbp_per_sample_median":2.27,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":316},"intervention_design":"randomized_controlled_trial","intervention_detail":"Complex oligosaccharide with/without probiotic in antibiotic-treated healthy volunteers","interventions":["antibiotic","prebiotic_or_fibre","probiotic"],"n_samples":316,"papers":[{"doi":"10.1016/j.chom.2023.08.004","pmcid":null,"pmid":"37657443","title":"Precision modulation of dysbiotic adult microbiomes with a human-milk-derived synbiotic reshapes gut microbial composition and metabolites."}],"sample_intervention_arms":{},"sex":{"female":148,"male":168},"title":"Impact of complex oligosaccharides and a probiotic on the antibiotic-treated human microbiome","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA993161","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA993161_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA993161.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA993161.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA993161.csv.gz"}},{"accession":"PRJNA486009","age_categories":{"adolescent":18,"adult":67,"child":65,"elderly":7,"infant":140,"neonate":18},"countries":{"EC":315},"first_public_year":"2019","gbp_per_sample_median":0.06,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"gi_infection_or_diarrhoea":55,"healthy_control":56},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":315,"papers":[{"doi":"10.1128/aem.01820-19","pmcid":"PMC6881795","pmid":"31585992","title":"Metagenomic Signatures of Gut Infections Caused by Different Escherichia coli Pathotypes."},{"doi":"10.1128/aem.02593-20","pmcid":"PMC8105024","pmid":"33452027","title":"The Reliability of Metagenome-Assembled Genomes (MAGs) in Representing Natural Populations: Insights from Comparing MAGs against Isolate Genomes Derived from the Same Fecal Sample."},{"doi":"10.4269/ajtmh.20-0831","pmcid":"PMC8176484","pmid":"33872206","title":"Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador."},{"doi":"10.1016/j.meegid.2023.105476","pmcid":"PMC10599324","pmid":"37392822","title":"Population genomics of diarrheagenic Escherichia coli uncovers high connectivity between urban and rural communities in Ecuador."},{"doi":"10.4269/ajtmh.23-0167","pmcid":"PMC10484266","pmid":"37549901","title":"Distribution of Escherichia coli Pathotypes along an Urban-Rural Gradient in Ecuador."}],"sample_intervention_arms":{},"sex":{"female":140,"male":175},"title":"Genome diversity of pathogenic Escherichia coli in Ecuador","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA486009","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA486009_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA486009.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA486009.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA486009.csv.gz"}},{"accession":"PRJNA615162","age_categories":{"adult":231,"elderly":82},"countries":{"US":313},"first_public_year":"2021","gbp_per_sample_median":2.01,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":148,"healthy_control":165},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":313,"papers":[{"doi":"10.1186/s13073-021-00853-7","pmcid":"PMC7919092","pmid":"33648559","title":"Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis."},{"doi":"10.1016/j.jaci.2021.03.025","pmcid":"PMC8429070","pmid":"33819509","title":"Cytokine-specific autoantibodies shape the gut microbiome in autoimmune polyendocrine syndrome type 1."},{"doi":"10.1186/s12859-025-06286-y","pmcid":"PMC12659350","pmid":"41299229","title":"Protein language models uncover carbohydrate-active enzyme function in metagenomics."}],"sample_intervention_arms":{},"sex":{"female":210,"male":103},"title":"Gut Microbiome characterization of IgG4 patients and Systemic Sclerosis patients","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA615162","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA615162_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA615162.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA615162.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA615162.csv.gz"}},{"accession":"PRJEB6337","age_categories":{"adult":292,"elderly":20},"countries":{"CN":312},"first_public_year":"2014","gbp_per_sample_median":3.1,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":143,"liver_disease":169},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":312,"papers":[{"doi":"10.1186/s40168-017-0283-5","pmcid":"PMC5501583","pmid":"28683828","title":"VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data."},{"doi":"10.3389/fmicb.2018.03166","pmcid":"PMC6315199","pmid":"30631318","title":"Disorganized Gut Microbiome Contributed to Liver Cirrhosis Progression: A Meta-Omics-Based Study."},{"doi":"10.1093/gigascience/giz020","pmcid":"PMC6446249","pmid":"30942867","title":"MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs."},{"doi":"10.3390/ijms222212431","pmcid":"PMC8625315","pmid":"34830313","title":"Aryl Hydrocarbon Receptor (AhR) Activation by 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) Dose-Dependently Shifts the Gut Microbiome Consistent with the Progression of Non-Alcoholic Fatty Liver Disease"},{"doi":"10.3389/fmicb.2023.1169811","pmcid":"PMC10170289","pmid":"37180228","title":"Alterations in the intestinal microbiome and metabolic profile of patients with cirrhosis supplemented with lactulose, Clostridium butyricum, and Bifidobacterium longum infantis: a randomized placebo-"}],"sample_intervention_arms":{},"sex":{"female":108,"male":204},"title":"Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide. Previous studies have shown an association between the gut microbiota and liver complications such as cirrhosis and other liver injuries. We therefore undertook a whole gut microbiome wide association study of stool samples from 98 liver cirrhosis patients and 83 healthy controls to characterise the faecal microbial communities and their functional composition. In total, we generated 860 Gb of high-quality sequence data and built a reference gene set for the liver cirrhosis cohort containing 2.69 million genes, 36.1% of which was not covered by previously published gene catalogues.","trial_population_condition":"liver_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB6337","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB6337_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB6337.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB6337.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB6337.csv.gz"}},{"accession":"PRJEB39661","age_categories":{"adult":43,"child":38,"elderly":45,"infant":8,"unknown":170},"countries":{"ES":304},"first_public_year":"2023","gbp_per_sample_median":0.19,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":304},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":304,"papers":[{"doi":"10.1038/s41598-026-35033-3","pmcid":"PMC12873169","pmid":"41513932","title":"Lifetime existence of a core of mutualistic symbionts and functionally uncoupled taxa in the gut of a Mediterranean cohort."}],"sample_intervention_arms":{},"sex":{"female":181,"male":123},"title":"Changes in the microbiota across life: the existence of a core of microbial taxa and decoupling taxa.","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB39661","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB39661_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB39661.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB39661.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB39661.csv.gz"}},{"accession":"PRJNA822660","age_categories":{"adult":281,"elderly":21},"countries":{"US":302},"first_public_year":"2023","gbp_per_sample_median":4.59,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":302},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":302,"papers":[{"doi":"10.1038/s42255-023-00777-z","pmcid":"PMC10229427","pmid":"37165176","title":"Human metabolome variation along the upper intestinal tract."},{"doi":"10.1038/s41586-023-05989-7","pmcid":"PMC10191855","pmid":"37165188","title":"Profiling the human intestinal environment under physiological conditions."},{"doi":"10.1080/19490976.2024.2405547","pmcid":"PMC11459740","pmid":"39679619","title":"Comparative analysis of the duodenojejunal microbiome with the oral and fecal microbiomes reveals its stronger association with obesity and nutrition."}],"sample_intervention_arms":{},"sex":{"female":141,"male":161},"title":"Profiling the human intestinal environment under physiologic conditions","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA822660","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA822660_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA822660.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA822660.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA822660.csv.gz"}},{"accession":"PRJNA389280","age_categories":{"adolescent":69,"adult":141,"child":43,"elderly":14,"unknown":33},"countries":{"US":300},"first_public_year":"2017","gbp_per_sample_median":2.79,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":143,"healthy_control":56,"ibd_unspecified":23,"ulcerative_colitis":78},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":300,"papers":[{"doi":"10.1038/s41564-017-0089-z","pmcid":"PMC6131705","pmid":"29311644","title":"Dynamics of metatranscription in the inflammatory bowel disease gut microbiome."},{"doi":"10.3389/fbinf.2022.828703","pmcid":"PMC9580954","pmid":"36304322","title":"GMEmbeddings: An R Package to Apply Embedding Techniques to Microbiome Data."},{"doi":"10.1186/s40168-024-01750-y","pmcid":"PMC10949743","pmid":"38504383","title":"Microbiota-derived indoles alleviate intestinal inflammation and modulate microbiome by microbial cross-feeding."},{"doi":"10.1038/s41467-024-53670-y","pmcid":"PMC11525784","pmid":"39477928","title":"Biosynthetic enzyme analysis identifies a protective role for TLR4-acting gut microbial sulfonolipids in inflammatory bowel disease."},{"doi":"10.1093/nar/gkag227","pmcid":"PMC12993454","pmid":"41841491","title":"ABaCo: addressing heterogeneity challenges in metagenomic data integration with adversarial generative models."}],"sample_intervention_arms":{},"sex":{"female":165,"male":112},"title":"Human gut metagenome and metatranscriptome in the inflammatory bowel disease (iHMP/HMP2)","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA389280","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA389280_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA389280.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA389280.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA389280.csv.gz"}},{"accession":"PRJNA449784","age_categories":{"adult":257,"elderly":35},"countries":{"CN":292},"first_public_year":"2019","gbp_per_sample_median":11.32,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":69,"kidney_disease":223},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":292,"papers":[{"doi":"10.1136/gutjnl-2019-319766","pmcid":"PMC7677483","pmid":"32241904","title":"Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents."},{"doi":"10.1126/science.abb3763","pmcid":"PMC8178816","pmid":"32943527","title":"Diet posttranslationally modifies the mouse gut microbial proteome to modulate renal function."},{"doi":"10.1186/s12967-024-05004-1","pmcid":"PMC10894479","pmid":"38403655","title":"Altered gut mycobiome in patients with end-stage renal disease and its correlations with serum and fecal metabolomes."},{"doi":"10.1128/mbio.00735-24","pmcid":"PMC11253615","pmid":"38819146","title":"Guild-level signature of gut microbiome for diabetic kidney disease."},{"doi":"10.1053/j.gastro.2021.04.013","pmcid":"PMC9069394","pmid":"33857456","title":"Impact of Antibiotic Resistance Genes in Gut Microbiome of Patients With Cirrhosis."}],"sample_intervention_arms":{},"sex":{"female":108,"male":184},"title":"human gut metagenome Raw sequence reads","trial_population_condition":"kidney_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA449784","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA449784_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA449784.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA449784.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA449784.csv.gz"}},{"accession":"PRJNA1088844","age_categories":{"adult":232,"elderly":50},"countries":{"NZ":282},"first_public_year":"2024","gbp_per_sample_median":1.85,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":113,"ibs":112,"other_disease":50},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":282,"papers":[{"doi":"10.1080/19490976.2025.2604871","pmcid":"PMC12758187","pmid":"41431864","title":"Integrated multi-omic and symptom clustering reveals lower-gastrointestinal disorders of gut-brain interaction heterogeneity."}],"sample_intervention_arms":{},"sex":{"female":196,"male":79},"title":"Characterization of the fecal microbial taxonomic composition and functional potential and integrative analysis with gastrointestinal and non-gastrointestinal symptoms in subjects with disorders of gut-brain interactions","trial_population_condition":"ibs","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1088844","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1088844_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1088844.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1088844.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1088844.csv.gz"}},{"accession":"PRJNA1295573","age_categories":{"adult":204,"elderly":74},"countries":{"US":278},"first_public_year":"2026","gbp_per_sample_median":11.17,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":278},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":278,"papers":[{"doi":"10.1038/s41523-026-00922-3","pmcid":"PMC13066469","pmid":"41760690","title":"The landscape of the intestinal microbiome among patients with newly diagnosed invasive breast cancer and ductal carcinoma in situ (DCIS)."}],"sample_intervention_arms":{},"sex":{"female":278},"title":"The intestinal microbiome of patients with newly diagnosed invasive breast cancer and ductal carcinoma in situ","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1295573","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1295573_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1295573.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1295573.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1295573.csv.gz"}},{"accession":"PRJEB76817","age_categories":{"adult":261,"elderly":10},"countries":{"ES":271},"first_public_year":"2024","gbp_per_sample_median":6.72,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_infection":271},"intervention_design":"randomized_controlled_trial","intervention_detail":"Lamivudine/abacavir plus dolutegravir vs ritonavir-boosted darunavir (ART)","interventions":["drug_therapy"],"n_samples":271,"papers":[{"doi":"10.1038/s41467-026-69846-7","pmcid":"PMC12960958","pmid":"41781390","title":"Dolutegravir restores gut microbiota in late-stage HIV-1 unlike darunavir: an open-label, randomized clinical trial."}],"sample_intervention_arms":{"drug_therapy":263},"sex":{"female":34,"male":229},"title":"WMGS data from two-year, two-arm, randomized clinical trial comparing first-line antiretroviral therapy including dolutegravir vs. ritonavir-boosted darunavir in subjects with very advanced HIV-1 late presentation.","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB76817","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB76817_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB76817.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB76817.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB76817.csv.gz"}},{"accession":"PRJEB87602","age_categories":{"adult":180,"elderly":83},"countries":{"NL":263},"first_public_year":"2025","gbp_per_sample_median":0.02,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":58,"ulcerative_colitis":178},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":263,"papers":[{"doi":"10.1093/ecco-jcc/jjad092","pmcid":"PMC10673813","pmid":"37243505","title":"Bacterial Oncotraits Rather than Spatial Organization Are Associated with Dysplasia in Ulcerative Colitis."}],"sample_intervention_arms":{},"sex":{"female":128,"male":135},"title":"Bacteria in colitis associated cancer development","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB87602","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB87602_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB87602.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB87602.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB87602.csv.gz"}},{"accession":"PRJNA1269031","age_categories":{"adult":253,"elderly":5},"countries":{"DK":258},"first_public_year":"2025","gbp_per_sample_median":0.6,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"ibs":258},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":258,"papers":[{"doi":"10.3389/fnut.2025.1701341","pmcid":"PMC12869991","pmid":"41648756","title":"Eight weeks of treatment with probiotic &lt;i&gt;Bifidobacterium breve&lt;/i&gt;, Bif195 lowers fatigue scores in patients with diarrhoea-predominant irritable bowel syndrome: results from a randomise"}],"sample_intervention_arms":{"no_intervention":52,"placebo":107,"probiotic":99},"sex":{"female":155,"male":103},"title":"Randomised, clinical trial: Eight weeks of treatment with probiotic Bifidobacterium breve, Bif195 lowers fatigue scores in patients with diarrhoea-predominant irritable bowel syndrome","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1269031","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1269031_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1269031.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1269031.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1269031.csv.gz"}},{"accession":"PRJNA745329","age_categories":{"adult":151,"elderly":100},"countries":{"US":251},"first_public_year":"2021","gbp_per_sample_median":0.32,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":80,"colorectal_cancer":2,"healthy_control":83,"other_disease":59},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":251,"papers":[{"doi":"10.1038/s41522-022-00328-6","pmcid":"PMC9424272","pmid":"36038569","title":"Distinct colon mucosa microbiomes associated with tubular adenomas and serrated polyps."},{"doi":"10.1080/19490976.2023.2245562","pmcid":"PMC10464540","pmid":"37635357","title":"Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer."},{"doi":"10.1038/s41522-026-01001-y","pmcid":"PMC13381771","pmid":"42106361","title":"Instance-based transfer learning enables cross-cohort early detection of colorectal cancer."}],"sample_intervention_arms":{"bowel_preparation":126},"sex":{"female":101,"male":117},"title":"Fecal and colon mucosa sequencing of tubular adenoma, serrated, and polyp-free individuals","trial_population_condition":"colorectal_adenoma","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA745329","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA745329_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA745329.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA745329.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA745329.csv.gz"}},{"accession":"PRJEB9576","age_categories":{"adult":178,"elderly":72},"countries":{"GB":250},"first_public_year":"2016","gbp_per_sample_median":7.12,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"allergy_or_atopy":24,"healthy_control":169,"neurological_psychiatric":36,"other_disease":8},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":250,"papers":[{"doi":"10.1371/journal.pbio.3000102","pmcid":"PMC6361464","pmid":"30673701","title":"Evolutionary dynamics of bacteria in the gut microbiome within and across hosts."},{"doi":"10.3389/fmicb.2021.740990","pmcid":"PMC8511818","pmid":"34659174","title":"Characterizing Enterotypes in Human Metagenomics: A Viral Perspective."},{"doi":"10.1186/s12864-022-09087-2","pmcid":"PMC9789565","pmid":"36564713","title":"Machine learning framework for gut microbiome biomarkers discovery and modulation analysis in large-scale obese population."},{"doi":"10.1016/j.xgen.2022.100219","pmcid":"PMC9903723","pmid":"36778050","title":"Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases."},{"doi":"10.1038/s43587-022-00306-9","pmcid":"PMC10154212","pmid":"37118093","title":"Toward an improved definition of a healthy microbiome for healthy aging."}],"sample_intervention_arms":{},"sex":{"female":250},"title":"Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB9576","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB9576_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB9576.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB9576.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB9576.csv.gz"}},{"accession":"PRJEB33500","age_categories":{"adult":241,"elderly":3},"countries":{"IT":244},"first_public_year":"2020","gbp_per_sample_median":3.12,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"obesity":244},"intervention_design":"randomized_controlled_trial","intervention_detail":"Personalized isocaloric Mediterranean diet, 8 weeks, vs habitual diet control","interventions":["diet_intervention"],"n_samples":244,"papers":[{"doi":"10.1136/gutjnl-2019-320438","pmcid":"PMC7306983","pmid":"32075887","title":"Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake."},{"doi":"10.1007/s00394-021-02538-8","pmcid":"PMC8437855","pmid":"33763720","title":"Mediterranean diet consumption affects the endocannabinoid system in overweight and obese subjects: possible links with gut microbiome, insulin resistance and inflammation."},{"doi":"10.3390/life11111246","pmcid":"PMC8620312","pmid":"34833122","title":"Lacticaseibacillus paracasei: Occurrence in the Human Gut Microbiota and K-Mer-Based Assessment of Intraspecies Diversity."},{"doi":"10.1038/s41467-022-34405-3","pmcid":"PMC9649010","pmid":"36357393","title":"Faecal microbiome-based machine learning for multi-class disease diagnosis."},{"doi":"10.1186/s40168-023-01667-y","pmcid":"PMC10588041","pmid":"37858269","title":"Four functional profiles for fibre and mucin metabolism in the human gut microbiome."}],"sample_intervention_arms":{"diet_intervention":85,"no_intervention":159},"sex":{"female":128,"male":116},"title":"Mediterranean diet intervention in overweight and obese subjects leads to multiple beneficial shifts in gut microbiome and metabolome independently from energy intake","trial_population_condition":"obesity","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB33500","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB33500_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB33500.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB33500.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB33500.csv.gz"}},{"accession":"PRJEB38625","age_categories":{"adult":157,"elderly":87},"countries":{"ES":244},"first_public_year":"2022","gbp_per_sample_median":1.84,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"allergy_or_atopy":1,"healthy_control":33,"obesity":8,"other_cancer":25,"other_disease":8,"type2_diabetes":2},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":244,"papers":[{"doi":"10.1136/gutjnl-2021-324755","pmcid":"PMC9185815","pmid":"35260444","title":"A faecal microbiota signature with high specificity for pancreatic cancer."},{"doi":"10.1016/j.isci.2024.109294","pmcid":"PMC10915599","pmid":"38450156","title":"Highly accurate diagnosis of pancreatic cancer by integrative modeling using gut microbiome and exposome data."},{"doi":"10.1097/js9.0000000000001762","pmcid":"PMC11487005","pmid":"38874485","title":"The microbial composition of pancreatic ductal adenocarcinoma: a systematic review of 16S rRNA gene sequencing."},{"doi":"10.1016/j.cpblue.2026.100034","pmcid":"PMC13269251","pmid":"42312244","title":"Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals."}],"sample_intervention_arms":{},"sex":{"female":49,"male":87},"title":"The oral and fecal microbiome in chronic pancreatitis and pancreatic cancer.","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB38625","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB38625_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB38625.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB38625.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB38625.csv.gz"}},{"accession":"PRJEB81519","age_categories":{"adult":197,"elderly":41},"countries":{"NL":238},"first_public_year":"2025","gbp_per_sample_median":0.42,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"healthy_control":238},"intervention_design":"crossover","intervention_detail":"Acacia gum and carrot powder fibre mixture vs placebo, 12 weeks crossover","interventions":["prebiotic_or_fibre"],"n_samples":238,"papers":[{"doi":"10.3389/fmicb.2025.1708906","pmcid":"PMC12756460","pmid":"41488312","title":"Translating &lt;i&gt;in vitro&lt;/i&gt; gut microbiota models to human context: compositional correlations under dietary fiber intervention."}],"sample_intervention_arms":{"no_intervention":121,"placebo":58,"prebiotic_or_fibre":59},"sex":{"female":113,"male":125},"title":"Effects of a Fiber Mixture on Gut Microbiome Diversity and Short-Chain Fatty Acids in Adults with Increased Metabolic Risk: A Randomized Cross-over Study","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB81519","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB81519_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB81519.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB81519.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB81519.csv.gz"}},{"accession":"PRJNA878603","age_categories":{"adult":231,"elderly":7},"countries":{"US":238},"first_public_year":"2023","gbp_per_sample_median":2.33,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":92,"other_disease":146},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":238,"papers":[{"doi":"10.1016/j.chom.2023.01.001","pmcid":"PMC10353054","pmid":"36758521","title":"Multi-'omics of gut microbiome-host interactions in short- and long-term myalgic encephalomyelitis/chronic fatigue syndrome patients."},{"doi":"10.1142/9789811286421_0039","pmcid":"PMC10764071","pmid":"38160303","title":"KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome."}],"sample_intervention_arms":{},"sex":{"female":162,"male":76},"title":"Multi-omics of host-microbiome interactions in short- and long-term Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA878603","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA878603_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA878603.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA878603.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA878603.csv.gz"}},{"accession":"PRJEB49124","age_categories":{"elderly":234},"countries":{"SG":234},"first_public_year":"2021","gbp_per_sample_median":1.12,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":234},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":234,"papers":[{"doi":"10.1038/s41467-024-52097-9","pmcid":"PMC11377447","pmid":"39237540","title":"Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes."}],"sample_intervention_arms":{},"sex":{"female":139,"male":95},"title":"Gut metagenomes of Asian octogenarians from SG90 cohort","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB49124","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB49124_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB49124.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB49124.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB49124.csv.gz"}},{"accession":"PRJNA524170","age_categories":{"adult":102,"elderly":21,"unknown":111},"countries":{"IL":234},"first_public_year":"2019","gbp_per_sample_median":1.0,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":21,"healthy_control":39,"ibd_unspecified":35},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":234,"papers":[{"doi":"10.1053/j.gastro.2019.10.001","pmcid":null,"pmid":"31605691","title":"Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy."},{"doi":"10.1128/msystems.00984-20","pmcid":"PMC8546988","pmid":"33653942","title":"Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn's Disease."}],"sample_intervention_arms":{},"sex":{"female":73,"male":50},"title":"Resistant microbiome underlies antibiotic therapy in pouchitis","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA524170","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA524170_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA524170.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA524170.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA524170.csv.gz"}},{"accession":"PRJNA297252","age_categories":{"adult":16,"elderly":213},"countries":{"CA":229},"first_public_year":"2015","gbp_per_sample_median":2.3,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":182,"other_disease":4,"other_infection":43},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":229,"papers":[{"doi":"10.1186/s40168-016-0156-3","pmcid":"PMC4791782","pmid":"26975510","title":"Bloom and bust: intestinal microbiota dynamics in response to hospital exposures and Clostridium difficile colonization or infection."},{"doi":"10.1007/s00248-018-1155-7","pmcid":"PMC6132499","pmid":"29445826","title":"Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes."},{"doi":"10.1186/s13059-019-1841-x","pmcid":"PMC6833257","pmid":"31690338","title":"Mash Screen: high-throughput sequence containment estimation for genome discovery."},{"doi":"10.1038/s43587-022-00306-9","pmcid":"PMC10154212","pmid":"37118093","title":"Toward an improved definition of a healthy microbiome for healthy aging."},{"doi":"10.1016/j.cpblue.2026.100034","pmcid":"PMC13269251","pmid":"42312244","title":"Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals."}],"sample_intervention_arms":{},"sex":{"female":105,"male":124},"title":"Intestinal microbiota dynamics in hospitalized patients","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA297252","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA297252_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA297252.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA297252.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA297252.csv.gz"}},{"accession":"PRJEB55648","age_categories":{"adolescent":28,"adult":96,"child":72,"elderly":2,"infant":28},"countries":{"VE":226},"first_public_year":"2023","gbp_per_sample_median":1.9,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":226},"intervention_design":"unknown","intervention_detail":"Ivermectin treatment given to villages between 2015 and 2016 sampling","interventions":[],"n_samples":226,"papers":[],"sample_intervention_arms":{},"sex":{"female":108,"male":80},"title":"multi bodi site study of Bolivar amerindian microbiome","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB55648","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB55648_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB55648.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB55648.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB55648.csv.gz"}},{"accession":"PRJNA400072","age_categories":{"adult":191,"elderly":29},"countries":{"NL":65,"US":155},"first_public_year":"2018","gbp_per_sample_median":3.11,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":88,"healthy_control":56,"ulcerative_colitis":76},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":220,"papers":[{"doi":"10.1038/s41564-018-0306-4","pmcid":"PMC6342642","pmid":"30531976","title":"Gut microbiome structure and metabolic activity in inflammatory bowel disease."},{"doi":"10.1038/s41467-019-10927-1","pmcid":"PMC6637180","pmid":"31316056","title":"Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences."},{"doi":"10.3389/fmicb.2020.595910","pmcid":"PMC7746778","pmid":"33343536","title":"A Comparative Evaluation of Tools to Predict Metabolite Profiles From Microbiome Sequencing Data."},{"doi":"10.7554/elife.58609","pmcid":"PMC8177889","pmid":"34085924","title":"Reshaping of bacterial molecular hydrogen metabolism contributes to the outgrowth of commensal E. coli during gut inflammation."},{"doi":"10.1016/j.chom.2021.07.013","pmcid":"PMC9064000","pmid":"34416161","title":"A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1."}],"sample_intervention_arms":{},"sex":{},"title":"Gut microbiome structure and metabolic activity in inflammatory bowel disease","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA400072","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA400072_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA400072.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA400072.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA400072.csv.gz"}},{"accession":"PRJEB22863","age_categories":{"adult":125,"elderly":94},"countries":{"FR":219},"first_public_year":"2017","gbp_per_sample_median":2.99,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"other_cancer":219},"intervention_design":"observational_with_procedure","intervention_detail":"Anti-PD-1 therapy; FMT and A. muciniphila supplementation in mouse models","interventions":["drug_therapy","fmt","probiotic"],"n_samples":219,"papers":[{"doi":"10.1126/science.aan3706","pmcid":null,"pmid":"29097494","title":"Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors."},{"doi":"10.3389/fonc.2022.837525","pmcid":"PMC9069064","pmid":"35530307","title":"Distinct Functional Metagenomic Markers Predict the Responsiveness to Anti-PD-1 Therapy in Chinese Non-Small Cell Lung Cancer Patients."},{"doi":"10.1186/s12967-025-06370-0","pmcid":"PMC11916936","pmid":"40098172","title":"Prioritizing gut microbial SNPs linked to immunotherapy outcomes in NSCLC patients by integrative bioinformatics analysis."},{"doi":"10.1126/sciadv.aaz2299","pmcid":"PMC7176420","pmid":"32494636","title":"Metagenomic growth rate inferences of strains in situ."},{"doi":"10.1084/jem.20200606","pmcid":"PMC7664509","pmid":"33175106","title":"Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers."}],"sample_intervention_arms":{"drug_therapy":92,"no_intervention":127},"sex":{"female":47,"male":127},"title":"Gut mictobiota composition correlation with the clinical outcome of NSCLC and RCC patients treated with anti-PD-1 mAB","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB22863","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB22863_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB22863.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB22863.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB22863.csv.gz"}},{"accession":"PRJNA672867","age_categories":{"adult":134,"elderly":82},"countries":{"US":216},"first_public_year":"2020","gbp_per_sample_median":2.19,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"other_cancer":216},"intervention_design":"single_arm_before_after","intervention_detail":"Responder-derived FMT combined with anti-PD-1 therapy in refractory melanoma","interventions":["drug_therapy","fmt"],"n_samples":216,"papers":[{"doi":"10.1126/science.abf3363","pmcid":"PMC8097968","pmid":"33542131","title":"Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients."},{"doi":"10.1371/journal.pone.0274633","pmcid":"PMC9477264","pmid":"36107983","title":"Time series strain tracking analysis post fecal transplantation identifies individual specific patterns of fecal dominant donor, recipient, and unrelated microbial strains."},{"doi":"10.1186/s12866-021-02312-0","pmcid":"PMC8454007","pmid":"34544375","title":"Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy."},{"doi":"10.1126/science.aaz7015","pmcid":"PMC8970537","pmid":"34941392","title":"Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response."},{"doi":"10.1126/sciimmunol.abn0704","pmcid":"PMC9925043","pmid":"36083892","title":"The microbiome-derived metabolite TMAO drives immune activation and boosts responses to immune checkpoint blockade in pancreatic cancer."}],"sample_intervention_arms":{"fmt":167,"no_intervention":49},"sex":{"female":65,"male":151},"title":"Effectiveness of Fecal Microbiota Transplant together with PD-1 blockade in overcoming resistance to anti-PD-1 therapy in advanced melanoma patients","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA672867","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA672867_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA672867.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA672867.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA672867.csv.gz"}},{"accession":"PRJEB37017","age_categories":{"adult":7,"elderly":207},"countries":{"IE":214},"first_public_year":"2020","gbp_per_sample_median":4.24,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":214,"papers":[{"doi":"10.1080/19490976.2023.2282796","pmcid":"PMC10854441","pmid":"38010168","title":"Engraftment of aging-related human gut microbiota and the effect of a seven-species consortium in a pre-clinical model."},{"doi":"10.1080/19490976.2023.2297852","pmcid":"PMC10829834","pmid":"38289284","title":"A gut aging clock using microbiome multi-view profiles is associated with health and frail risk."},{"doi":"10.7554/elife.50240","pmcid":"PMC7065848","pmid":"32159510","title":"Adjusting for age improves identification of gut microbiome alterations in multiple diseases."},{"doi":"10.1038/s43587-022-00306-9","pmcid":"PMC10154212","pmid":"37118093","title":"Toward an improved definition of a healthy microbiome for healthy aging."}],"sample_intervention_arms":{},"sex":{"female":104,"male":84},"title":"Identifying frailty-associated markers in Elderly Irish Individuals","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB37017","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB37017_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB37017.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB37017.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB37017.csv.gz"}},{"accession":"PRJNA375935","age_categories":{"adolescent":2,"adult":208,"elderly":1},"countries":{"CN":211},"first_public_year":"2017","gbp_per_sample_median":3.64,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":97,"healthy_control":114},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":211,"papers":[{"doi":"10.1186/s13059-017-1271-6","pmcid":"PMC5530561","pmid":"28750650","title":"Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis."},{"doi":"10.1016/j.isci.2020.101199","pmcid":"PMC7298543","pmid":"32534441","title":"Human Gut Microbiome Aging Clock Based on Taxonomic Profiling and Deep Learning."},{"doi":"10.1038/s41396-021-01016-7","pmcid":"PMC8528855","pmid":"34079079","title":"Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers."},{"doi":"10.1038/s41522-021-00235-2","pmcid":"PMC8352958","pmid":"34373464","title":"Metagenomic analysis revealed the potential role of gut microbiome in gout."},{"doi":"10.1186/s12866-021-02321-z","pmcid":"PMC8485520","pmid":"34592929","title":"MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen."}],"sample_intervention_arms":{},"sex":{"female":41,"male":56},"title":"human gut Metagenome","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA375935","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA375935_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA375935.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA375935.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA375935.csv.gz"}},{"accession":"PRJEB42155","age_categories":{"adult":195,"child":1,"elderly":12,"infant":2},"countries":{"US":210},"first_public_year":"2023","gbp_per_sample_median":0.25,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":118,"healthy_control":18,"ulcerative_colitis":74},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":210,"papers":[{"doi":"10.1038/s41564-021-01050-3","pmcid":"PMC8852248","pmid":"35087228","title":"Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity."},{"doi":"10.1186/s40168-022-01331-x","pmcid":"PMC9400277","pmid":"35999575","title":"Location-specific signatures of Crohn's disease at a multi-omics scale."},{"doi":"10.20517/mrr.2024.09","pmcid":"PMC11480726","pmid":"39421249","title":"Pangenomic analysis identifies correlations between &lt;i&gt;Akkermansia&lt;/i&gt; species and subspecies and human health outcomes."},{"doi":"10.1128/msystems.01453-25","pmcid":"PMC12710343","pmid":"41283667","title":"Phylo-Spec: a phylogeny-fusion deep learning model advances microbiome status identification."}],"sample_intervention_arms":{},"sex":{"female":101,"male":87},"title":"UCSD IBD 200 Patient Cohort Multi-omic Project","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB42155","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB42155_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB42155.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB42155.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB42155.csv.gz"}},{"accession":"PRJNA381333","age_categories":{"adolescent":11,"adult":140,"child":23,"elderly":25,"infant":9},"countries":{"CN":208},"first_public_year":"2018","gbp_per_sample_median":0.04,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":208},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":208,"papers":[{"doi":"10.1080/19490976.2024.2350151","pmcid":"PMC11086029","pmid":"38715346","title":"Meta-analysis identifying gut microbial biomarkers of Qinghai-Tibet Plateau populations and the functionality of microbiota-derived butyrate in high-altitude adaptation."},{"doi":"10.1038/s41598-023-47748-8","pmcid":"PMC10696028","pmid":"38049420","title":"Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits."}],"sample_intervention_arms":{},"sex":{"female":113,"male":95},"title":"Tibetan Gut Miicrobiota Metagenome","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA381333","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA381333_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA381333.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA381333.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA381333.csv.gz"}},{"accession":"PRJNA491335","age_categories":{"adult":200,"elderly":8},"countries":{"DK":208},"first_public_year":"2018","gbp_per_sample_median":7.08,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"healthy_control":208},"intervention_design":"crossover","intervention_detail":"Low-gluten (2g/day) vs high-gluten (18g/day) diet, 8-week periods","interventions":["diet_intervention"],"n_samples":208,"papers":[{"doi":"10.1038/s41467-018-07019-x","pmcid":"PMC6234216","pmid":"30425247","title":"A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults."},{"doi":"10.1038/s41598-020-76097-z","pmcid":"PMC7674420","pmid":"33208769","title":"Data integration for prediction of weight loss in randomized controlled dietary trials."},{"doi":"10.1038/s43587-022-00306-9","pmcid":"PMC10154212","pmid":"37118093","title":"Toward an improved definition of a healthy microbiome for healthy aging."},{"doi":"10.1038/s41467-023-44636-7","pmcid":"PMC10770139","pmid":"38182626","title":"Functional host-specific adaptation of the intestinal microbiome in hominids."},{"doi":"10.1038/s41522-026-00935-7","pmcid":"PMC13039869","pmid":"41730870","title":"pH regulates gut bacterial tryptophan metabolism."}],"sample_intervention_arms":{"diet_intervention":101,"no_intervention":107},"sex":{"female":116,"male":92},"title":"3G low-gluten cross-over trial - faeces metagenome data","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA491335","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA491335_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA491335.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA491335.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA491335.csv.gz"}},{"accession":"PRJEB72524","age_categories":{"adult":78,"elderly":125},"countries":{},"first_public_year":"2025","gbp_per_sample_median":3.74,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":2,"colorectal_cancer":201},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":203,"papers":[{"doi":"10.1038/s41591-025-03693-9","pmcid":"PMC12283368","pmid":"40461820","title":"Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer."}],"sample_intervention_arms":{},"sex":{"female":91,"male":112},"title":"Gut microbiome samples from a cohort of CRC patients in Brno, Czech Republic.","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB72524","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB72524_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB72524.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB72524.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB72524.csv.gz"}},{"accession":"PRJEB83322","age_categories":{"elderly":203},"countries":{"ES":203},"first_public_year":"2025","gbp_per_sample_median":1.21,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":203,"papers":[{"doi":"10.1111/acel.70365","pmcid":"PMC12790095","pmid":"41518158","title":"The Role of the Gut Microbiome in the Complex Network of Frailty Syndrome and Associated Comorbidities in Aging."}],"sample_intervention_arms":{},"sex":{},"title":"The gut microbiome, frailty syndrome and comorbidities: a complex network in aging","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB83322","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB83322_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB83322.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB83322.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB83322.csv.gz"}},{"accession":"PRJEB76236","age_categories":{"elderly":200},"countries":{"IT":200},"first_public_year":"2024","gbp_per_sample_median":0.85,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{},"intervention_design":"crossover","intervention_detail":"Polyphenol-rich diet vs control diet, 8 weeks","interventions":["diet_intervention"],"n_samples":200,"papers":[{"doi":"10.20517/mrr.2025.33","pmcid":"PMC12702650","pmid":"41403880","title":"Effect of a polyphenol-rich dietary pattern on subjects aged ≥ 60 years with higher levels of inflammatory markers: insights into microbiome and metabolome."}],"sample_intervention_arms":{"diet_intervention":72,"no_intervention":100},"sex":{},"title":"MaPLE insights into microbiome and metabolome.","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB76236","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB76236_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB76236.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB76236.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB76236.csv.gz"}},{"accession":"PRJNA1453174","age_categories":{"adult":146,"elderly":54},"countries":{"KE":200},"first_public_year":"2026","gbp_per_sample_median":7.39,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":113,"other_disease":87},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":200,"papers":[],"sample_intervention_arms":{},"sex":{"female":92,"male":108},"title":"Gut microbiome of subjects with either gastric cancer or gastritis","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1453174","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1453174_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1453174.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1453174.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1453174.csv.gz"}},{"accession":"PRJNA862629","age_categories":{"adolescent":21,"adult":140,"child":13,"elderly":26},"countries":{"MY":200},"first_public_year":"2023","gbp_per_sample_median":7.77,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":200},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":200,"papers":[{"doi":"10.1038/s41522-023-00425-0","pmcid":"PMC10423249","pmid":"37573460","title":"Social demographics determinants for resistome and microbiome variation of a multiethnic community in Southern Malaysia."}],"sample_intervention_arms":{},"sex":{"female":107,"male":93},"title":"Segamat Resistome Profiling","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA862629","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA862629_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA862629.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA862629.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA862629.csv.gz"}},{"accession":"PRJEB6070","age_categories":{"adult":116,"elderly":83},"countries":{"DE":43,"FR":156},"first_public_year":"2014","gbp_per_sample_median":5.24,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":42,"healthy_control":66,"other_cancer":91},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":199,"papers":[{"doi":"10.1038/s41467-019-08844-4","pmcid":"PMC6399450","pmid":"30833550","title":"Microbial abundance, activity and population genomic profiling with mOTUs2."},{"doi":"10.7717/peerj.7315","pmcid":"PMC6673421","pmid":"31392094","title":"Association network analysis identifies enzymatic components of gut microbiota that significantly differ between colorectal cancer patients and healthy controls."},{"doi":"10.1093/bioinformatics/btz686","pmcid":null,"pmid":"31504188","title":"Phylogenetic tree-based microbiome association test."},{"doi":"10.1073/pnas.1912129116","pmcid":"PMC6883805","pmid":"31712445","title":"Colorectal cancer-associated microbiota contributes to oncogenic epigenetic signatures."},{"doi":"10.3892/ol.2020.11967","pmcid":"PMC7439112","pmid":"32831925","title":"Alteration of the abundance of Parvimonas micra in the gut along the adenoma-carcinoma sequence."}],"sample_intervention_arms":{},"sex":{"female":82,"male":117},"title":"Potential of fecal microbiota for early stage detection of colorectal cancer","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB6070","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB6070_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB6070.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB6070.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB6070.csv.gz"}},{"accession":"PRJNA751448","age_categories":{"adult":181,"elderly":16},"countries":{"US":197},"first_public_year":"2021","gbp_per_sample_median":1.84,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":91,"other_disease":106},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":197,"papers":[{"doi":"10.1016/j.chom.2023.01.004","pmcid":"PMC10183837","pmid":"36758522","title":"Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS."},{"doi":"10.1038/s41598-026-56821-x","pmcid":"PMC13526866","pmid":"42289444","title":"Fatigue-associated gut bacteria in Japanese healthy adults characterized by metagenomic analysis."}],"sample_intervention_arms":{},"sex":{"female":144,"male":53},"title":"gut microbiome of Myalgic Encephlomyelitis/Chronic Fatigue Syndrome patients","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA751448","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA751448_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA751448.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA751448.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA751448.csv.gz"}},{"accession":"PRJNA429097","age_categories":{"adult":167,"elderly":20,"unknown":7},"countries":{"CN":194},"first_public_year":"2019","gbp_per_sample_median":5.77,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":99},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":194,"papers":[{"doi":"10.1080/19490976.2020.1712986","pmcid":"PMC7524397","pmid":"31971861","title":"Establishing high-accuracy biomarkers for colorectal cancer by comparing fecal microbiomes in patients with healthy families."},{"doi":"10.3389/fmicb.2023.1261889","pmcid":"PMC10556866","pmid":"37808286","title":"Machine learning approaches in microbiome research: challenges and best practices."},{"doi":"10.1038/s42003-023-05714-0","pmcid":"PMC10770074","pmid":"38182885","title":"Multi-kingdom microbial signatures in excess body weight colorectal cancer based on global metagenomic analysis."},{"doi":"10.1093/nar/gkae515","pmcid":"PMC11317153","pmid":"38884260","title":"Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome."},{"doi":"10.3390/microorganisms12102086","pmcid":"PMC11510655","pmid":"39458395","title":"Oral Microbial Translocation Genes in Gastrointestinal Cancers: Insights from Metagenomic Analysis."}],"sample_intervention_arms":{},"sex":{"female":76,"male":117},"title":"Microbiota Research on Chinses Colorectal Cancer","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA429097","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA429097_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA429097.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA429097.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA429097.csv.gz"}},{"accession":"PRJNA895487","age_categories":{"adult":51,"child":94,"elderly":39,"infant":10},"countries":{"BB":2,"BS":2,"CA":4,"CN":2,"FR":4,"GB":2,"MX":2,"PA":4,"RU":2,"TC":2,"TH":2,"US":164,"VN":2},"first_public_year":"2023","gbp_per_sample_median":1.53,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":95,"neurological_psychiatric":77,"other_disease":4},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":194,"papers":[{"doi":"10.1038/s41598-023-38228-0","pmcid":"PMC10345091","pmid":"37443184","title":"Topic modeling for multi-omic integration in the human gut microbiome and implications for Autism."},{"doi":"10.1038/s41598-022-21327-9","pmcid":"PMC9554176","pmid":"36220843","title":"Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups"},{"doi":"10.1038/s43705-021-00080-6","pmcid":"PMC9723651","pmid":"37938270","title":"Longitudinal study of stool-associated microbial taxa in sibling pairs with and without autism spectrum disorder"},{"doi":"10.1101/2022.09.30.509056","pmcid":null,"pmid":null,"title":"Topic modeling for multi-omic integration in the human gut microbiome and implications for Autism"},{"doi":"10.1186/s12859-021-04427-7","pmcid":"PMC8527694","pmid":"34666677","title":"Improved detection of disease-associated gut microbes using 16S sequence-based biomarkers"}],"sample_intervention_arms":{},"sex":{"female":54,"male":140},"title":"Multi-omic gut microbiomes of autistic children and their typically developing siblings","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA895487","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA895487_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA895487.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA895487.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA895487.csv.gz"}},{"accession":"PRJEB43611","age_categories":{"adolescent":22,"adult":142,"child":16,"elderly":12},"countries":{"FR":192},"first_public_year":"2022","gbp_per_sample_median":2.99,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"allergy_or_atopy":192},"intervention_design":"single_arm_before_after","intervention_detail":"3-week balneotherapy (thermal spring water treatment)","interventions":["other_intervention"],"n_samples":192,"papers":[{"doi":"10.2147/ccid.s342104","pmcid":"PMC8818552","pmid":"35140493","title":"Changes in Gut Microbiota of Patients with Atopic Dermatitis During Balneotherapy."}],"sample_intervention_arms":{"no_intervention":96,"other_intervention":96},"sex":{"female":102,"male":90},"title":"Changes in gut microbiota during balneotherapy","trial_population_condition":"allergy_or_atopy","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB43611","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB43611_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB43611.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB43611.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB43611.csv.gz"}},{"accession":"PRJEB53403","age_categories":{"adult":136,"elderly":56},"countries":{"US":192},"first_public_year":"2022","gbp_per_sample_median":2.98,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":79,"neurological_psychiatric":55},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":192,"papers":[{"doi":"10.1038/s41467-025-56829-3","pmcid":"PMC12059030","pmid":"40335465","title":"Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease."},{"doi":"10.1101/2023.12.05.569565","pmcid":null,"pmid":null,"title":"Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson’s disease"}],"sample_intervention_arms":{},"sex":{"female":45,"male":76},"title":"PD Shotgun Metagenomics Data","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB53403","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB53403_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB53403.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB53403.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB53403.csv.gz"}},{"accession":"PRJNA909223","age_categories":{"adult":108,"elderly":84},"countries":{"DE":192},"first_public_year":"2024","gbp_per_sample_median":3.5,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":192,"papers":[{"doi":"10.1038/s41522-024-00538-0","pmcid":"PMC11291933","pmid":"39085233","title":"Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19."}],"sample_intervention_arms":{},"sex":{"female":57,"male":135},"title":"Study of microbiome alterations in hospitalized COVID-19 patients and non-infected controls","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA909223","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA909223_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA909223.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA909223.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA909223.csv.gz"}},{"accession":"PRJNA300541","age_categories":{"adolescent":12,"adult":103,"child":34,"elderly":16,"infant":25,"neonate":1},"countries":{"PE":77,"SV":114},"first_public_year":"2016","gbp_per_sample_median":0.73,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":191},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":191,"papers":[{"doi":null,"pmcid":null,"pmid":null,"title":""},{"doi":null,"pmcid":null,"pmid":null,"title":""},{"doi":"10.3389/fmicb.2022.1006721","pmcid":"PMC9512645","pmid":"36177457","title":"Gut microbe metabolism of small molecules supports human development across the early stages of life."},{"doi":null,"pmcid":null,"pmid":null,"title":""},{"doi":"10.1128/spectrum.00665-23","pmcid":"PMC10269646","pmid":"37191543","title":"Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria."}],"sample_intervention_arms":{},"sex":{"female":96,"male":92},"title":"Antibiotic resistance exchange between microbiota in resource-poor settings in Latin America","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA300541","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA300541_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA300541.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA300541.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA300541.csv.gz"}},{"accession":"PRJEB12124","age_categories":{"adult":186,"elderly":2},"countries":{"CN":188},"first_public_year":"2016","gbp_per_sample_median":5.7,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"type2_diabetes":188},"intervention_design":"randomized_controlled_trial","intervention_detail":"Acarbose vs Glipizide (sulfonylurea) oral antidiabetic drugs in treatment-naive T2D patients","interventions":["drug_therapy"],"n_samples":188,"papers":[{"doi":"10.1038/s41467-017-01682-2","pmcid":"PMC5702614","pmid":"29176714","title":"Analyses of gut microbiota and plasma bile acids enable stratification of patients for antidiabetic treatment."},{"doi":"10.1128/mbio.00095-20","pmcid":"PMC7157763","pmid":"32265336","title":"Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides."},{"doi":"10.1128/mbio.03628-20","pmcid":"PMC8262883","pmid":"34061597","title":"Human Gut Faecalibacterium prausnitzii Deploys a Highly Efficient Conserved System To Cross-Feed on β-Mannan-Derived Oligosaccharides."},{"doi":"10.1016/j.chom.2022.02.001","pmcid":"PMC9096808","pmid":"35240043","title":"Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria."},{"doi":"10.1038/s41467-024-47272-x","pmcid":"PMC11009399","pmid":"38605009","title":"Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases."}],"sample_intervention_arms":{"drug_therapy":94},"sex":{"female":72,"male":116},"title":"Gut microbiome-dependent stratification of patients for anti-diabetic treatment","trial_population_condition":"type2_diabetes","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB12124","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB12124_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB12124.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB12124.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB12124.csv.gz"}},{"accession":"PRJEB52891","age_categories":{"adult":175,"elderly":11},"countries":{},"first_public_year":"2024","gbp_per_sample_median":12.37,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":27,"liver_disease":141,"sepsis_or_infection":14},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":186,"papers":[{"doi":"10.1101/2023.08.06.552152","pmcid":null,"pmid":null,"title":"Pathogenic entero- and salivatypes harbour changes in microbiome virulence and antimicrobial resistance genes with increasing chronic liver disease severity"},{"doi":"10.1038/s41564-025-02223-0","pmcid":"PMC12768972","pmid":"41461922","title":"Microbial collagenase activity is linked to oral-gut translocation in advanced chronic liver disease."},{"doi":"10.1002/imt2.70131","pmcid":"PMC13377410","pmid":"42491347","title":"Integrative host-microbiome modeling uncovers the implication of oral-gut translocation in advanced cirrhosis."}],"sample_intervention_arms":{},"sex":{"female":60,"male":122},"title":"Oral-gut microbiome interactions in advanced cirrhosis: characterisation of pathogenic enterotypes and salivatypes, virulence factors and antimicrobial resistance","trial_population_condition":"liver_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB52891","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB52891_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB52891.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB52891.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB52891.csv.gz"}},{"accession":"PRJNA1398904","age_categories":{"adolescent":2,"adult":147,"child":4,"elderly":31,"infant":1},"countries":{"US":185},"first_public_year":"2026","gbp_per_sample_median":2.18,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"liver_disease":42,"transplant_or_immunocompromised":143},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":185,"papers":[],"sample_intervention_arms":{},"sex":{"female":78,"male":107},"title":"Enterococcus faecium Driven Metabolic Dysbiosis is Linked to Mortality following Liver Transplant","trial_population_condition":"transplant_or_immunocompromised","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1398904","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1398904_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1398904.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1398904.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1398904.csv.gz"}},{"accession":"PRJNA289586","age_categories":{"adolescent":37,"adult":112,"child":19,"elderly":10,"infant":6},"countries":{"LU":184},"first_public_year":"2016","gbp_per_sample_median":3.73,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":87,"type1_diabetes":81},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":184,"papers":[{"doi":"10.1038/nmicrobiol.2016.180","pmcid":null,"pmid":"27723761","title":"Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes."},{"doi":"10.1073/pnas.2023202118","pmcid":"PMC8201803","pmid":"34083435","title":"A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases."},{"doi":"10.3389/fmicb.2016.00884","pmcid":"PMC4914512","pmid":"27445992","title":"Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract."},{"doi":"10.7554/elife.42693","pmcid":"PMC6424576","pmid":"30747106","title":"Extensive transmission of microbes along the gastrointestinal tract."},{"doi":"10.3390/microorganisms7090367","pmcid":"PMC6780314","pmid":"31546776","title":"Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome."}],"sample_intervention_arms":{},"sex":{"female":109,"male":74},"title":"Human Gut Microbiome in a Multiplex Family Study of Type 1 Diabetes Mellitus","trial_population_condition":"type1_diabetes","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA289586","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA289586_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA289586.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA289586.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA289586.csv.gz"}},{"accession":"PRJNA1236664","age_categories":{"adult":159,"elderly":23},"countries":{"CA":182},"first_public_year":"2025","gbp_per_sample_median":2.78,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_infection":182},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":182,"papers":[{"doi":"10.21203/rs.3.rs-8876425/v1","pmcid":null,"pmid":null,"title":"Microbiota-derived extracellular vesicles mediate gut-brain axis dysfunction in long COVID"},{"doi":"10.64898/2026.02.28.708602","pmcid":null,"pmid":null,"title":"Microbiota-derived extracellular vesicles link intestinal dysbiosis to neuroimmune activation in long COVID"}],"sample_intervention_arms":{},"sex":{"female":114,"male":68},"title":"Intestinal dysbiosis promotes gut permeability and neurological sequelae in individuals with long COVID via gut microbiota-derived extracellular vesicles","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1236664","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1236664_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1236664.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1236664.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1236664.csv.gz"}},{"accession":"PRJNA389927","age_categories":{"adult":58,"elderly":19,"unknown":104},"countries":{"CA":57,"US":124},"first_public_year":"2017","gbp_per_sample_median":0.63,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":56,"healthy_control":69,"other_cancer":56},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":181,"papers":[{"doi":"10.1128/mbio.02248-18","pmcid":"PMC6247079","pmid":"30459201","title":"Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome."},{"doi":"10.1128/mbio.01454-19","pmcid":"PMC6606814","pmid":"31266879","title":"Fecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community Structure."},{"doi":"10.1186/s13059-024-03236-4","pmcid":"PMC11020464","pmid":"38622738","title":"Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes."},{"doi":"10.1038/s41467-021-23265-y","pmcid":"PMC8144394","pmid":"34031391","title":"Identification of microbial markers across populations in early detection of colorectal cancer."},{"doi":"10.3389/fmicb.2021.765291","pmcid":"PMC8715872","pmid":"34975790","title":"Species-Level Analysis of the Human Gut Microbiome Shows Antibiotic Resistance Genes Associated With Colorectal Cancer."}],"sample_intervention_arms":{},"sex":{"female":35,"male":46},"title":"Viral and Bacterial Communities of Colorectal Cancer","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA389927","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA389927_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA389927.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA389927.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA389927.csv.gz"}},{"accession":"PRJNA826552","age_categories":{"adult":173,"elderly":8},"countries":{"CN":181},"first_public_year":"2022","gbp_per_sample_median":9.26,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"type2_diabetes":181},"intervention_design":"randomized_controlled_trial","intervention_detail":"Acarbose vs vildagliptin, 24-week RCT in T2D patients","interventions":["drug_therapy"],"n_samples":181,"papers":[{"doi":"10.1007/s00125-022-05768-5","pmcid":"PMC9477956","pmid":"35930018","title":"Metagenomic analysis reveals crosstalk between gut microbiota and glucose-lowering drugs targeting the gastrointestinal tract in Chinese patients with type 2 diabetes: a 6 month, two-arm randomised tr"},{"doi":"10.1002/imt2.179","pmcid":"PMC11170963","pmid":"38882498","title":"Deciphering unique and shared interactions between the human gut microbiota and oral antidiabetic drugs."}],"sample_intervention_arms":{"drug_therapy":82,"no_intervention":82},"sex":{"female":72,"male":92},"title":"human gut metagenome Raw sequence reads","trial_population_condition":"type2_diabetes","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA826552","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA826552_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA826552.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA826552.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA826552.csv.gz"}},{"accession":"PRJNA487636","age_categories":{"adult":157,"elderly":23},"countries":{"US":180},"first_public_year":"2018","gbp_per_sample_median":0.51,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":25,"crohns_disease":55,"healthy_control":64,"ibd_unspecified":5,"ulcerative_colitis":31},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":180,"papers":[{"doi":"10.1093/ibd/izy318","pmcid":"PMC6458525","pmid":"30321331","title":"An Increased Abundance of Clostridiaceae Characterizes Arthritis in Inflammatory Bowel Disease and Rheumatoid Arthritis: A Cross-sectional Study."},{"doi":"10.1126/scitranslmed.abl3927","pmcid":"PMC9741845","pmid":"35976997","title":"The systemic anti-microbiota IgG repertoire can identify gut bacteria that translocate across gut barrier surfaces."},{"doi":"10.1016/j.chom.2025.01.002","pmcid":"PMC12268991","pmid":"39947133","title":"A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules."}],"sample_intervention_arms":{},"sex":{"female":106,"male":74},"title":"An increased abundance of Clostridiaceae characterizes arthritis in inflammatory bowel disease and rheumatoid arthritis: a cross-sectional study","trial_population_condition":"ibd_or_gi_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA487636","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA487636_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA487636.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA487636.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA487636.csv.gz"}},{"accession":"PRJNA547591","age_categories":{"adolescent":10,"adult":136,"child":19,"elderly":15},"countries":{"CM":180},"first_public_year":"2020","gbp_per_sample_median":2.11,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"gi_infection_or_diarrhoea":89,"healthy_control":91},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":180,"papers":[{"doi":"10.1186/s13059-020-02020-4","pmcid":"PMC7249393","pmid":"32450885","title":"Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians."},{"doi":"10.1186/s12866-025-03974-w","pmcid":"PMC12051316","pmid":"40320537","title":"The altitudinal patterns of global human gut microbial diversity."},{"doi":"10.1101/2024.07.31.605962","pmcid":null,"pmid":null,"title":"Nanopore-based analysis unravels the genetic landscape and phylogenetic relationships of human-infecting  Trichuris incognita  and  Trichuris trichiura  in Côte d’Ivoire, Uganda, Tanzania, and Laos"},{"doi":"10.1038/s43587-022-00306-9","pmcid":"PMC10154212","pmid":"37118093","title":"Toward an improved definition of a healthy microbiome for healthy aging."},{"doi":"10.1038/s41598-023-47748-8","pmcid":"PMC10696028","pmid":"38049420","title":"Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits."}],"sample_intervention_arms":{},"sex":{"female":98,"male":77},"title":"Cameroon, U.S. fecal V4 amplicon sequencing of 16S rRNA and shotgun sequencing","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA547591","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA547591_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA547591.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA547591.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA547591.csv.gz"}},{"accession":"PRJEB47976","age_categories":{"adult":23,"elderly":152},"countries":{"DE":175},"first_public_year":"2022","gbp_per_sample_median":5.13,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":100,"neurological_psychiatric":75},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":175,"papers":[{"doi":"10.3389/fnins.2022.792996","pmcid":"PMC9063165","pmid":"35516807","title":"Signature of Alzheimer's Disease in Intestinal Microbiome: Results From the AlzBiom Study."},{"doi":"10.1186/s13195-023-01285-8","pmcid":"PMC10464408","pmid":"37608325","title":"A metagenomic study of gut viral markers in amyloid-positive Alzheimer's disease patients."},{"doi":"10.1128/msystems.00295-24","pmcid":"PMC11334437","pmid":"39078158","title":"Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases."},{"doi":"10.1186/s40168-025-02080-3","pmcid":"PMC11954268","pmid":"40158141","title":"Modeling microbiome-trait associations with taxonomy-adaptive neural networks."},{"doi":"10.1038/s41467-026-69711-7","pmcid":"PMC13035836","pmid":"41720792","title":"Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems."}],"sample_intervention_arms":{},"sex":{"female":88,"male":87},"title":"Alzheimer signature in intestinal microbiome: Results from the AlzBiom study.","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB47976","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB47976_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB47976.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB47976.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB47976.csv.gz"}},{"accession":"PRJEB110936","age_categories":{"adult":51,"elderly":123},"countries":{"KR":174},"first_public_year":"2026","gbp_per_sample_median":10.49,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_disease":174},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":174,"papers":[],"sample_intervention_arms":{},"sex":{"female":32,"male":142},"title":"Comparative Analysis of Urinary, Bladder Tissue, and Stool Microbiota in Bladder Cancer Using Shotgun Metagenomics","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB110936","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB110936_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB110936.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB110936.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB110936.csv.gz"}},{"accession":"PRJNA384246","age_categories":{"adult":159,"elderly":15},"countries":{"US":174},"first_public_year":"2019","gbp_per_sample_median":2.66,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":88,"ulcerative_colitis":86},"intervention_design":"single_arm_before_after","intervention_detail":"Vedolizumab therapy in IBD patients, sampled over treatment","interventions":["drug_therapy"],"n_samples":174,"papers":[{"doi":"10.1038/s41579-019-0213-6","pmcid":"PMC6759048","pmid":"31249397","title":"Microbial genes and pathways in inflammatory bowel disease."},{"doi":"10.1186/s12864-020-6749-z","pmcid":"PMC7216530","pmid":"32393180","title":"Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment."},{"doi":"10.1016/j.chom.2025.01.002","pmcid":"PMC12268991","pmid":"39947133","title":"A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules."}],"sample_intervention_arms":{},"sex":{"female":84,"male":90},"title":"Studies of metagenomes of inflammatory bowel disease patient receiving vedolizamub therapy","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA384246","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA384246_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA384246.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA384246.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA384246.csv.gz"}},{"accession":"PRJNA1198725","age_categories":{"adult":122,"elderly":49,"unknown":2},"countries":{"CN":173},"first_public_year":"2025","gbp_per_sample_median":12.02,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":53,"colorectal_cancer":70,"healthy_control":48},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":173,"papers":[{"doi":"10.1186/s12859-025-06156-7","pmcid":"PMC12107961","pmid":"40419960","title":"TaxaCal: enhancing species-level profiling accuracy of 16S amplicon data."},{"doi":"10.1038/s41522-026-01001-y","pmcid":"PMC13381771","pmid":"42106361","title":"Instance-based transfer learning enables cross-cohort early detection of colorectal cancer."}],"sample_intervention_arms":{},"sex":{"female":71,"male":100},"title":"Human gut metagenome","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1198725","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1198725_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1198725.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1198725.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1198725.csv.gz"}},{"accession":"PRJNA1056768","age_categories":{"adolescent":7,"adult":75,"child":1,"elderly":88,"infant":1},"countries":{"US":172},"first_public_year":"2025","gbp_per_sample_median":8.5,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"gi_infection_or_diarrhoea":172},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":172,"papers":[{"doi":"10.1128/msphere.00435-25","pmcid":"PMC12570482","pmid":"40996044","title":"Microbiome signatures of &lt;i&gt;Clostridioides difficile&lt;/i&gt; toxin production and toxin gene presence: a shotgun metagenomic approach."}],"sample_intervention_arms":{},"sex":{"female":85,"male":87},"title":"Relationships between the gastrointestinal microbiome and Clostridiodes difficile toxin production and expression","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1056768","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1056768_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1056768.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1056768.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1056768.csv.gz"}},{"accession":"PRJNA731589","age_categories":{"adult":134,"elderly":38},"countries":{"CN":172},"first_public_year":"2022","gbp_per_sample_median":10.97,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":84,"healthy_control":86},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":172,"papers":[{"doi":"10.1016/j.isci.2026.114664","pmcid":"PMC12907713","pmid":"41704769","title":"Gut fungal landscape in colorectal cancer and its cross-kingdom interplay with gut microbial ecology."},{"doi":"10.1128/aem.01903-25","pmcid":"PMC13188911","pmid":"41940696","title":"Enhanced microbiota-derived mucinases in colorectal cancer patients revealed by gut metagenome probing coupled with functional validation."},{"doi":"10.1038/s41564-021-01030-7","pmcid":"PMC8813618","pmid":"35087227","title":"Multi-kingdom microbiota analyses identify bacterial-fungal interactions and biomarkers of colorectal cancer across cohorts."},{"doi":"10.3389/fmicb.2023.1130446","pmcid":"PMC10239823","pmid":"37283932","title":"Metagenomic analysis reveals gut plasmids as diagnosis markers for colorectal cancer."},{"doi":"10.3389/fonc.2023.1218056","pmcid":"PMC10436198","pmid":"37601681","title":"Taxonomic and functional profiling of fecal metagenomes for the early detection of colorectal cancer."}],"sample_intervention_arms":{},"sex":{"female":65,"male":103},"title":"Metagenomic sequencing of microbial DNA extracted from stool samples of CRC and HS","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA731589","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA731589_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA731589.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA731589.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA731589.csv.gz"}},{"accession":"PRJEB83971","age_categories":{"adult":20,"elderly":148},"countries":{"CH":168},"first_public_year":"2025","gbp_per_sample_median":3.39,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":50,"neurological_psychiatric":118},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":168,"papers":[{"doi":"10.1371/journal.pone.0330251","pmcid":"PMC12435679","pmid":"40953029","title":"Gut microbiome signatures in iNPH: Insights from a shotgun metagenomics study."}],"sample_intervention_arms":{},"sex":{"female":90,"male":78},"title":"Gut Microbiome Signatures in iNPH: Insights from a Shotgun Metagenomics Study","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB83971","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB83971_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB83971.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB83971.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB83971.csv.gz"}},{"accession":"PRJNA356102","age_categories":{"adult":167,"elderly":1},"countries":{"CN":168},"first_public_year":"2016","gbp_per_sample_median":6.39,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":90,"healthy_control":72},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":168,"papers":[{"doi":"10.3389/fmicb.2022.839015","pmcid":"PMC9024311","pmid":"35464950","title":"The Potential of Gut Microbiota Metabolic Capability to Detect Drug Response in Rheumatoid Arthritis Patients."},{"doi":"10.1038/s41467-024-47272-x","pmcid":"PMC11009399","pmid":"38605009","title":"Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases."},{"doi":"10.21203/rs.3.rs-3272455/v1","pmcid":null,"pmid":null,"title":"Plasmid dispersal and recombination across human gut microbiomes is neutral, but overpowered by inflammatory diseases"}],"sample_intervention_arms":{},"sex":{"female":122,"male":40},"title":"human gut metagenome in RA","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA356102","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA356102_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA356102.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA356102.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA356102.csv.gz"}},{"accession":"PRJDB15956","age_categories":{"adult":46,"elderly":115,"unknown":6},"countries":{"JP":167},"first_public_year":"2023","gbp_per_sample_median":2.47,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":73,"neurological_psychiatric":94},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":167,"papers":[{"doi":"10.1038/s41531-024-00724-z","pmcid":"PMC11109112","pmid":"38773112","title":"Meta-analysis of shotgun sequencing of gut microbiota in Parkinson's disease."}],"sample_intervention_arms":{},"sex":{},"title":"Shotgun data in the gut of Parkinson's disease","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB15956","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB15956_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB15956.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB15956.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB15956.csv.gz"}},{"accession":"PRJNA504921","age_categories":{"adult":48,"elderly":11,"unknown":108},"countries":{"CN":56,"HK":111},"first_public_year":"2019","gbp_per_sample_median":9.39,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":76,"ulcerative_colitis":91},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":167,"papers":[{"doi":"10.1073/pnas.2023202118","pmcid":"PMC8201803","pmid":"34083435","title":"A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases."},{"doi":"10.1136/gutjnl-2018-318131","pmcid":"PMC6582748","pmid":"30842211","title":"Gut mucosal virome alterations in ulcerative colitis."}],"sample_intervention_arms":{},"sex":{"female":18,"male":45},"title":"viral metagenome Metagenome","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA504921","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA504921_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA504921.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA504921.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA504921.csv.gz"}},{"accession":"PRJNA770295","age_categories":{"adult":83,"elderly":84},"countries":{"US":167},"first_public_year":"2021","gbp_per_sample_median":2.62,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":167},"intervention_design":"observational_with_procedure","intervention_detail":"Observed dietary fiber/probiotic use; preclinical low-fiber diet/probiotic feeding in mice","interventions":["diet_intervention","probiotic"],"n_samples":167,"papers":[{"doi":"10.1126/science.aaz7015","pmcid":"PMC8970537","pmid":"34941392","title":"Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response."},{"doi":"10.1128/msystems.01023-22","pmcid":"PMC10134792","pmid":"36809182","title":"Consistent Stool Metagenomic Biomarkers Associated with the Response To Melanoma Immunotherapy."},{"doi":"10.1038/s41467-023-42997-7","pmcid":"PMC10654443","pmid":"37973916","title":"Gut microbial structural variation associates with immune checkpoint inhibitor response."},{"doi":"10.1038/s41591-024-02803-3","pmcid":"PMC10957474","pmid":"38365950","title":"Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma."},{"doi":"10.26508/lsa.202302480","pmcid":"PMC10917649","pmid":"38448159","title":"Systemic metabolic depletion of gut microbiome undermines responsiveness to melanoma immunotherapy."}],"sample_intervention_arms":{},"sex":{"female":58,"male":109},"title":"Dietary fiber and probiotics impact the gut microbiome and melanoma immunotherapy response","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA770295","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA770295_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA770295.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA770295.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA770295.csv.gz"}},{"accession":"PRJEB43119","age_categories":{"adolescent":1,"adult":67,"elderly":95,"unknown":2},"countries":{"ES":12,"GB":98,"NL":55},"first_public_year":"2021","gbp_per_sample_median":6.2,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":165},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":165,"papers":[{"doi":"10.1016/j.xcrm.2026.102921","pmcid":"PMC13400165","pmid":"42447866","title":"Tryptophan degradation by intestinal Bacteroides induces anti-tumor immunity and limits melanoma growth."},{"doi":"10.1038/s41591-022-01695-5","pmcid":"PMC8938272","pmid":"35228751","title":"Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma."},{"doi":"10.1128/msystems.01023-22","pmcid":"PMC10134792","pmid":"36809182","title":"Consistent Stool Metagenomic Biomarkers Associated with the Response To Melanoma Immunotherapy."},{"doi":"10.1038/s41467-023-42997-7","pmcid":"PMC10654443","pmid":"37973916","title":"Gut microbial structural variation associates with immune checkpoint inhibitor response."},{"doi":"10.1038/s41591-024-02803-3","pmcid":"PMC10957474","pmid":"38365950","title":"Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma."}],"sample_intervention_arms":{},"sex":{"female":65,"male":100},"title":"Predicting Response to Immunotherapy for Melanoma With Gut Microbiome and Metabolomics","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB43119","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB43119_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB43119.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB43119.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB43119.csv.gz"}},{"accession":"PRJNA798058","age_categories":{"elderly":164},"countries":{"US":164},"first_public_year":"2022","gbp_per_sample_median":4.97,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":114,"neurological_psychiatric":49},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":164,"papers":[{"doi":"10.1126/scitranslmed.abo2984","pmcid":"PMC10680783","pmid":"37315112","title":"Gut microbiome composition may be an indicator of preclinical Alzheimer's disease."},{"doi":"10.1038/s41467-026-69711-7","pmcid":"PMC13035836","pmid":"41720792","title":"Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems."}],"sample_intervention_arms":{},"sex":{"female":90,"male":73},"title":"The gut microbiome in preclinical Alzheimer Disease","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA798058","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA798058_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA798058.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA798058.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA798058.csv.gz"}},{"accession":"PRJNA972625","age_categories":{"adult":119,"elderly":45},"countries":{"PL":164},"first_public_year":"2024","gbp_per_sample_median":2.46,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":164,"papers":[{"doi":"10.1007/s00262-024-03918-9","pmcid":"PMC11861499","pmid":"39998665","title":"Exploring correlations between gut mycobiome and lymphocytes in melanoma patients undergoing anti-PD-1 therapy."},{"doi":"10.1158/2326-6066.cir-23-0592","pmcid":"PMC10985481","pmid":"38315788","title":"Gut Mycobiota Dysbiosis Is Associated with Melanoma and Response to Anti-PD-1 Therapy."}],"sample_intervention_arms":{},"sex":{"female":33,"male":60},"title":"Changes in gut mycobiome in Polish melanoma patients","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA972625","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA972625_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA972625.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA972625.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA972625.csv.gz"}},{"accession":"PRJEB72523","age_categories":{"adult":115,"elderly":48},"countries":{"IT":163},"first_public_year":"2025","gbp_per_sample_median":4.28,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":163},"intervention_design":"randomized_controlled_trial","intervention_detail":"Atezolizumab added to FOLFOXIRI plus bevacizumab in mCRC","interventions":["drug_therapy"],"n_samples":163,"papers":[{"doi":"10.1038/s41591-025-03693-9","pmcid":"PMC12283368","pmid":"40461820","title":"Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer."}],"sample_intervention_arms":{},"sex":{"female":67,"male":96},"title":"Gut microbiome samples from the AtezoTRIBE phase-II clinical trial","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB72523","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB72523_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB72523.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB72523.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB72523.csv.gz"}},{"accession":"PRJNA1216426","age_categories":{"adult":123,"elderly":40},"countries":{"DK":163},"first_public_year":"2025","gbp_per_sample_median":0.56,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"crohns_disease":163},"intervention_design":"randomized_controlled_trial","intervention_detail":"Bifidobacterium breve Bif195 vs placebo, 8 weeks, Crohn's disease","interventions":["probiotic"],"n_samples":163,"papers":[{"doi":"10.1186/s13099-025-00692-6","pmcid":"PMC11984114","pmid":"40205497","title":"The effects of probiotic treatment with Bifidobacterium breve, Bif195 for small intestinal Crohn's disease and the gut microbiome: results from a randomised, double-blind, placebo-controlled trial."}],"sample_intervention_arms":{"placebo":85,"probiotic":62},"sex":{"female":94,"male":69},"title":"The effects of probiotic treatment with Bifidobacterium breve, Bif195 for small intestinal Crohn's disease and the gut microbiome: Results from a randomised, double-blind, placebo-controlled trial","trial_population_condition":"crohns_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1216426","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1216426_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1216426.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1216426.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1216426.csv.gz"}},{"accession":"PRJEB113836","age_categories":{"adult":158,"elderly":2},"countries":{"RO":160},"first_public_year":"2026","gbp_per_sample_median":8.42,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":160},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":160,"papers":[{"doi":"10.1128/spectrum.00528-26","pmcid":"PMC13532179","pmid":"42578673","title":"Resistome and microbiome-immune interactions in an Eastern European population with high antibiotic use."}],"sample_intervention_arms":{},"sex":{"female":106,"male":54},"title":"Resistome and microbiome-immune interactions in an Eastern European population with high antibiotic use","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB113836","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB113836_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB113836.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB113836.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB113836.csv.gz"}},{"accession":"PRJEB48663","age_categories":{"adult":152,"elderly":4},"countries":{"FR":156},"first_public_year":"2021","gbp_per_sample_median":3.09,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"cardiometabolic_other":156},"intervention_design":"crossover","intervention_detail":"Daily 150g bread: standard (5.55g fiber) vs 7-fiber-enriched (16.05g fiber), 8-week crossover","interventions":["diet_intervention","prebiotic_or_fibre"],"n_samples":156,"papers":[{"doi":"10.1080/19490976.2022.2044722","pmcid":"PMC8942430","pmid":"35311446","title":"Increasing the diversity of dietary fibers in a daily-consumed bread modifies gut microbiota and metabolic profile in subjects at cardiometabolic risk."}],"sample_intervention_arms":{"no_intervention":78,"prebiotic_or_fibre":78},"sex":{"female":88,"male":68},"title":"Increasing the diversity of dietary fibres in a daily-consumed bread modifies gut microbiota and metabolic profile in subjects at cardiometabolic risk","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB48663","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB48663_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB48663.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB48663.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB48663.csv.gz"}},{"accession":"PRJEB7774","age_categories":{"adult":60,"elderly":96},"countries":{"AT":156},"first_public_year":"2015","gbp_per_sample_median":5.0,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":47,"colorectal_cancer":46,"healthy_control":31},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":156,"papers":[{"doi":"10.3389/fgene.2020.00445","pmcid":"PMC7283552","pmid":"32582274","title":"HARMONIES: A Hybrid Approach for Microbiome Networks Inference via Exploiting Sparsity."},{"doi":"10.1186/s40168-021-01213-8","pmcid":"PMC8851854","pmid":"35172890","title":"METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks."},{"doi":"10.3390/microorganisms11082037","pmcid":"PMC10457972","pmid":"37630597","title":"Gut Microbial and Associated Metabolite Markers for Colorectal Cancer Diagnosis."},{"doi":"10.1017/gmb.2025.3","pmcid":"PMC12035788","pmid":"40297307","title":"Association of &lt;i&gt;Fusobacterium nucleatum&lt;/i&gt; with colorectal cancer molecular subtypes and its outcome: a systematic review."},{"doi":"10.1186/s13099-025-00712-5","pmcid":"PMC12539022","pmid":"41121269","title":"Gut microbiota alterations and their association with tumorigenic pathways in colorectal cancer: insights from a pooled analysis of 109 microbiome datasets."}],"sample_intervention_arms":{},"sex":{"female":68,"male":88},"title":"Gut microbiome development along the colorectal adenoma-carcinoma sequence","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB7774","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB7774_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB7774.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB7774.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB7774.csv.gz"}},{"accession":"PRJNA307231","age_categories":{"adult":155,"elderly":1},"countries":{"ES":156},"first_public_year":"2018","gbp_per_sample_median":3.63,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":27,"other_infection":129},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":156,"papers":[{"doi":"10.1016/j.ebiom.2016.01.032","pmcid":"PMC4816837","pmid":"27077120","title":"Gut Microbiota Linked to Sexual Preference and HIV Infection."},{"doi":"10.1128/msystems.00053-18","pmcid":"PMC6050633","pmid":"30035234","title":"Balances: a New Perspective for Microbiome Analysis."},{"doi":"10.1038/s41598-019-46249-x","pmcid":"PMC6629854","pmid":"31308384","title":"Establishment and evaluation of prediction model for multiple disease classification based on gut microbial data."},{"doi":"10.1111/1755-0998.13704","pmcid":"PMC9744196","pmid":"36001047","title":"SCNIC: Sparse correlation network investigation for compositional data."},{"doi":"10.1093/bib/bbaf111","pmcid":"PMC11899578","pmid":"40072847","title":"Disrupted microbial cross-feeding and altered L-phenylalanine consumption in people living with HIV."}],"sample_intervention_arms":{},"sex":{"female":31,"male":125},"title":"Human feces metagenome 16s rDNA sequencing","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA307231","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA307231_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA307231.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA307231.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA307231.csv.gz"}},{"accession":"PRJNA521587","age_categories":{"adult":150,"elderly":5,"infant":1},"countries":{"CA":156},"first_public_year":"2019","gbp_per_sample_median":2.43,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":79,"other_disease":77},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":156,"papers":[],"sample_intervention_arms":{},"sex":{"female":156},"title":"Gut microbiome in individuals with fibromyalgia - WGS","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA521587","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA521587_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA521587.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA521587.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA521587.csv.gz"}},{"accession":"PRJNA629755","age_categories":{"adolescent":9,"adult":96,"child":4,"elderly":14,"infant":3,"unknown":28},"countries":{"US":154},"first_public_year":"2020","gbp_per_sample_median":1.71,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":27,"other_disease":127},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":154,"papers":[{"doi":"10.1038/s41467-020-16436-w","pmcid":"PMC7253448","pmid":"32461638","title":"Permissive microbiome characterizes human subjects with a neurovascular disease cavernous angioma."},{"doi":"10.1038/s43856-023-00265-1","pmcid":"PMC9984539","pmid":"36869161","title":"Plasma metabolites with mechanistic and clinical links to the neurovascular disease cavernous angioma."},{"doi":"10.1128/msystems.00515-24","pmcid":"PMC11264914","pmid":"38912768","title":"Unassigning bacterial species for microbiome studies."},{"doi":"10.1177/0271678x251314366","pmcid":"PMC11748132","pmid":"39829356","title":"Circulating molecules reflect imaging biomarkers of hemorrhage in cerebral cavernous malformations."}],"sample_intervention_arms":{},"sex":{"female":88,"male":39},"title":"Microbiome Signatures of Cavernous Angioma","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA629755","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA629755_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA629755.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA629755.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA629755.csv.gz"}},{"accession":"PRJNA1001944","age_categories":{"adult":122,"elderly":31},"countries":{"PL":153},"first_public_year":"2024","gbp_per_sample_median":3.79,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":3,"healthy_control":10,"ibs":51,"other_cancer":80},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":153,"papers":[{"doi":"10.3389/fonc.2024.1279132","pmcid":"PMC10848918","pmid":"38327745","title":"Breast cancer but not the menopausal status is associated with small changes of the gut microbiota."},{"doi":"10.3390/ijms25158026","pmcid":"PMC11311272","pmid":"39125593","title":"Microbial and Metabolic Gut Profiling across Seven Malignancies Identifies Fecal Faecalibacillus intestinalis and Formic Acid as Commonly Altered in Cancer Patients."}],"sample_intervention_arms":{},"sex":{"female":153},"title":"Breast cancer but not the menopausal status is associated with small changes of the gut microbiota","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1001944","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1001944_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1001944.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1001944.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1001944.csv.gz"}},{"accession":"PRJNA542578","age_categories":{"adult":51,"elderly":100},"countries":{"CN":151},"first_public_year":"2024","gbp_per_sample_median":13.05,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":151},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":151,"papers":[{"doi":"10.1111/acel.14028","pmcid":"PMC10726799","pmid":"38015106","title":"Age-dependent changes in the gut microbiota and serum metabolome correlate with renal function and human aging."}],"sample_intervention_arms":{},"sex":{},"title":"human gut metagenome Raw sequence reads","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA542578","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA542578_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA542578.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA542578.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA542578.csv.gz"}},{"accession":"PRJNA356225","age_categories":{"adolescent":3,"adult":135,"elderly":12},"countries":{"CN":150},"first_public_year":"2016","gbp_per_sample_median":5.71,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":94,"healthy_control":1,"other_disease":1},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":150,"papers":[{"doi":"10.1080/19490976.2019.1700754","pmcid":"PMC7524263","pmid":"31928124","title":"Altered gut microbiome composition in patients with Vogt-Koyanagi-Harada disease."},{"doi":"10.1186/s40168-018-0520-6","pmcid":"PMC6091101","pmid":"30077182","title":"A metagenomic study of the gut microbiome in Behcet's disease."},{"doi":"10.1038/s41522-025-00768-w","pmcid":"PMC12274573","pmid":"40681522","title":"Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation."},{"doi":"10.1371/journal.pone.0329457","pmcid":"PMC12316285","pmid":"40748897","title":"The porphyran degradation system is complete, phylogenetically and geographically diverse across the gut microbiota of East Asian populations."}],"sample_intervention_arms":{},"sex":{"female":36,"male":82},"title":"human gut metagenome Metagenome","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA356225","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA356225_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA356225.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA356225.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA356225.csv.gz"}},{"accession":"PRJDB40001","age_categories":{"elderly":148},"countries":{"JP":148},"first_public_year":"2026","gbp_per_sample_median":8.82,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":148,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Human gut metagenome from the elderly population in Ginowan City, Okinawa","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB40001","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB40001_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB40001.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB40001.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB40001.csv.gz"}},{"accession":"PRJNA1142892","age_categories":{"elderly":148},"countries":{"US":148},"first_public_year":"2025","gbp_per_sample_median":1.53,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":63,"neurological_psychiatric":36,"other_cancer":49},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":148,"papers":[{"doi":"10.1007/s11357-025-01917-x","pmcid":"PMC13575041","pmid":"41175312","title":"Gut microbiome signatures predict cognitive impairment in older cancer survivors."}],"sample_intervention_arms":{},"sex":{},"title":"Microbiome modulators in the prevention and mitigation of accelerated aging biology caused by cancer treatment","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1142892","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1142892_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1142892.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1142892.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1142892.csv.gz"}},{"accession":"PRJEB1786","age_categories":{"elderly":145},"countries":{"DE":4,"DK":2,"EE":1,"FI":1,"FR":1,"HU":1,"IS":1,"NO":1,"SE":130,"SK":3},"first_public_year":"2013","gbp_per_sample_median":2.81,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":43,"type2_diabetes":53},"intervention_design":"unknown","intervention_detail":"Observational case-control cohort, no administered intervention","interventions":[],"n_samples":145,"papers":[{"doi":"10.1073/pnas.2023202118","pmcid":"PMC8201803","pmid":"34083435","title":"A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases."},{"doi":"10.1186/s13059-015-0611-7","pmcid":"PMC4389708","pmid":"25853934","title":"Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome."},{"doi":"10.1371/journal.pone.0140827","pmcid":"PMC4610706","pmid":"26479726","title":"Type 2 Diabetes Biomarkers of Human Gut Microbiota Selected via Iterative Sure Independent Screening Method."},{"doi":"10.1186/s12859-020-3533-7","pmcid":"PMC7218625","pmid":"32397982","title":"TAMA: improved metagenomic sequence classification through meta-analysis."},{"doi":"10.1186/s40168-022-01237-8","pmcid":"PMC8908641","pmid":"35272700","title":"MetaDecoder: a novel method for clustering metagenomic contigs."}],"sample_intervention_arms":{},"sex":{"female":145},"title":"Gut metagenome in European women with normal, impaired and diabetic glucose control","trial_population_condition":"type2_diabetes","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB1786","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB1786_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB1786.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB1786.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB1786.csv.gz"}},{"accession":"PRJNA1356643","age_categories":{"adult":138,"elderly":7},"countries":{"SA":145},"first_public_year":"2025","gbp_per_sample_median":2.16,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":145},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":145,"papers":[{"doi":"10.3389/fragi.2026.1733638","pmcid":"PMC13013359","pmid":"41889698","title":"First metagenomic analysis of age-associated changes in the gut microbiome among healthy Saudi adults: SAMS pilot study."}],"sample_intervention_arms":{},"sex":{"female":70,"male":75},"title":"Profiling the gut microbiota with Saudi healthy aging","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1356643","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1356643_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1356643.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1356643.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1356643.csv.gz"}},{"accession":"PRJNA531316","age_categories":{"elderly":144},"countries":{"FR":144},"first_public_year":"2019","gbp_per_sample_median":0.2,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":144,"papers":[{"doi":"10.1186/s13756-020-00773-y","pmcid":"PMC7359458","pmid":"32665016","title":"Gut microbiome signatures of nursing home residents carrying Enterobacteria producing extended-spectrum β-lactamases."}],"sample_intervention_arms":{},"sex":{},"title":"CARBEPAD","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA531316","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA531316_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA531316.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA531316.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA531316.csv.gz"}},{"accession":"PRJNA1491285","age_categories":{"adult":64,"elderly":79},"countries":{"US":143},"first_public_year":"2026","gbp_per_sample_median":0.77,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"liver_disease":143},"intervention_design":"single_arm_before_after","intervention_detail":"Lactulose given to cirrhosis patients, sampled at baseline and 4 weeks","interventions":["drug_therapy"],"n_samples":143,"papers":[],"sample_intervention_arms":{},"sex":{"female":114,"male":29},"title":"Gut microbiota in patients with cirrhosis and portal hypertension receiving lactulose","trial_population_condition":"liver_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1491285","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1491285_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1491285.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1491285.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1491285.csv.gz"}},{"accession":"PRJNA397450","age_categories":{"adult":92,"elderly":51},"countries":{"US":143},"first_public_year":"2017","gbp_per_sample_median":0.12,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"healthy_control":143},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":143,"papers":[{"doi":"10.1038/s41598-018-22408-4","pmcid":"PMC5841359","pmid":"29515151","title":"Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples."},{"doi":null,"pmcid":"PMC10913632","pmid":null,"title":"Proportion-based normalizations outperform compositional data transformations in machine learning applications"}],"sample_intervention_arms":{"bowel_preparation":34,"no_intervention":72,"placebo":37},"sex":{"female":54,"male":89},"title":"Human gut microbial community assessment using stool, rectal swab, and mucosal samples","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA397450","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA397450_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA397450.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA397450.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA397450.csv.gz"}},{"accession":"PRJNA928758","age_categories":{"adolescent":1,"adult":102,"child":1,"elderly":37,"infant":2},"countries":{"US":143},"first_public_year":"2023","gbp_per_sample_median":2.18,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"transplant_or_immunocompromised":143},"intervention_design":"observational_with_procedure","intervention_detail":"Gut microbiome sampled in liver transplant recipients","interventions":["surgery"],"n_samples":143,"papers":[{"doi":"10.1016/j.chom.2023.11.016","pmcid":null,"pmid":"38103544","title":"Fecal metabolite profiling identifies liver transplant recipients at risk for postoperative infection."}],"sample_intervention_arms":{},"sex":{"female":63,"male":80},"title":"Microbiome in Liver Transplant Infections","trial_population_condition":"transplant_or_immunocompromised","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA928758","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA928758_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA928758.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA928758.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA928758.csv.gz"}},{"accession":"PRJNA447983","age_categories":{"adult":80,"elderly":59,"unknown":1},"countries":{"IT":140},"first_public_year":"2018","gbp_per_sample_median":3.76,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":27,"colorectal_cancer":61,"healthy_control":52},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":140,"papers":[{"doi":"10.1038/s41591-019-0405-7","pmcid":"PMC9533319","pmid":"30936548","title":"Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation."},{"doi":"10.1128/msystems.00289-19","pmcid":"PMC6749105","pmid":"31530647","title":"Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples."},{"doi":"10.1080/19490976.2025.2611544","pmcid":"PMC12818822","pmid":"41530917","title":"metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches."},{"doi":"10.1038/s41591-019-0406-6","pmcid":"PMC7984229","pmid":"30936547","title":"Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer."},{"doi":"10.1186/s12864-020-6749-z","pmcid":"PMC7216530","pmid":"32393180","title":"Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment."}],"sample_intervention_arms":{},"sex":{"female":49,"male":91},"title":"Whole-metagenome shotgun sequencing of two Italian fecal CRC cohorts","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA447983","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA447983_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA447983.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA447983.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA447983.csv.gz"}},{"accession":"PRJNA608022","age_categories":{"adult":132,"elderly":7},"countries":{"BE":44,"ES":6,"FR":19,"GB":10,"MX":5,"US":50},"first_public_year":"2020","gbp_per_sample_median":0.29,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"liver_disease":88,"other_disease":36},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":139,"papers":[{"doi":"10.1002/hep.31459","pmcid":"PMC8159727","pmid":"32654263","title":"Intestinal Virome in Patients With Alcoholic Hepatitis."}],"sample_intervention_arms":{},"sex":{"female":37,"male":101},"title":"human viral metagenome Raw sequence reads","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA608022","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA608022_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA608022.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA608022.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA608022.csv.gz"}},{"accession":"PRJEB81804","age_categories":{"adult":124,"elderly":14},"countries":{"US":138},"first_public_year":"2024","gbp_per_sample_median":0.03,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":138,"papers":[{"doi":"10.1007/s11033-025-10330-8","pmcid":"PMC11845529","pmid":"39982577","title":"ChIP provides 10-fold microbial DNA enrichment from tissue while minimizing bias."}],"sample_intervention_arms":{},"sex":{"female":110,"male":28},"title":"Host depletion in pig and human colon samples","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB81804","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB81804_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB81804.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB81804.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB81804.csv.gz"}},{"accession":"PRJEB72531","age_categories":{"elderly":137},"countries":{"GB":137},"first_public_year":"2024","gbp_per_sample_median":6.11,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":137},"intervention_design":"randomized_controlled_trial","intervention_detail":"Prebiotic vs placebo 12 weeks, with resistance exercise and BCAA supplementation for all","interventions":["dietary_supplement","exercise","prebiotic_or_fibre"],"n_samples":137,"papers":[{"doi":"10.1038/s41467-024-46116-y","pmcid":"PMC10904794","pmid":"38424099","title":"Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial."}],"sample_intervention_arms":{},"sex":{},"title":"Prebiotic intervention for muscle function and cognition","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB72531","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB72531_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB72531.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB72531.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB72531.csv.gz"}},{"accession":"PRJEB39813","age_categories":{"adult":130,"elderly":4},"countries":{"SG":134},"first_public_year":"2021","gbp_per_sample_median":0.03,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":84,"healthy_control":50},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":134,"papers":[{"doi":"10.1186/s13099-021-00409-5","pmcid":"PMC7905567","pmid":"33632307","title":"Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn's disease."},{"doi":"10.1093/ecco-jcc/jjac063","pmcid":"PMC9624293","pmid":"35511486","title":"Oral Microbiome of Crohn's Disease Patients With and Without Oral Manifestations."}],"sample_intervention_arms":{},"sex":{"female":66,"male":64},"title":"A metagenomic study of the oral (saliva) and Gut (stool) microbiome in subjects with Crohn's Disease.","trial_population_condition":"crohns_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB39813","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB39813_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB39813.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB39813.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB39813.csv.gz"}},{"accession":"PRJNA954584","age_categories":{"adult":8,"elderly":124},"countries":{"BG":10,"DE":116,"FI":6},"first_public_year":"2023","gbp_per_sample_median":6.43,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":66,"healthy_control":1,"other_disease":65},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":132,"papers":[{"doi":"10.3389/fimmu.2023.1212551","pmcid":"PMC10668026","pmid":"38022583","title":"The gut microbiome in bullous pemphigoid: implications of the gut-skin axis for disease susceptibility."}],"sample_intervention_arms":{},"sex":{"female":46,"male":86},"title":"The gut microbiome in bullous pemphigoid","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA954584","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA954584_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA954584.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA954584.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA954584.csv.gz"}},{"accession":"PRJEB46778","age_categories":{"adult":126,"elderly":4},"countries":{"NL":130},"first_public_year":"2022","gbp_per_sample_median":6.47,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"cardiometabolic_other":130},"intervention_design":"randomized_controlled_trial","intervention_detail":"Lean donor (allogenic) vs autologous FMT in metabolic syndrome patients","interventions":["fmt"],"n_samples":130,"papers":[{"doi":"10.1126/science.aad8852","pmcid":null,"pmid":"27126044","title":"Durable coexistence of donor and recipient strains after fecal microbiota transplantation."},{"doi":"10.1016/j.cmet.2017.09.008","pmcid":null,"pmid":"28978426","title":"Improvement of Insulin Sensitivity after Lean Donor Feces in Metabolic Syndrome Is Driven by Baseline Intestinal Microbiota Composition."},{"doi":"10.1038/s41591-022-01913-0","pmcid":"PMC9499871","pmid":"36109636","title":"Drivers and determinants of strain dynamics following fecal microbiota transplantation."}],"sample_intervention_arms":{"fmt":88,"no_intervention":26},"sex":{"male":121},"title":"Fecal Microbiota Transplantation for Metabolic Syndrome","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB46778","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB46778_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB46778.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB46778.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB46778.csv.gz"}},{"accession":"PRJEB10878","age_categories":{"adult":80,"elderly":48},"countries":{"CN":128},"first_public_year":"2015","gbp_per_sample_median":5.59,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":74,"healthy_control":37},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":128,"papers":[{"doi":"10.1126/sciadv.aba1590","pmcid":"PMC7228756","pmid":"32440552","title":"Bioinorganic hybrid bacteriophage for modulation of intestinal microbiota to remodel tumor-immune microenvironment against colorectal cancer."},{"doi":"10.1186/s13059-024-03320-9","pmcid":"PMC11229495","pmid":"38965579","title":"VirRep: a hybrid language representation learning framework for identifying viruses from human gut metagenomes."},{"doi":"10.1016/j.cmet.2025.06.002","pmcid":"PMC12365777","pmid":"40609532","title":"Microbial riboflavin inhibits ceramide synthase 3 to lower ceramide (d18:1/26:0) and delay colorectal cancer progression."},{"doi":"10.1093/nargab/lqaf158","pmcid":"PMC12639245","pmid":"41278541","title":"MeTAline: enabling reproducible and scalable metagenomic analyses."},{"doi":"10.1038/s42003-026-10278-w","pmcid":"PMC13434703","pmid":"42141123","title":"Decoding the human gut bacterial plasmids in colorectal cancer."}],"sample_intervention_arms":{},"sex":{"female":47,"male":81},"title":"Metagenomic analysis of fecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB10878","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB10878_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB10878.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB10878.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB10878.csv.gz"}},{"accession":"PRJNA1169096","age_categories":{"adult":118,"elderly":9},"countries":{"US":127},"first_public_year":"2025","gbp_per_sample_median":6.11,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"ulcerative_colitis":127},"intervention_design":"randomized_controlled_trial","intervention_detail":"Single-dose FMT vs placebo, with/without psyllium fiber, 8 weeks","interventions":["fmt","prebiotic_or_fibre"],"n_samples":127,"papers":[{"doi":"10.1016/j.medj.2025.100707","pmcid":"PMC12353604","pmid":"40460824","title":"Donor composition and fiber promote strain engraftment in a randomized controlled trial of fecal microbiota transplant for ulcerative colitis."}],"sample_intervention_arms":{"fmt":67,"placebo":35},"sex":{"female":40,"male":86},"title":"Donor Composition and Fiber Promote Strain Engraftment in a Randomized Controlled Trial of Fecal Transplant with Dietary Fiber for Ulcerative Colitis (MINDFUL)","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1169096","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1169096_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1169096.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1169096.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1169096.csv.gz"}},{"accession":"PRJNA890008","age_categories":{"adult":123,"elderly":2},"countries":{"LU":125},"first_public_year":"2022","gbp_per_sample_median":2.71,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":57,"other_infection":61},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":125,"papers":[{"doi":"10.1186/s40168-023-01472-7","pmcid":"PMC9995755","pmid":"36894986","title":"Altered infective competence of the human gut microbiome in COVID-19."},{"doi":"10.1101/2022.10.20.512999","pmcid":null,"pmid":null,"title":"Altered infective competence of the human gut microbiome in COVID-19"}],"sample_intervention_arms":{},"sex":{"female":44,"male":74},"title":"Altered infective proficiency of the gut microbiome in COVID-19","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA890008","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA890008_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA890008.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA890008.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA890008.csv.gz"}},{"accession":"PRJEB122858","age_categories":{"adult":121,"elderly":3},"countries":{"IL":124},"first_public_year":"2026","gbp_per_sample_median":0.47,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":43,"healthy_control":49,"ulcerative_colitis":32},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":124,"papers":[{"doi":"10.3389/fmicb.2026.1871609","pmcid":"PMC13526984","pmid":"42676636","title":"Disrupted terminal bilirubin catabolism links &lt;i&gt;Lachnospiraceae&lt;/i&gt; depletion to inflammatory bowel disease."}],"sample_intervention_arms":{},"sex":{"female":68,"male":54},"title":"Disrupted Terminal Bilirubin Catabolism Links Lachnospiraceae Depletion to Inflammatory Bowel Disease","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB122858","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB122858_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB122858.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB122858.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB122858.csv.gz"}},{"accession":"PRJEB2054","age_categories":{"adult":110,"elderly":13,"neonate":1},"countries":{"DK":85,"ES":39},"first_public_year":"2010","gbp_per_sample_median":3.3,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":123},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":124,"papers":[{"doi":"10.1038/nmeth.2066","pmcid":"PMC3443552","pmid":"22688413","title":"Metagenomic microbial community profiling using unique clade-specific marker genes."},{"doi":"10.1371/journal.pcbi.1002863","pmcid":"PMC3542080","pmid":"23326225","title":"A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets."},{"doi":"10.1093/gbe/evu073","pmcid":"PMC4040986","pmid":"24709563","title":"An expanded genomic representation of the phylum cyanobacteria."},{"doi":"10.1186/s13059-015-0646-9","pmcid":"PMC4428241","pmid":"25896518","title":"Inter-individual differences in the gene content of human gut bacterial species."},{"doi":"10.1073/pnas.1423854112","pmcid":"PMC4460507","pmid":"25964341","title":"Identifying personal microbiomes using metagenomic codes."}],"sample_intervention_arms":{},"sex":{"female":69,"male":55},"title":"A human gut microbial gene catalog established by deep metagenomic sequencing","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB2054","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB2054_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB2054.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB2054.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB2054.csv.gz"}},{"accession":"PRJEB72525","age_categories":{"adult":68,"elderly":56},"countries":{},"first_public_year":"2025","gbp_per_sample_median":3.65,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":19,"colorectal_cancer":59,"healthy_control":46},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":124,"papers":[{"doi":"10.1038/s41591-025-03693-9","pmcid":"PMC12283368","pmid":"40461820","title":"Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer."}],"sample_intervention_arms":{},"sex":{"female":54,"male":70},"title":"Gut microbiome samples from a cohort of CRC patients in two hospitals in Prague and Plzen, Czech Republic.","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB72525","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB72525_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB72525.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB72525.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB72525.csv.gz"}},{"accession":"PRJNA762543","age_categories":{"adult":70,"elderly":54},"countries":{"SG":124},"first_public_year":"2021","gbp_per_sample_median":1.3,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":124},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":124,"papers":[{"doi":"10.1080/19490976.2022.2070392","pmcid":"PMC9116421","pmid":"35549618","title":"Integrative multiomics analysis reveals host-microbe-metabolite interplays associated with the aging process in Singaporeans."}],"sample_intervention_arms":{},"sex":{"male":124},"title":"human fecal and saliva metagenome Raw sequence reads","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA762543","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA762543_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA762543.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA762543.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA762543.csv.gz"}},{"accession":"PRJNA739858","age_categories":{"elderly":121},"countries":{"SG":121},"first_public_year":"2022","gbp_per_sample_median":1.42,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":121},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":121,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Gut microbiome analysis of the Brain, Adipocyte, Microbiome, Muscle, Bone, Exercise (BAMMBE) elderly Singapore Cohort","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA739858","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA739858_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA739858.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA739858.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA739858.csv.gz"}},{"accession":"PRJNA1160256","age_categories":{"adult":24,"elderly":28,"infant":47,"unknown":21},"countries":{"BE":120},"first_public_year":"2025","gbp_per_sample_median":2.52,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":120},"intervention_design":"observational_with_procedure","intervention_detail":"Ex vivo fecal fermentation dosed with sodium benzoate food additive","interventions":["other_intervention"],"n_samples":120,"papers":[{"doi":"10.3390/foods14172949","pmcid":"PMC12428287","pmid":"40941064","title":"The Effect of Sodium Benzoate on the Gut Microbiome Across Age Groups."},{"doi":"10.3390/foods14172949","pmcid":"PMC12428287","pmid":"40941064","title":"The Effect of Sodium Benzoate on the Gut Microbiome Across Age Groups."}],"sample_intervention_arms":{},"sex":{},"title":"The effects of selected food components and additives on the human gut microbiome","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1160256","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1160256_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1160256.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1160256.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1160256.csv.gz"}},{"accession":"PRJNA1210004","age_categories":{"elderly":120},"countries":{"US":120},"first_public_year":"2025","gbp_per_sample_median":2.72,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":120},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":120,"papers":[{"doi":"10.1158/1055-9965.epi-24-1770","pmcid":"PMC12247528","pmid":"40402042","title":"Stability and Variability of the Human Fecal Microbiome over 2 Years in the Multiethnic Cohort Study: A Metagenomic Analysis."}],"sample_intervention_arms":{},"sex":{},"title":"Temporal Stability of the Fecal Microbiome in Older Adults","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1210004","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1210004_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1210004.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1210004.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1210004.csv.gz"}},{"accession":"PRJDB16443","age_categories":{"adult":4,"elderly":114},"countries":{"JP":118},"first_public_year":"2023","gbp_per_sample_median":11.7,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"neurological_psychiatric":63},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":118,"papers":[{"doi":"10.1099/mgen.0.001180","pmcid":"PMC10926694","pmid":"38376378","title":"Exploring the effects of antimicrobial treatment on the gut and oral microbiomes and resistomes from elderly long-term care facility residents via shotgun DNA sequencing."}],"sample_intervention_arms":{},"sex":{"female":46,"male":28},"title":"Shotgun metagenome sequencing of oral and stool samples from Japanese long-term care facility residents","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB16443","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB16443_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB16443.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB16443.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB16443.csv.gz"}},{"accession":"PRJDB7767","age_categories":{"adult":116,"elderly":2},"countries":{"JP":118},"first_public_year":"2020","gbp_per_sample_median":1.74,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":20,"neurological_psychiatric":98},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":118,"papers":[{"doi":"10.1038/s41522-026-01030-7","pmcid":"PMC13519030","pmid":"42218218","title":"Multikingdom microbiome-based machine learning enables multiple sclerosis diagnosis."},{"doi":"10.1073/pnas.2011703117","pmcid":"PMC7486801","pmid":"32839304","title":"Alterations of the gut ecological and functional microenvironment in different stages of multiple sclerosis."}],"sample_intervention_arms":{},"sex":{"female":88,"male":30},"title":"Gut Microbiota dysbiosis leads to the development and progression of multiple sclerosis","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB7767","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB7767_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB7767.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB7767.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB7767.csv.gz"}},{"accession":"PRJEB36820","age_categories":{"adult":109,"elderly":2,"unknown":7},"countries":{"IE":118},"first_public_year":"2020","gbp_per_sample_median":3.24,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":117},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":118,"papers":[{"doi":"10.1186/s40168-022-01335-7","pmcid":"PMC9469561","pmid":"36100953","title":"Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population."},{"doi":"10.1038/s43587-022-00306-9","pmcid":"PMC10154212","pmid":"37118093","title":"Toward an improved definition of a healthy microbiome for healthy aging."}],"sample_intervention_arms":{},"sex":{"female":65,"male":52},"title":"Investigating the health status and microbiota in members of the Irish Travelling community","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB36820","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB36820_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB36820.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB36820.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB36820.csv.gz"}},{"accession":"PRJEB53401","age_categories":{"adult":70,"elderly":48},"countries":{"US":118},"first_public_year":"2022","gbp_per_sample_median":1.6,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":27,"neurological_psychiatric":48},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":118,"papers":[{"doi":"10.1038/s41467-025-56829-3","pmcid":"PMC12059030","pmid":"40335465","title":"Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease."},{"doi":"10.1038/s41467-026-69711-7","pmcid":"PMC13035836","pmid":"41720792","title":"Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems."},{"doi":"10.1101/2023.12.05.569565","pmcid":null,"pmid":null,"title":"Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson’s disease"}],"sample_intervention_arms":{},"sex":{"female":60,"male":58},"title":"PD Shotgun Metagenomics - TBC","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB53401","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB53401_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB53401.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB53401.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB53401.csv.gz"}},{"accession":"PRJNA637365","age_categories":{"adult":102,"elderly":15,"unknown":1},"countries":{"IL":118},"first_public_year":"2021","gbp_per_sample_median":1.18,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":4,"ibd_unspecified":76},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":118,"papers":[{"doi":"10.1128/msystems.00984-20","pmcid":"PMC8546988","pmid":"33653942","title":"Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn's Disease."}],"sample_intervention_arms":{},"sex":{"female":36,"male":81},"title":"Dysbiosis in metabolic genes of the gut microbiomes of patients with a Pouch","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA637365","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA637365_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA637365.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA637365.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA637365.csv.gz"}},{"accession":"PRJEB21612","age_categories":{"adult":97,"elderly":20},"countries":{"CN":117},"first_public_year":"2022","gbp_per_sample_median":5.44,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":61,"healthy_control":37,"type2_diabetes":19},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":117,"papers":[{"doi":"10.3389/fcimb.2017.00381","pmcid":"PMC5573791","pmid":"28884091","title":"Alterations of the Gut Microbiome in Hypertension."},{"doi":"10.3389/fmicb.2023.1309709","pmcid":"PMC10753005","pmid":"38156010","title":"Antibiotic resistance profiles of gut microbiota across various primate species in Guangxi."},{"doi":"10.1186/s12866-025-04500-8","pmcid":"PMC13001194","pmid":"41654729","title":"A validation for sex differences in gut microbiome of essential hypertension based on cohort analysis."},{"doi":"10.4103/mgr.medgasres-d-25-00128","pmcid":"PMC13456470","pmid":"42493771","title":"Hypertension and gut microbial hydrogenases: a comparison of hydrogen metabolism and etiology."}],"sample_intervention_arms":{},"sex":{"female":51,"male":65},"title":"Alterations of the gut microbiome in hypertension","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB21612","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB21612_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB21612.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB21612.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB21612.csv.gz"}},{"accession":"PRJNA714678","age_categories":{"adult":114,"elderly":2},"countries":{"IL":116},"first_public_year":"2021","gbp_per_sample_median":1.38,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":116,"papers":[{"doi":"10.1096/fj.202100857rr","pmcid":null,"pmid":"34695305","title":"Metagenomic analysis reveals the signature of gut microbiota associated with human chronotypes."},{"doi":"10.1101/2021.03.16.435653","pmcid":null,"pmid":null,"title":"Metagenomic analysis reveals the signature of gut microbiota associated with human chronotypes"}],"sample_intervention_arms":{},"sex":{},"title":"Metagenomic analysis reveals the signature of gut microbiota associated with human chronotypes","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA714678","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA714678_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA714678.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA714678.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA714678.csv.gz"}},{"accession":"PRJNA1181655","age_categories":{"adult":109,"elderly":6},"countries":{"NL":115},"first_public_year":"2026","gbp_per_sample_median":7.47,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_infection":115},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":115,"papers":[{"doi":"10.3390/ijms26041781","pmcid":"PMC11855614","pmid":"40004244","title":"Exploring Heterogeneity of Fecal Microbiome in Long COVID Patients at 3 to 6 Months After Infection."}],"sample_intervention_arms":{},"sex":{"female":60,"male":50},"title":"Fecal shotgun microbiome P4O2 COVID-19","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1181655","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1181655_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1181655.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1181655.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1181655.csv.gz"}},{"accession":"PRJNA1300320","age_categories":{"adult":89,"elderly":25},"countries":{"SE":114},"first_public_year":"2026","gbp_per_sample_median":9.16,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":75,"other_infection":39},"intervention_design":"observational_with_procedure","intervention_detail":"SARS-CoV-2 vaccination in PLWH and healthy controls","interventions":["vaccine"],"n_samples":114,"papers":[],"sample_intervention_arms":{},"sex":{"female":58,"male":56},"title":"Association of metabolic pathways and antibiotic resistance gene dynamics with SARS-CoV-2 vaccine efficacy in PLWH","trial_population_condition":"transplant_or_immunocompromised","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1300320","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1300320_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1300320.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1300320.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1300320.csv.gz"}},{"accession":"PRJNA685168","age_categories":{"adult":102,"elderly":12},"countries":{"US":114},"first_public_year":"2021","gbp_per_sample_median":2.9,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":65,"ulcerative_colitis":49},"intervention_design":"observational_with_procedure","intervention_detail":"Anti-TNF, anti-IL12/23, or anti-integrin biologic therapy","interventions":["drug_therapy"],"n_samples":114,"papers":[{"doi":"10.1016/j.chom.2021.06.019","pmcid":"PMC8366279","pmid":"34297922","title":"Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease."},{"doi":"10.1016/j.chom.2024.05.022","pmcid":"PMC11239293","pmid":"38917808","title":"Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases."},{"doi":"10.1016/j.chom.2025.01.002","pmcid":"PMC12268991","pmid":"39947133","title":"A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules."}],"sample_intervention_arms":{"drug_therapy":114},"sex":{"female":59,"male":55},"title":"Multi-omics suggest diverse mechanisms for response to biologic therapies in IBD","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA685168","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA685168_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA685168.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA685168.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA685168.csv.gz"}},{"accession":"PRJNA1107274","age_categories":{"adult":65,"elderly":48},"countries":{"US":113},"first_public_year":"2024","gbp_per_sample_median":7.24,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"other_cancer":113},"intervention_design":"single_arm_before_after","intervention_detail":"Neoadjuvant TLR9 agonist vidutolimod plus anti-PD-1 nivolumab","interventions":["drug_therapy"],"n_samples":113,"papers":[{"doi":"10.1016/j.ccell.2024.10.007","pmcid":"PMC11560503","pmid":"39486411","title":"Neoadjuvant vidutolimod and nivolumab in high-risk resectable melanoma: A prospective phase II trial."}],"sample_intervention_arms":{"drug_therapy":87,"no_intervention":26},"sex":{"female":45,"male":68},"title":"Neoadjuvant Vidutolimod and Nivolumab in High-Risk Resectable Melanoma","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1107274","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1107274_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1107274.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1107274.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1107274.csv.gz"}},{"accession":"PRJNA929328","age_categories":{"adult":112,"elderly":1},"countries":{"DE":113},"first_public_year":"2023","gbp_per_sample_median":2.16,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"transplant_or_immunocompromised":113},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":113,"papers":[{"doi":"10.1038/s41598-024-53506-1","pmcid":"PMC10876974","pmid":"38374282","title":"Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing."},{"doi":"10.1093/bib/bbaf535","pmcid":"PMC12510455","pmid":"41066697","title":"Quantifying antibiotic resistome risks across environmental niches: the L-ARRAP for long-read metagenomic profiling."},{"doi":"10.1038/s41467-025-57088-y","pmcid":"PMC11836353","pmid":"39966439","title":"Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo."}],"sample_intervention_arms":{"no_intervention":11,"other_intervention":101},"sex":{"female":65,"male":36},"title":"MetGut: ONT Sequencing of Stool Samples in alloHSCT patients","trial_population_condition":"transplant_or_immunocompromised","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA929328","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA929328_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA929328.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA929328.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA929328.csv.gz"}},{"accession":"PRJDB10829","age_categories":{"adult":32,"elderly":12,"unknown":68},"countries":{"JP":112},"first_public_year":"2022","gbp_per_sample_median":6.43,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"colorectal_cancer":112},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":112,"papers":[{"doi":"10.1128/msystems.00018-22","pmcid":"PMC9040882","pmid":"35311577","title":"Surgical Treatment for Colorectal Cancer Partially Restores Gut Microbiome and Metabolome Traits."}],"sample_intervention_arms":{"no_intervention":44,"other_intervention":11,"surgery":57},"sex":{"female":45,"male":67},"title":"Generic sample from human gut metagenome","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB10829","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB10829_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB10829.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB10829.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB10829.csv.gz"}},{"accession":"PRJDB18854","age_categories":{"adolescent":2,"adult":107,"elderly":3},"countries":{"JP":112},"first_public_year":"2025","gbp_per_sample_median":7.26,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":112},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":112,"papers":[{"doi":"10.1186/s40168-025-02168-w","pmcid":"PMC12302451","pmid":"40721806","title":"Metabolite-mediated interactions and direct contact between Fusobacterium varium and Faecalibacterium prausnitzii."}],"sample_intervention_arms":{},"sex":{"female":34,"male":78},"title":"Gut microbiota of healthy Japanese adult","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB18854","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB18854_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB18854.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB18854.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB18854.csv.gz"}},{"accession":"PRJNA485056","age_categories":{"adolescent":1,"adult":110,"elderly":1},"countries":{"MG":112},"first_public_year":"2018","gbp_per_sample_median":4.56,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":112},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":112,"papers":[{"doi":"10.1016/j.cell.2019.01.001","pmcid":"PMC6349461","pmid":"30661755","title":"Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle."},{"doi":"10.1038/s41467-022-30686-w","pmcid":"PMC9174155","pmid":"35672407","title":"Temporal changes in gastrointestinal fungi and the risk of autoimmunity during early childhood: the TEDDY study."},{"doi":"10.1080/19490976.2023.2207455","pmcid":"PMC10187079","pmid":"37188713","title":"Characterization of Bifidobacterium kashiwanohense that utilizes both milk- and plant-derived oligosaccharides."},{"doi":"10.1038/s41564-023-01549-x","pmcid":"PMC10769871","pmid":"38172624","title":"BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen."},{"doi":"10.3389/fmicb.2024.1349391","pmcid":"PMC10902438","pmid":"38426063","title":"Genomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota."}],"sample_intervention_arms":{},"sex":{"female":54,"male":58},"title":"Metagenomic sequencing of stool samples from rural communities from north-eastern Madagascar","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA485056","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA485056_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA485056.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA485056.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA485056.csv.gz"}},{"accession":"PRJDB38865","age_categories":{"elderly":110},"countries":{},"first_public_year":"2025","gbp_per_sample_median":12.02,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"randomized_controlled_trial","intervention_detail":"Bifidobacterium animalis subsp. lactis BL-99 supplementation vs placebo in older adults","interventions":["probiotic"],"n_samples":110,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Efficacy and mechanism of Bifidobacterium animalis subsp. lactis BL-99 in promoting age-related intestinal peristalsis in older adults (PRJCA042472)","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB38865","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB38865_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB38865.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB38865.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB38865.csv.gz"}},{"accession":"PRJEB12449","age_categories":{"adult":69,"elderly":41},"countries":{"US":110},"first_public_year":"2016","gbp_per_sample_median":5.68,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":52,"healthy_control":58},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":110,"papers":[{"doi":"10.1371/journal.pone.0155362","pmcid":"PMC4865240","pmid":"27171425","title":"Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing."},{"doi":"10.3389/fgene.2019.00631","pmcid":"PMC6629961","pmid":"31354787","title":"Hotspots of Sequence Variability in Gut Microbial Genes Encoding Pro-Inflammatory Factors Revealed by Oligotyping."},{"doi":"10.1038/s41591-019-0406-6","pmcid":"PMC7984229","pmid":"30936547","title":"Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer."},{"doi":"10.1186/s40168-019-0722-6","pmcid":"PMC6670193","pmid":"31370880","title":"Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease."},{"doi":"10.1186/s12864-020-6749-z","pmcid":"PMC7216530","pmid":"32393180","title":"Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment."}],"sample_intervention_arms":{},"sex":{"female":30,"male":74},"title":"Reproducibility of associations between the human gut microbiome and colorectal cancer assessed in a patient population from Washington, DC, USA","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB12449","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB12449_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB12449.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB12449.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB12449.csv.gz"}},{"accession":"PRJNA397112","age_categories":{"adolescent":4,"adult":87,"child":14,"elderly":1,"infant":4},"countries":{"IN":110},"first_public_year":"2018","gbp_per_sample_median":1.12,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":110},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":110,"papers":[{"doi":"10.1093/gigascience/giz004","pmcid":"PMC6394208","pmid":"30698687","title":"The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches."},{"doi":"10.1128/msystems.00438-19","pmcid":"PMC7407896","pmid":"31719139","title":"Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India."},{"doi":"10.1038/s41598-021-82449-0","pmcid":"PMC7854710","pmid":"33531651","title":"Bacterial associations in the healthy human gut microbiome across populations."},{"doi":"10.1080/19490976.2021.1902705","pmcid":"PMC8023248","pmid":"33794735","title":"The Impact of Migration on the Gut Metagenome of South Asian Canadians."},{"doi":"10.1186/s13073-021-00893-z","pmcid":"PMC8182900","pmid":"34092249","title":"Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers."}],"sample_intervention_arms":{},"sex":{"female":57,"male":53},"title":"Indian Human Gut Microbiome","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA397112","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA397112_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA397112.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA397112.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA397112.csv.gz"}},{"accession":"PRJNA762484","age_categories":{"adult":35,"elderly":43,"unknown":30},"countries":{},"first_public_year":"2022","gbp_per_sample_median":8.69,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":49,"neurological_psychiatric":59},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":108,"papers":[{"doi":"10.1212/wnl.0000000000013225","pmcid":"PMC8883514","pmid":"34996879","title":"Association of Fecal and Plasma Levels of Short-Chain Fatty Acids With Gut Microbiota and Clinical Severity in Parkinson Disease Patients."}],"sample_intervention_arms":{},"sex":{"female":32,"male":46},"title":"Gut microbiota in patients with Parkinson disease","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA762484","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA762484_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA762484.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA762484.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA762484.csv.gz"}},{"accession":"PRJNA928211","age_categories":{"adult":69,"elderly":39},"countries":{"KR":108},"first_public_year":"2023","gbp_per_sample_median":2.04,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":108},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":108,"papers":[{"doi":"10.4143/crt.2024.675","pmcid":"PMC12016819","pmid":"39164084","title":"Clinical Impact of Microbiome Characteristics in Treatment-Naïve Extranodal NK/T-Cell Lymphoma Patients."}],"sample_intervention_arms":{},"sex":{},"title":"Gut microbiome of DLBCL patients","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA928211","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA928211_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA928211.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA928211.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA928211.csv.gz"}},{"accession":"PRJEB49516","age_categories":{"adult":68,"elderly":39},"countries":{"AU":107},"first_public_year":"2024","gbp_per_sample_median":6.15,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":107},"intervention_design":"single_arm_before_after","intervention_detail":"Combination ipilimumab and nivolumab immune checkpoint blockade in rare cancers","interventions":["drug_therapy"],"n_samples":107,"papers":[{"doi":"10.1038/s41591-024-02823-z","pmcid":"PMC10957475","pmid":"38429524","title":"A gut microbial signature for combination immune checkpoint blockade across cancer types."},{"doi":"10.1016/j.isci.2025.112162","pmcid":"PMC11937697","pmid":"40151642","title":"Enriched pathways in gut microbiome predict response to immune checkpoint inhibitor treatment across demographic regions and various cancer types."},{"doi":"10.1002/advs.202520095","pmcid":"PMC13334858","pmid":"41972457","title":"A Microbial Lipid-ATP Synthase Axis Fuels NK Cell Antitumor Activity."},{"doi":"10.1080/19490976.2026.2662690","pmcid":"PMC13114121","pmid":"42026803","title":"Gene-level gut microbiome signatures as predictive biomarkers for response to immune checkpoint inhibitors across multiple cancer types."},{"doi":"10.34133/csbj.0065","pmcid":"PMC13173278","pmid":"42146906","title":"Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types."}],"sample_intervention_arms":{},"sex":{"female":68,"male":36},"title":"Role_of_microbiome_in_rare_cancers_in_Australia","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB49516","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB49516_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB49516.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB49516.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB49516.csv.gz"}},{"accession":"PRJNA401385","age_categories":{"adolescent":1,"adult":101,"elderly":5},"countries":{"CN":107},"first_public_year":"2017","gbp_per_sample_median":6.35,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":31,"other_infection":76},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":107,"papers":[{"doi":"10.3389/fcimb.2019.00090","pmcid":"PMC6456665","pmid":"31001490","title":"The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients."},{"doi":"10.1038/s41467-022-32991-w","pmcid":"PMC9446638","pmid":"36068270","title":"Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes."},{"doi":"10.3390/microorganisms12061058","pmcid":"PMC11205787","pmid":"38930440","title":"Deciphering Microbial Shifts in the Gut and Lung Microbiomes of COVID-19 Patients."}],"sample_intervention_arms":{},"sex":{"female":25,"male":52},"title":"Human gut microbiota Raw sequence reads","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA401385","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA401385_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA401385.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA401385.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA401385.csv.gz"}},{"accession":"PRJDB17221","age_categories":{"adult":104,"elderly":2},"countries":{"JP":106},"first_public_year":"2024","gbp_per_sample_median":13.42,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":29,"neurological_psychiatric":77},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":106,"papers":[{"doi":"10.21203/rs.3.rs-3716024/v1","pmcid":null,"pmid":null,"title":"Horizontal gene transfer shapes pathogenic bacteria in multiple sclerosis"},{"doi":"10.1016/j.celrep.2024.114785","pmcid":null,"pmid":"39341204","title":"Tyzzerella nexilis strains enriched in mobile genetic elements are involved in progressive multiple sclerosis."}],"sample_intervention_arms":{},"sex":{"female":72,"male":34},"title":"Horizontal gene transfer shapes pathogenic bacteria in multiple sclerosis_fecal metagenome","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB17221","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB17221_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB17221.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB17221.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB17221.csv.gz"}},{"accession":"PRJEB115114","age_categories":{"adult":89,"elderly":14},"countries":{"FR":103},"first_public_year":"2026","gbp_per_sample_median":15.78,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":103},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":103,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Gut microbiota analysis in FMF, CAPS, and MKD","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB115114","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB115114_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB115114.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB115114.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB115114.csv.gz"}},{"accession":"PRJNA918651","age_categories":{"adult":59,"elderly":44},"countries":{"US":103},"first_public_year":"2023","gbp_per_sample_median":0.77,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":103},"intervention_design":"randomized_controlled_trial","intervention_detail":"Mediterranean diet counseling vs USDA diet, 15 weeks","interventions":["diet_intervention"],"n_samples":103,"papers":[{"doi":"10.1128/mbio.02308-23","pmcid":"PMC10746218","pmid":"37877698","title":"Characterizing the microbiome of patients with myeloproliferative neoplasms during a Mediterranean diet intervention."},{"doi":"10.1158/2767-9764.crc-23-0380","pmcid":"PMC10913729","pmid":"38391189","title":"The NUTRIENT Trial (NUTRitional Intervention among myEloproliferative Neoplasms): Results from a Randomized Phase I Pilot Study for Feasibility and Adherence."}],"sample_intervention_arms":{},"sex":{"female":72,"male":28},"title":"Characterizing the microbiome of patients with myeloproliferative neoplasms during a Mediterranean diet intervention","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA918651","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA918651_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA918651.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA918651.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA918651.csv.gz"}},{"accession":"PRJNA934363","age_categories":{"adult":65,"elderly":38},"countries":{"PL":103},"first_public_year":"2023","gbp_per_sample_median":1.2,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_disease":103},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":103,"papers":[{"doi":"10.3390/cells12151997","pmcid":"PMC10417112","pmid":"37566076","title":"New Phage-Derived Antibacterial Enzyme PolaR Targeting Rothia spp."}],"sample_intervention_arms":{},"sex":{"female":57,"male":44},"title":"Phageomes from human stomach","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA934363","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA934363_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA934363.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA934363.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA934363.csv.gz"}},{"accession":"PRJNA1088414","age_categories":{"adult":101,"elderly":1},"countries":{"ES":102},"first_public_year":"2024","gbp_per_sample_median":1.56,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"transplant_or_immunocompromised":102},"intervention_design":"observational_with_procedure","intervention_detail":"Allogeneic hematopoietic stem cell transplantation, sampled following procedure","interventions":["surgery"],"n_samples":102,"papers":[{"doi":"10.1186/s40168-024-01948-0","pmcid":"PMC11542268","pmid":"39511587","title":"Multimodal analysis identifies microbiome changes linked to stem cell transplantation-associated diseases."}],"sample_intervention_arms":{},"sex":{"female":39,"male":63},"title":"Microbiome changes during stem cell transplantation","trial_population_condition":"transplant_or_immunocompromised","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1088414","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1088414_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1088414.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1088414.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1088414.csv.gz"}},{"accession":"PRJEB56919","age_categories":{"elderly":101},"countries":{"ES":101},"first_public_year":"2023","gbp_per_sample_median":1.33,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":101,"papers":[{"doi":"10.3389/fmicb.2023.1094071","pmcid":"PMC10062206","pmid":"37007475","title":"Influence of mental health medication on microbiota in the elderly population in the Valencian region."}],"sample_intervention_arms":{},"sex":{},"title":"Microbiota and mental health medication","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB56919","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB56919_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB56919.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB56919.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB56919.csv.gz"}},{"accession":"PRJEB72526","age_categories":{"adult":54,"elderly":47},"countries":{"IT":101},"first_public_year":"2025","gbp_per_sample_median":3.32,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":8,"colorectal_cancer":59,"healthy_control":34},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":101,"papers":[{"doi":"10.1038/s41591-025-03693-9","pmcid":"PMC12283368","pmid":"40461820","title":"Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer."}],"sample_intervention_arms":{},"sex":{"female":50,"male":51},"title":"Gut microbiome samples from CRC patients and controls from the Clinica Santa Rita, Vercelli, Italy.","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB72526","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB72526_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB72526.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB72526.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB72526.csv.gz"}},{"accession":"PRJEB76849","age_categories":{"adult":73,"elderly":28},"countries":{"US":101},"first_public_year":"2024","gbp_per_sample_median":7.19,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":true,"health_conditions":{"cardiometabolic_other":8,"healthy_control":55,"neurological_psychiatric":38},"intervention_design":"single_arm_before_after","intervention_detail":"Diet intervention in cognitive impairment/AD patients","interventions":["diet_intervention"],"n_samples":101,"papers":[{"doi":"10.1038/s44324-024-00016-3","pmcid":"PMC11216994","pmid":"38962750","title":"Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer's disease."}],"sample_intervention_arms":{"diet_intervention":54,"no_intervention":39},"sex":{"female":69,"male":24},"title":"Gut microbiome alterations in Alzheimers disease _WF-BEAM","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB76849","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB76849_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB76849.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB76849.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB76849.csv.gz"}},{"accession":"PRJNA1155319","age_categories":{"adult":80,"elderly":21},"countries":{"IE":101},"first_public_year":"2025","gbp_per_sample_median":3.59,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_infection":101},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":101,"papers":[],"sample_intervention_arms":{},"sex":{"female":51,"male":50},"title":"Characterisation of the gut and oral microbiome during SARS-COV-2 infection","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1155319","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1155319_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1155319.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1155319.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1155319.csv.gz"}},{"accession":"PRJNA1195999","age_categories":{"elderly":100},"countries":{"CN":100},"first_public_year":"2025","gbp_per_sample_median":14.21,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":100},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":100,"papers":[{"doi":"10.3389/fmicb.2025.1629811","pmcid":"PMC12490327","pmid":"41048504","title":"Gut microbiome dynamics and functional shifts in healthy aging: insights from a metagenomic study."}],"sample_intervention_arms":{},"sex":{},"title":"Gut Microbiome Dynamics and Functional Shifts in Healthy Aging","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1195999","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1195999_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1195999.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1195999.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1195999.csv.gz"}},{"accession":"PRJNA1446200","age_categories":{"adolescent":3,"adult":59,"elderly":38},"countries":{"US":100},"first_public_year":"2026","gbp_per_sample_median":5.03,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"gi_infection_or_diarrhoea":50},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":100,"papers":[],"sample_intervention_arms":{},"sex":{"female":51,"male":49},"title":"Matched Metagenomic and Metatranscriptomic Profiling of CDI","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1446200","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1446200_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1446200.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1446200.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1446200.csv.gz"}},{"accession":"PRJNA503909","age_categories":{"adolescent":8,"adult":78,"elderly":14},"countries":{"AU":100},"first_public_year":"2020","gbp_per_sample_median":2.39,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":100,"papers":[{"doi":"10.7554/elife.58407","pmcid":"PMC7572126","pmid":"33074097","title":"Intestinal microbiology shapes population health impacts of diet and lifestyle risk exposures in Torres Strait Islander communities."}],"sample_intervention_arms":{},"sex":{"female":51,"male":49},"title":"Torres Strait Islands Health Surveys, 2016","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA503909","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA503909_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA503909.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA503909.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA503909.csv.gz"}},{"accession":"PRJNA176385","age_categories":{"adolescent":16,"adult":73,"elderly":7,"unknown":2},"countries":{"RU":98},"first_public_year":"2013","gbp_per_sample_median":2.49,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":98},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":98,"papers":[{"doi":"10.1038/ncomms3469","pmcid":"PMC3778515","pmid":"24036685","title":"Human gut microbiota community structures in urban and rural populations in Russia."}],"sample_intervention_arms":{},"sex":{"female":48,"male":48},"title":"Human gut microbiome of Russian population","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA176385","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA176385_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA176385.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA176385.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA176385.csv.gz"}},{"accession":"PRJEB34333","age_categories":{"elderly":1,"unknown":96},"countries":{"ES":97},"first_public_year":"2021","gbp_per_sample_median":0.84,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":97},"intervention_design":"observational_with_procedure","intervention_detail":"Tumour vs distal tissue sampled from surgical resection","interventions":["surgery"],"n_samples":97,"papers":[{"doi":"10.1038/s41598-020-79874-y","pmcid":"PMC7801721","pmid":"33432015","title":"Metagenomic analysis of formalin-fixed paraffin-embedded tumor and normal mucosa reveals differences in the microbiome of colorectal cancer patients."}],"sample_intervention_arms":{},"sex":{"female":42,"male":55},"title":"The metagenomic analysis of formalin-fixed paraffin-embedded tumour and distal tissue from colorectal cancer patients reveals differences in the microbiome","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB34333","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB34333_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB34333.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB34333.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB34333.csv.gz"}},{"accession":"PRJNA353560","age_categories":{"adolescent":3,"adult":93,"elderly":1},"countries":{"CN":97},"first_public_year":"2016","gbp_per_sample_median":4.13,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":97},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":97,"papers":[{"doi":"10.1186/s13059-017-1271-6","pmcid":"PMC5530561","pmid":"28750650","title":"Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis."}],"sample_intervention_arms":{},"sex":{"female":40,"male":57},"title":"Human gut microbiome in AS","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA353560","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA353560_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA353560.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA353560.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA353560.csv.gz"}},{"accession":"PRJNA598452","age_categories":{"elderly":97},"countries":{"SE":97},"first_public_year":"2020","gbp_per_sample_median":12.18,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":97,"papers":[{"doi":"10.3390/nu12092610","pmcid":"PMC7551621","pmid":"32867153","title":"Differences in Gut Microbiome Composition between Senior Orienteering Athletes and Community-Dwelling Older Adults."}],"sample_intervention_arms":{},"sex":{},"title":"Elderly Gut Microbiota FMM","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA598452","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA598452_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA598452.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA598452.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA598452.csv.gz"}},{"accession":"PRJNA1096686","age_categories":{"adult":53,"elderly":43},"countries":{"US":96},"first_public_year":"2024","gbp_per_sample_median":0.64,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":6,"crohns_disease":16,"healthy_control":12,"ibd_unspecified":3,"neurological_psychiatric":36,"other_cancer":10,"other_disease":1,"type2_diabetes":3,"ulcerative_colitis":5},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":96,"papers":[{"doi":"10.1038/s41531-025-00894-4","pmcid":"PMC11923181","pmid":"40108151","title":"Comparative analysis of Parkinson's and inflammatory bowel disease gut microbiomes reveals shared butyrate-producing bacteria depletion."}],"sample_intervention_arms":{},"sex":{"female":47,"male":49},"title":"A comparative analysis of Parkinson's disease, inflammatory bowel disease, and control gut microbiomes with shotgun metagenomics","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1096686","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1096686_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1096686.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1096686.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1096686.csv.gz"}},{"accession":"PRJNA624763","age_categories":{"adult":27,"elderly":68},"countries":{"CN":95},"first_public_year":"2020","gbp_per_sample_median":11.69,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":3,"cardiometabolic_other":2,"healthy_control":86,"liver_disease":1,"other_infection":2,"type2_diabetes":1},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":95,"papers":[{"doi":"10.1080/19490976.2024.2393756","pmcid":"PMC11364081","pmid":"39197040","title":"Consistent signatures in the human gut microbiome of longevous populations."},{"doi":"10.1371/journal.pone.0305583","pmcid":"PMC11488730","pmid":"39423213","title":"Comprehensive gut microbiota composition and microbial interactions among the three age groups."},{"doi":"10.3389/fnagi.2026.1745455","pmcid":"PMC13021664","pmid":"41907847","title":"Examination of shared gut microbiome signatures in aging and Parkinson's disease."},{"doi":"10.1038/s41467-026-71521-w","pmcid":"PMC13079874","pmid":"41980943","title":"Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery."}],"sample_intervention_arms":{},"sex":{"female":56,"male":39},"title":"Shotgun metagenomics of human gut microbiota in China high longevity area","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA624763","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA624763_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA624763.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA624763.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA624763.csv.gz"}},{"accession":"PRJNA728680","age_categories":{"adult":51,"elderly":44},"countries":{"US":95},"first_public_year":"2022","gbp_per_sample_median":4.07,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"other_infection":14,"transplant_or_immunocompromised":23,"type2_diabetes":52},"intervention_design":"randomized_controlled_trial","intervention_detail":"FMT vs delayed FMT for MDRO decolonization in transplant recipients","interventions":["fmt"],"n_samples":95,"papers":[{"doi":"10.1126/scitranslmed.abo2750","pmcid":"PMC10821315","pmid":"37910603","title":"Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement."},{"doi":"10.1186/s40168-025-02046-5","pmcid":"PMC12180181","pmid":"40542451","title":"Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation."}],"sample_intervention_arms":{"fmt":51,"no_intervention":44},"sex":{"female":52,"male":43},"title":"PREMIX","trial_population_condition":"transplant_or_immunocompromised","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA728680","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA728680_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA728680.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA728680.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA728680.csv.gz"}},{"accession":"PRJNA762360","age_categories":{"adult":28,"elderly":66},"countries":{"US":94},"first_public_year":"2022","gbp_per_sample_median":8.9,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"other_cancer":65,"other_disease":29},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":94,"papers":[{"doi":"10.1136/jitc-2026-015617","pmcid":"PMC13384208","pmid":"42463281","title":"&lt;i&gt;Blautia coccoides&lt;/i&gt;-derived acetate potentiates anti-PD-1 immunotherapy in melanoma by activating cytotoxic CD8&lt;sup&gt;+&lt;/sup&gt; T cells."},{"doi":"10.1038/s41591-022-01698-2","pmcid":"PMC10246505","pmid":"35228752","title":"Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1."},{"doi":"10.18632/oncotarget.28252","pmcid":"PMC9295706","pmid":"35875611","title":"Predicting cancer immunotherapy response from gut microbiomes using machine learning models."},{"doi":"10.1126/sciimmunol.abn0704","pmcid":"PMC9925043","pmid":"36083892","title":"The microbiome-derived metabolite TMAO drives immune activation and boosts responses to immune checkpoint blockade in pancreatic cancer."},{"doi":"10.1038/s41467-023-42997-7","pmcid":"PMC10654443","pmid":"37973916","title":"Gut microbial structural variation associates with immune checkpoint inhibitor response."}],"sample_intervention_arms":{"drug_therapy":67,"no_intervention":27},"sex":{"female":28,"male":66},"title":"Intestinal Microbiota Signatures Predict Clinical Outcome and Immune-related Adverse Events in PD-1 Treated Melanoma Patients","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA762360","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA762360_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA762360.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA762360.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA762360.csv.gz"}},{"accession":"PRJEB59450","age_categories":{"adult":51,"elderly":42},"countries":{"DE":93},"first_public_year":"2023","gbp_per_sample_median":0.07,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":4,"cardiometabolic_other":15,"crohns_disease":41,"neurological_psychiatric":2,"other_cancer":1,"other_disease":30},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":93,"papers":[{"doi":"10.1093/bjs/znad129","pmcid":null,"pmid":"37260059","title":"Whole 16S rRNA sequencing of the oral microbiome predicts postoperative pancreatic fistula: prospective observational cohort study."}],"sample_intervention_arms":{},"sex":{"female":25,"male":37},"title":"PDA-MAPS - Pancreatic Ductal Adenocarcinoma - Microbiome As Predictor of Subtypes - Fistula","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB59450","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB59450_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB59450.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB59450.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB59450.csv.gz"}},{"accession":"PRJNA1210837","age_categories":{"adult":67,"elderly":26},"countries":{"CN":93},"first_public_year":"2025","gbp_per_sample_median":6.9,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":48,"healthy_control":45},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":93,"papers":[],"sample_intervention_arms":{},"sex":{"female":23,"male":70},"title":"Metagenomic sequencing of gut virus in heart failure patients","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1210837","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1210837_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1210837.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1210837.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1210837.csv.gz"}},{"accession":"PRJNA1404669","age_categories":{"adult":75,"elderly":17},"countries":{"US":92},"first_public_year":"2026","gbp_per_sample_median":8.4,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"neurological_psychiatric":92},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":92,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Microbiome-Gut-Brain Axis Biomarkers Associated with Brain Health in those with History of Traumatic Brain Injury: A US-VMP Study","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1404669","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1404669_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1404669.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1404669.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1404669.csv.gz"}},{"accession":"PRJNA413659","age_categories":{"adult":81,"elderly":11},"countries":{"RU":92},"first_public_year":"2017","gbp_per_sample_median":1.42,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"gi_infection_or_diarrhoea":92},"intervention_design":"single_arm_before_after","intervention_detail":"Quadruple HP eradication: amoxicillin, clarithromycin, PPI, bismuth subsalicylate","interventions":["antibiotic","drug_therapy"],"n_samples":92,"papers":[{"doi":"10.3389/fmicb.2019.01902","pmcid":"PMC6718723","pmid":"31507546","title":"Shifts in the Human Gut Microbiota Structure Caused by Quadruple Helicobacter pylori Eradication Therapy."}],"sample_intervention_arms":{},"sex":{"female":46,"male":46},"title":"Shifts of the intestinal microbiota and resistome caused by Helicobacter pylori eradication therapy","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA413659","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA413659_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA413659.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA413659.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA413659.csv.gz"}},{"accession":"PRJNA445968","age_categories":{"adolescent":11,"adult":77,"child":3,"elderly":1},"countries":{"HT":92},"first_public_year":"2018","gbp_per_sample_median":0.69,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":29},"intervention_design":"single_arm_before_after","intervention_detail":"Multidrug anti-TB antibiotic therapy (6 months standard regimen, or short-course monotherapy) with pre/post sampling","interventions":["antibiotic"],"n_samples":92,"papers":[{"doi":"10.1038/s41598-017-10346-6","pmcid":"PMC5589918","pmid":"28883399","title":"Antibiotic treatment for Tuberculosis induces a profound dysbiosis of the microbiome that persists long after therapy is completed."},{"doi":"10.1172/jci.insight.121899","pmcid":"PMC6237486","pmid":"30282828","title":"Mucosal-associated invariant and γδ T cell subsets respond to initial Mycobacterium tuberculosis infection."},{"doi":"10.1038/s41467-021-21475-y","pmcid":"PMC7892575","pmid":"33602926","title":"Gastrointestinal microbiota composition predicts peripheral inflammatory state during treatment of human tuberculosis."},{"doi":"10.3390/cells10102704","pmcid":"PMC8534371","pmid":"34685683","title":"Transcriptomic Biomarkers for Tuberculosis: Validation of NPC2 as a Single mRNA Biomarker to Diagnose TB, Predict Disease Progression, and Monitor Treatment Response."}],"sample_intervention_arms":{},"sex":{"female":54,"male":38},"title":"Innate, Transcriptomic, and Microbiomic Correlates of Tuberculosis Infection and Disease","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA445968","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA445968_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA445968.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA445968.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA445968.csv.gz"}},{"accession":"PRJNA682730","age_categories":{"adult":88,"elderly":4},"countries":{"US":92},"first_public_year":"2021","gbp_per_sample_median":2.63,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":69},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":92,"papers":[{"doi":"10.1002/art.41622","pmcid":"PMC11293279","pmid":"33314800","title":"The Pretreatment Gut Microbiome Is Associated With Lack of Response to Methotrexate in New-Onset Rheumatoid Arthritis."},{"doi":"10.3389/fmicb.2022.839015","pmcid":"PMC9024311","pmid":"35464950","title":"The Potential of Gut Microbiota Metabolic Capability to Detect Drug Response in Rheumatoid Arthritis Patients."},{"doi":"10.7554/elife.82401","pmcid":"PMC10289814","pmid":"37306300","title":"SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations."}],"sample_intervention_arms":{},"sex":{"female":55,"male":13},"title":"human gut microbiome predicts response to MTX treatment","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA682730","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA682730_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA682730.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA682730.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA682730.csv.gz"}},{"accession":"PRJNA1125836","age_categories":{"adult":88,"elderly":2,"neonate":1},"countries":{"PL":91},"first_public_year":"2024","gbp_per_sample_median":3.95,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":28,"obesity":63},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":91,"papers":[{"doi":"10.3390/nu17142320","pmcid":"PMC12298630","pmid":"40732945","title":"The Gut Microbiome Obesity Index: A New Analytical Tool in the Metagenomics Workflow for the Evaluation of Gut Dysbiosis in Obese Humans"}],"sample_intervention_arms":{},"sex":{"female":38,"male":35},"title":"Gut microbiome obesity index, a new analytical part of the metagenomics workflow to evaluate gut dysbiosis in obese humans","trial_population_condition":"obesity","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1125836","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1125836_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1125836.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1125836.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1125836.csv.gz"}},{"accession":"PRJNA690543","age_categories":{"adolescent":1,"adult":56,"child":7,"elderly":17,"unknown":9},"countries":{"BF":90},"first_public_year":"2021","gbp_per_sample_median":7.12,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":90},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":90,"papers":[{"doi":"10.1038/s41598-021-81257-w","pmcid":"PMC7813856","pmid":"33462272","title":"Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle."},{"doi":"10.1038/s41467-024-47272-x","pmcid":"PMC11009399","pmid":"38605009","title":"Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases."},{"doi":"10.21203/rs.3.rs-3272455/v1","pmcid":null,"pmid":null,"title":"Plasmid dispersal and recombination across human gut microbiomes is neutral, but overpowered by inflammatory diseases"}],"sample_intervention_arms":{},"sex":{"female":31,"male":59},"title":"Human Gut Microbiomes from Burkina Faso","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA690543","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA690543_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA690543.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA690543.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA690543.csv.gz"}},{"accession":"PRJNA786875","age_categories":{"adult":82,"elderly":8},"countries":{"BE":90},"first_public_year":"2022","gbp_per_sample_median":0.4,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":1,"other_disease":89},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":90,"papers":[{"doi":"10.1002/hep4.1947","pmcid":"PMC9315129","pmid":"35368152","title":"Intestinal virome in patients with alcohol use disorder and after abstinence."},{"doi":"10.1097/hep.0000000000000238","pmcid":"PMC10192041","pmid":"36631002","title":"Any alcohol use in NAFLD patients is associated with significant changes to the intestinal virome."}],"sample_intervention_arms":{},"sex":{"female":28,"male":62},"title":"Intestinal virome in alcohol use disorder and abstinence Raw sequence reads","trial_population_condition":"liver_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA786875","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA786875_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA786875.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA786875.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA786875.csv.gz"}},{"accession":"PRJNA1229669","age_categories":{"adult":64,"elderly":25},"countries":{"KR":89},"first_public_year":"2025","gbp_per_sample_median":10.64,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_disease":89},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":89,"papers":[{"doi":"10.1182/bloodadvances.2025016858","pmcid":"PMC12955626","pmid":"41364878","title":"Microbiome and metabolite biomarkers of CAR T-cell therapy outcomes in relapsed/refractory diffuse large B-cell lymphoma."}],"sample_intervention_arms":{},"sex":{},"title":"Gut microbiome shotgun metagenome data from DLBCL patients receiving CAR-T therapy","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1229669","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1229669_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1229669.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1229669.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1229669.csv.gz"}},{"accession":"PRJNA1255639","age_categories":{"adult":42,"elderly":40,"unknown":7},"countries":{"BR":89},"first_public_year":"2026","gbp_per_sample_median":0.16,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_disease":50,"other_infection":38},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":89,"papers":[{"doi":"10.3389/fcimb.2025.1622866","pmcid":"PMC12411461","pmid":"40918250","title":"Microbial diversity and composition in the gut microbiome of patients during systemic inflammatory response syndrome: can we use gut bacteria as potential biomarkers to characterize sepsis?"}],"sample_intervention_arms":{},"sex":{"female":43,"male":45},"title":"Gut microbiota of SIRS and sepsis patients","trial_population_condition":"sepsis_or_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1255639","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1255639_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1255639.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1255639.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1255639.csv.gz"}},{"accession":"PRJNA1203401","age_categories":{"adult":78,"elderly":9},"countries":{"HK":87},"first_public_year":"2025","gbp_per_sample_median":12.04,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"liver_disease":87},"intervention_design":"single_arm_before_after","intervention_detail":"Empagliflozin treatment, baseline to week 52, in MASLD patients","interventions":["drug_therapy"],"n_samples":87,"papers":[{"doi":"10.1111/liv.70023","pmcid":"PMC11827547","pmid":"39950834","title":"Gut Microbiota Predicts Treatment Response to Empagliflozin Among MASLD Patients Without Diabetes Mellitus."}],"sample_intervention_arms":{},"sex":{},"title":"Gut microbiota predicts treatment response to empagliflozin among MASLD patients without diabetes mellitus","trial_population_condition":"liver_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1203401","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1203401_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1203401.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1203401.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1203401.csv.gz"}},{"accession":"PRJNA1291832","age_categories":{"adult":33,"elderly":54},"countries":{"AU":87},"first_public_year":"2025","gbp_per_sample_median":7.33,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"other_cancer":87},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":87,"papers":[],"sample_intervention_arms":{"drug_therapy":48,"no_intervention":39},"sex":{"female":36,"male":51},"title":"Shotgun metagenomics data of melanoma patients undergoing ICB","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1291832","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1291832_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1291832.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1291832.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1291832.csv.gz"}},{"accession":"PRJNA1090271","age_categories":{"adult":81,"elderly":5},"countries":{"IN":86},"first_public_year":"2025","gbp_per_sample_median":5.44,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":16},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":86,"papers":[{"doi":"10.1093/ofid/ofae654","pmcid":"PMC11568386","pmid":"39553288","title":"Gut Microbiome in Human Melioidosis: Composition and Resistome Dynamics from Diagnosis to Discovery."}],"sample_intervention_arms":{},"sex":{"female":10,"male":76},"title":"Whole Genome Metagenomics of Human Fecal Sample: Melioidosis","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1090271","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1090271_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1090271.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1090271.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1090271.csv.gz"}},{"accession":"PRJNA672125","age_categories":{"adult":58,"elderly":28},"countries":{"NZ":86},"first_public_year":"2021","gbp_per_sample_median":2.77,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_disease":86},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":86,"papers":[{"doi":"10.1002/jbm4.10452","pmcid":"PMC7990138","pmid":"33778322","title":"The Gut Microbiome Is Altered in Postmenopausal Women With Osteoporosis and Osteopenia."}],"sample_intervention_arms":{},"sex":{"female":86},"title":"Bugs and Bones","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA672125","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA672125_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA672125.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA672125.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA672125.csv.gz"}},{"accession":"PRJNA811494","age_categories":{"adult":42,"elderly":41,"neonate":3},"countries":{"HU":86},"first_public_year":"2023","gbp_per_sample_median":7.77,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":86},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":86,"papers":[{"doi":"10.1038/s41467-023-38058-8","pmcid":"PMC10169812","pmid":"37160893","title":"Candida expansion in the gut of lung cancer patients associates with an ecological signature that supports growth under dysbiotic conditions."},{"doi":"10.1038/s41598-026-47296-x","pmcid":"PMC13319499","pmid":"42062386","title":"The gut mycobiome and inter-kingdom microbial networks are linked to COPD severity in lung cancer patients."},{"doi":"10.21203/rs.3.rs-7992928/v1","pmcid":null,"pmid":null,"title":"The Gut Mycobiome and Inter-kingdom Microbial Networks are linked to COPD Severity in Lung Cancer Patients"}],"sample_intervention_arms":{},"sex":{"female":34,"male":52},"title":"ITS2 and whole metagenomics from stool of human lung cancer patients from hungary","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA811494","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA811494_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA811494.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA811494.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA811494.csv.gz"}},{"accession":"PRJNA689476","age_categories":{"adult":80,"elderly":5},"countries":{"US":85},"first_public_year":"2022","gbp_per_sample_median":1.43,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":23,"crohns_disease":39,"healthy_control":23},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":85,"papers":[{"doi":"10.3389/fimmu.2021.587119","pmcid":"PMC7966505","pmid":"33746944","title":"Multi 'Omics Analysis of Intestinal Tissue in Ankylosing Spondylitis Identifies Alterations in the Tryptophan Metabolism Pathway."}],"sample_intervention_arms":{},"sex":{"female":43,"male":42},"title":"Metagenomic Sequencing of Bacteria from Subjects with CD and AS","trial_population_condition":"crohns_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA689476","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA689476_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA689476.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA689476.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA689476.csv.gz"}},{"accession":"PRJEB50260","age_categories":{"adult":82,"elderly":2},"countries":{"US":84},"first_public_year":"2022","gbp_per_sample_median":0.05,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"ulcerative_colitis":84},"intervention_design":"single_arm_before_after","intervention_detail":"Hyperbaric oxygen therapy as adjunct to steroids for UC flares","interventions":["other_intervention"],"n_samples":84,"papers":[{"doi":"10.1016/j.jcmgh.2022.03.008","pmcid":"PMC9117812","pmid":"35378331","title":"The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients."},{"doi":"10.1101/2022.01.14.22269325","pmcid":null,"pmid":null,"title":"Ulcerative Colitis Host-Microbiome Response to Hyperbaric Oxygen Therapy"}],"sample_intervention_arms":{"other_intervention":51,"placebo":11},"sex":{"female":29,"male":29},"title":"Hyperbaric Oxygen Therapy for Ulcerative Colitis","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB50260","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB50260_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB50260.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB50260.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB50260.csv.gz"}},{"accession":"PRJEB75958","age_categories":{"adult":83,"elderly":1},"countries":{"ES":84},"first_public_year":"2024","gbp_per_sample_median":0.43,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"other_infection":84},"intervention_design":"randomized_controlled_trial","intervention_detail":"Weekly oral FMT capsules vs placebo for 8 weeks","interventions":["fmt"],"n_samples":84,"papers":[{"doi":"10.1038/s41467-021-21472-1","pmcid":"PMC7892558","pmid":"33602945","title":"Fecal microbiota transplantation in HIV: A pilot placebo-controlled study."},{"doi":"10.1186/s40168-024-01919-5","pmcid":"PMC11494993","pmid":"39438902","title":"Fecal microbiota transplantation alters the proteomic landscape of inflammation in HIV: identifying bacterial drivers."}],"sample_intervention_arms":{"fmt":41,"no_intervention":27,"placebo":16},"sex":{"female":8,"male":73},"title":"REpeated Fecal microbiota REStoration in Hiv","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB75958","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB75958_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB75958.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB75958.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB75958.csv.gz"}},{"accession":"PRJNA1026631","age_categories":{"adult":33,"elderly":49,"unknown":1},"countries":{"US":83},"first_public_year":"2023","gbp_per_sample_median":1.67,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_infection":83},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":83,"papers":[],"sample_intervention_arms":{},"sex":{"female":82},"title":"Female Urogenital & Rectal Microbiomes of Individuals with UTI Symptoms Metagenome","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1026631","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1026631_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1026631.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1026631.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1026631.csv.gz"}},{"accession":"PRJNA353598","age_categories":{"adult":10,"elderly":8,"unknown":65},"countries":{},"first_public_year":"2017","gbp_per_sample_median":6.74,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"gi_infection_or_diarrhoea":24,"healthy_control":20},"intervention_design":"non_randomized_controlled","intervention_detail":"FMT vs vancomycin for recurrent C. difficile infection","interventions":["antibiotic","fmt"],"n_samples":83,"papers":[{"doi":"10.1136/gutjnl-2017-313952","pmcid":"PMC5868238","pmid":"28539351","title":"Bacteriophage transfer during faecal microbiota transplantation in &lt;i&gt;Clostridium difficile&lt;/i&gt; infection is associated with treatment outcome."}],"sample_intervention_arms":{"fmt":1},"sex":{"female":11,"male":7},"title":"viral metagenome Metagenome","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA353598","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA353598_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA353598.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA353598.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA353598.csv.gz"}},{"accession":"PRJEB27928","age_categories":{"adult":60,"elderly":22},"countries":{"DE":82},"first_public_year":"2018","gbp_per_sample_median":4.49,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":22,"healthy_control":60},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":82,"papers":[{"doi":"10.1038/s41591-019-0406-6","pmcid":"PMC7984229","pmid":"30936547","title":"Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer."},{"doi":"10.1038/s41467-021-23029-8","pmcid":"PMC8131609","pmid":"34006865","title":"Gene-level metagenomic architectures across diseases yield high-resolution microbiome diagnostic indicators."},{"doi":"10.1038/s41591-019-0405-7","pmcid":"PMC9533319","pmid":"30936548","title":"Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation."},{"doi":"10.3389/fmicb.2019.03117","pmcid":"PMC6990412","pmid":"32038558","title":"Beyond Taxonomic Analysis of Microbiomes: A Functional Approach for Revisiting Microbiome Changes in Colorectal Cancer."},{"doi":"10.1186/s12864-020-6749-z","pmcid":"PMC7216530","pmid":"32393180","title":"Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment."}],"sample_intervention_arms":{},"sex":{"female":39,"male":43},"title":"Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB27928","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB27928_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB27928.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB27928.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB27928.csv.gz"}},{"accession":"PRJNA1475610","age_categories":{"adult":81,"elderly":1},"countries":{"CN":82},"first_public_year":"2026","gbp_per_sample_median":7.51,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":41,"type2_diabetes":41},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":82,"papers":[{"doi":"10.3389/fmicb.2026.1902019","pmcid":"PMC13522148","pmid":"42666298","title":"Multi-layer gut microbiome variation in type 2 diabetes despite preserved higher-order community structure."}],"sample_intervention_arms":{},"sex":{"female":35,"male":47},"title":"Shotgun metagenomic profiling of the gut microbiome in type 2 diabetes mellitus and healthy controls","trial_population_condition":"type2_diabetes","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1475610","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1475610_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1475610.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1475610.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1475610.csv.gz"}},{"accession":"PRJNA1157583","age_categories":{"adult":39,"elderly":12,"unknown":30},"countries":{"CN":81},"first_public_year":"2025","gbp_per_sample_median":10.85,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":81,"papers":[{"doi":"10.1080/19490976.2025.2508949","pmcid":"PMC12118437","pmid":"40409349","title":"Indole-3-lactic acid suppresses colorectal cancer via metabolic reprogramming."}],"sample_intervention_arms":{},"sex":{"female":21,"male":30},"title":"metagenome Raw sequence reads","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1157583","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1157583_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1157583.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1157583.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1157583.csv.gz"}},{"accession":"PRJNA665245","age_categories":{"elderly":81},"countries":{"GB":81},"first_public_year":"2022","gbp_per_sample_median":7.82,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":81,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Gut-Brain axis in people at differential genetic risk for developing Alzheimer's disease","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA665245","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA665245_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA665245.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA665245.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA665245.csv.gz"}},{"accession":"PRJNA531921","age_categories":{"elderly":79},"countries":{"US":79},"first_public_year":"2019","gbp_per_sample_median":5.68,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":79,"papers":[{"doi":"10.3389/fmicb.2019.02260","pmcid":"PMC6777474","pmid":"31611867","title":"Fecal Microbiome Characteristics and the Resistome Associated With Acquisition of Multidrug-Resistant Organisms Among Elderly Subjects."},{"doi":"10.1016/j.isci.2020.100905","pmcid":"PMC7044522","pmid":"32106056","title":"Antimicrobial Resistance Gene Prevalence in a Population of Patients with Advanced Dementia Is Related to Specific Pathobionts."}],"sample_intervention_arms":{},"sex":{},"title":"Human Gut Metagenome Raw sequence reads","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA531921","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA531921_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA531921.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA531921.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA531921.csv.gz"}},{"accession":"PRJNA1145581","age_categories":{"adult":58,"elderly":19,"unknown":1},"countries":{"IL":78},"first_public_year":"2025","gbp_per_sample_median":35.52,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":24,"other_disease":54},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":78,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Gut Microbiome profile of Lynch syndrome mutations","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1145581","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1145581_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1145581.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1145581.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1145581.csv.gz"}},{"accession":"PRJNA588035","age_categories":{"adult":62,"elderly":16},"countries":{"CN":78},"first_public_year":"2021","gbp_per_sample_median":12.23,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":39,"neurological_psychiatric":39},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":78,"papers":[{"doi":"10.3389/fmicb.2021.728479","pmcid":"PMC8506127","pmid":"34650532","title":"Cross-Sectional Study on the Gut Microbiome of Parkinson's Disease Patients in Central China."},{"doi":"10.3389/fnint.2022.1054627","pmcid":"PMC9846222","pmid":"36686268","title":"High levels of Bifidobacteriaceae are associated with the pathogenesis of Parkinson's disease."},{"doi":"10.1371/journal.pone.0310005","pmcid":"PMC11706413","pmid":"39774383","title":"Deep learning-based differential gut flora for prediction of Parkinson's."},{"doi":"10.1038/s41531-024-00724-z","pmcid":"PMC11109112","pmid":"38773112","title":"Meta-analysis of shotgun sequencing of gut microbiota in Parkinson's disease."},{"doi":"10.1038/s41467-025-56829-3","pmcid":"PMC12059030","pmid":"40335465","title":"Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease."}],"sample_intervention_arms":{},"sex":{"female":18,"male":21},"title":"Cross-sectional study of intestinal flora in Parkinson's patients in central China","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA588035","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA588035_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA588035.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA588035.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA588035.csv.gz"}},{"accession":"PRJNA791751","age_categories":{"adult":17,"elderly":61},"countries":{"FR":78},"first_public_year":"2022","gbp_per_sample_median":7.05,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":78},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":78,"papers":[{"doi":"10.1136/jitc-2021-004191","pmcid":"PMC8928383","pmid":"35296557","title":"Immune system and intestinal microbiota determine efficacy of androgen deprivation therapy against prostate cancer."}],"sample_intervention_arms":{},"sex":{"male":78},"title":"Immune system and intestinal microbiota determine efficacy of androgen deprivation therapy against prostate cancer","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA791751","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA791751_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA791751.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA791751.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA791751.csv.gz"}},{"accession":"PRJNA962059","age_categories":{"adult":36,"elderly":38,"unknown":3},"countries":{"US":77},"first_public_year":"2024","gbp_per_sample_median":3.36,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":39,"neurological_psychiatric":35},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":77,"papers":[{"doi":"10.1016/j.parkreldis.2024.107176","pmcid":"PMC11614677","pmid":"39426329","title":"Taxonomic intestinal microbiota differences in Lewy body spectrum disease and cohabitant controls."}],"sample_intervention_arms":{},"sex":{"female":40,"male":34},"title":"Lewy Body Dementia Microbiome","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA962059","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA962059_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA962059.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA962059.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA962059.csv.gz"}},{"accession":"PRJEB42013","age_categories":{"adult":41,"elderly":35},"countries":{"DE":76},"first_public_year":"2022","gbp_per_sample_median":5.84,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":31,"other_cancer":45},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":76,"papers":[{"doi":"10.1128/msystems.01229-24","pmcid":"PMC11915875","pmid":"40013793","title":"Association of tumor microbiome with survival in resected early-stage PDAC."},{"doi":"10.1136/gutjnl-2021-324755","pmcid":"PMC9185815","pmid":"35260444","title":"A faecal microbiota signature with high specificity for pancreatic cancer."},{"doi":"10.1016/j.isci.2024.109294","pmcid":"PMC10915599","pmid":"38450156","title":"Highly accurate diagnosis of pancreatic cancer by integrative modeling using gut microbiome and exposome data."},{"doi":"10.1097/js9.0000000000001762","pmcid":"PMC11487005","pmid":"38874485","title":"The microbial composition of pancreatic ductal adenocarcinoma: a systematic review of 16S rRNA gene sequencing."},{"doi":"10.1016/j.cpblue.2026.100034","pmcid":"PMC13269251","pmid":"42312244","title":"Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals."}],"sample_intervention_arms":{},"sex":{"female":42,"male":34},"title":"Non-invasive, robust and specific fecal microbiota-based screening for the early detection of PDAC.","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB42013","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB42013_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB42013.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB42013.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB42013.csv.gz"}},{"accession":"PRJNA431482","age_categories":{"adult":71,"elderly":5},"countries":{"CN":76},"first_public_year":"2018","gbp_per_sample_median":5.97,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":24,"healthy_control":52},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":76,"papers":[{"doi":"10.1097/md.0000000000042698","pmcid":"PMC12338280","pmid":"40797468","title":"Investigating the mediating effect of plasma metabolites on the gut microbiome in influencing Behçet disease: A multi-omics validated Mendelian randomization study."},{"doi":"10.1186/s40168-018-0520-6","pmcid":"PMC6091101","pmid":"30077182","title":"A metagenomic study of the gut microbiome in Behcet's disease."}],"sample_intervention_arms":{},"sex":{"female":17,"male":55},"title":"human gut metagenome Metagenome-Behcet's disease","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA431482","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA431482_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA431482.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA431482.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA431482.csv.gz"}},{"accession":"PRJNA1240691","age_categories":{"adult":63,"elderly":12},"countries":{"CN":75},"first_public_year":"2025","gbp_per_sample_median":6.97,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":75},"intervention_design":"single_arm_before_after","intervention_detail":"5-aminosalicylic acid (5-ASA) standardized treatment for UC","interventions":["drug_therapy"],"n_samples":75,"papers":[{"doi":"10.1016/j.isci.2025.112568","pmcid":"PMC12159923","pmid":"40510115","title":"Gut microbiome signatures predict 5-ASA efficacy in ulcerative colitis."}],"sample_intervention_arms":{},"sex":{},"title":"Gut metagenome","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1240691","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1240691_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1240691.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1240691.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1240691.csv.gz"}},{"accession":"PRJNA904419","age_categories":{"elderly":75},"countries":{"CN":75},"first_public_year":"2023","gbp_per_sample_median":11.68,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":75},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":75,"papers":[{"doi":"10.1016/j.exger.2023.112356","pmcid":null,"pmid":"38185288","title":"A metagenomics study reveals the gut microbiome as a sex-specific modulator of healthy aging in Hainan centenarians."}],"sample_intervention_arms":{},"sex":{"female":59,"male":16},"title":"A metagenomics study reveals the gut microbiome as a sex-specific modulator of healthy aging in Hainan centenarians","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA904419","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA904419_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA904419.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA904419.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA904419.csv.gz"}},{"accession":"PRJNA347511","age_categories":{"adult":3,"elderly":71},"countries":{"IE":74},"first_public_year":"2020","gbp_per_sample_median":4.77,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":74,"papers":[{"doi":"10.1093/ajcn/nqz220","pmcid":"PMC6885478","pmid":"31518386","title":"Exploratory analysis of covariation of microbiota-derived vitamin K and cognition in older adults."}],"sample_intervention_arms":{},"sex":{"female":51,"male":23},"title":"Shotgun sequencing of the gut microbiome to look at vitamin K biosynthesis","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA347511","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA347511_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA347511.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA347511.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA347511.csv.gz"}},{"accession":"PRJNA749645","age_categories":{"adult":18,"elderly":55,"neonate":1},"countries":{"CH":29,"GB":45},"first_public_year":"2021","gbp_per_sample_median":2.96,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":74},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":74,"papers":[{"doi":"10.1093/nargab/lqag110","pmcid":"PMC13551040","pmid":"42712939","title":"Identifying fundamental gaps in functional metagenomics: a step towards unlocking microbiome research potential."},{"doi":"10.3389/fcimb.2026.1754671","pmcid":"PMC12876203","pmid":"41660426","title":"SSTDhunter: a curated gene database for investigating androgen producing potential in microbiota species."}],"sample_intervention_arms":{},"sex":{"male":74},"title":"Whole genome metagenome of gut microbiota from prostate cancer patients","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA749645","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA749645_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA749645.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA749645.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA749645.csv.gz"}},{"accession":"PRJNA1299468","age_categories":{"adult":42,"elderly":31},"countries":{"AU":73},"first_public_year":"2025","gbp_per_sample_median":3.22,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":55,"neurological_psychiatric":18},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":73,"papers":[{"doi":"10.1016/j.neuropharm.2023.109566","pmcid":null,"pmid":"37150399","title":"Differences in the gut microbiome across typical ageing and in Parkinson's disease."}],"sample_intervention_arms":{},"sex":{"female":38,"male":35},"title":"Gut Bacteria and Parkinson's disease","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1299468","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1299468_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1299468.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1299468.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1299468.csv.gz"}},{"accession":"PRJNA1390647","age_categories":{"elderly":73},"countries":{"US":73},"first_public_year":"2026","gbp_per_sample_median":1.3,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":43,"neurological_psychiatric":30},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":73,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Gut Barrier Dysfunction, Inflammation, and Cognitive Impairment in Aging","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1390647","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1390647_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1390647.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1390647.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1390647.csv.gz"}},{"accession":"PRJNA624223","age_categories":{"adult":55,"elderly":18},"countries":{"CN":70,"HK":3},"first_public_year":"2020","gbp_per_sample_median":3.5,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":15,"other_infection":57},"intervention_design":"observational_with_procedure","intervention_detail":"Empirical antibiotics received by COVID-19 patients (observed, not trial-assigned)","interventions":["antibiotic"],"n_samples":73,"papers":[{"doi":"10.1053/j.gastro.2020.05.048","pmcid":"PMC7237927","pmid":"32442562","title":"Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization."},{"doi":"10.1371/journal.pone.0248730","pmcid":"PMC7963026","pmid":"33725024","title":"Variability in digestive and respiratory tract Ace2 expression is associated with the microbiome."},{"doi":"10.1177/1177932221999428","pmcid":"PMC7961713","pmid":"33786001","title":"Metagenomics Approaches to Investigate the Gut Microbiome of COVID-19 Patients."},{"doi":"10.3389/fcimb.2021.790422","pmcid":"PMC8653907","pmid":"34900762","title":"Alterations in the Composition of Intestinal DNA Virome in Patients With COVID-19."},{"doi":"10.1016/j.ijheh.2021.113882","pmcid":"PMC8664710","pmid":"34915282","title":"Alterations of fecal antibiotic resistome in COVID-19 patients after empirical antibiotic exposure."}],"sample_intervention_arms":{},"sex":{"female":34,"male":39},"title":"Gut microbiome alterations and longitudinal kinetics in COVID-19 patients","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA624223","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA624223_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA624223.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA624223.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA624223.csv.gz"}},{"accession":"PRJDB17048","age_categories":{"adolescent":1,"adult":60,"elderly":10},"countries":{"JP":71},"first_public_year":"2024","gbp_per_sample_median":6.58,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":23,"colorectal_cancer":10,"other_disease":38},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":71,"papers":[{"doi":"10.1016/j.isci.2024.110181","pmcid":"PMC11237946","pmid":"38993678","title":"Fusobacterium species are distinctly associated with patients with Lynch syndrome colorectal cancer."}],"sample_intervention_arms":{},"sex":{"female":41,"male":29},"title":"Japanese Lynch Syndrome Gut Microbiome","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB17048","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB17048_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB17048.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB17048.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB17048.csv.gz"}},{"accession":"PRJEB123871","age_categories":{"adult":56,"elderly":15},"countries":{},"first_public_year":"2026","gbp_per_sample_median":2.13,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":11,"other_cancer":60},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":71,"papers":[{"doi":"10.1111/ejh.70121","pmcid":"PMC13050679","pmid":"41582602","title":"Microbiome-Based Modeling of CAR-T Therapy Response in Lymphoma: Insights From Shotgun Metagenomics Sequencing."}],"sample_intervention_arms":{},"sex":{"female":31,"male":40},"title":"Microbiome‐Based Modeling of CAR‐T Therapy Response in Lymphoma: Insights From Shotgun Metagenomics Sequencing","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB123871","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB123871_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB123871.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB123871.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB123871.csv.gz"}},{"accession":"PRJEB54724","age_categories":{"adult":7,"child":2,"elderly":38,"infant":21,"neonate":2,"unknown":1},"countries":{"NL":71},"first_public_year":"2023","gbp_per_sample_median":0.36,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"gi_infection_or_diarrhoea":71},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":71,"papers":[{"doi":"10.1128/spectrum.05022-22","pmcid":"PMC10434279","pmid":"37432120","title":"Metagenomic Surveillance of Viral Gastroenteritis in a Public Health Setting."},{"doi":"10.1038/s41598-024-73785-y","pmcid":"PMC11522440","pmid":"39472593","title":"Accessible viral metagenomics for public health and clinical domains with Jovian."}],"sample_intervention_arms":{},"sex":{"female":40,"male":30},"title":"Netherlands Norovirus surveillance, metagenomics, 2015-2019","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB54724","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB54724_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB54724.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB54724.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB54724.csv.gz"}},{"accession":"PRJNA494824","age_categories":{"adult":68,"elderly":3},"countries":{"US":71},"first_public_year":"2019","gbp_per_sample_median":7.14,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":12,"other_cancer":59},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":71,"papers":[{"doi":"10.1186/s40168-020-00811-2","pmcid":"PMC7059390","pmid":"32138779","title":"Predictable modulation of cancer treatment outcomes by the gut microbiota."},{"doi":"10.1002/advs.202411052","pmcid":"PMC12245021","pmid":"40285661","title":"β-Glucuronidase-Expressing Lactobacillus reuteri Triggers Irinotecan Enterotoxicity Through Depleting the Regenerative Epithelial Stem/Progenitor Pool."},{"doi":"10.1002/cam4.6503","pmcid":"PMC10557844","pmid":"37676050","title":"Identification of microbial markers associated with lung cancer based on multi-cohort 16 s rRNA analyses: A systematic review and meta-analysis."},{"doi":"10.3389/fcimb.2025.1591076","pmcid":"PMC12336193","pmid":"40792105","title":"Exploring fecal microbiota signatures associated with immune response and antibiotic impact in NSCLC: insights from metagenomic and machine learning approaches."},{"doi":"10.34133/csbj.0065","pmcid":"PMC13173278","pmid":"42146906","title":"Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types."}],"sample_intervention_arms":{"drug_therapy":23},"sex":{"female":40,"male":31},"title":"Gut metagenomic raw sequence reads of cancer patients","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA494824","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA494824_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA494824.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA494824.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA494824.csv.gz"}},{"accession":"PRJNA842425","age_categories":{"adult":39,"elderly":32},"countries":{"US":71},"first_public_year":"2022","gbp_per_sample_median":1.68,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_infection":71},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":71,"papers":[{"doi":"10.1038/s41467-022-34260-2","pmcid":"PMC9633022","pmid":"36329015","title":"Immunomodulatory fecal metabolites are associated with mortality in COVID-19 patients with respiratory failure."},{"doi":"10.1016/j.gastha.2025.100695","pmcid":"PMC12197998","pmid":"40574876","title":"Fecal Butyrate and Deoxycholic Acid Concentrations Correlate With Mortality in Patients With Liver Disease."}],"sample_intervention_arms":{},"sex":{"female":32,"male":37},"title":"Alterations of the Microbiome During Critical Illness with short and long term clinical outcomes","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA842425","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA842425_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA842425.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA842425.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA842425.csv.gz"}},{"accession":"PRJNA928744","age_categories":{"adult":27,"elderly":44},"countries":{"CA":71},"first_public_year":"2023","gbp_per_sample_median":5.2,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":11,"other_cancer":60},"intervention_design":"single_arm_before_after","intervention_detail":"FMT from healthy donor combined with anti-PD1 therapy in melanoma","interventions":["drug_therapy","fmt"],"n_samples":71,"papers":[{"doi":"10.1136/jitc-2025-012659","pmcid":"PMC12359429","pmid":"40759441","title":"Improved survival in advanced melanoma patients treated with fecal microbiota transplantation using healthy donor stool in combination with anti-PD1: final results of the MIMic phase 1 trial."},{"doi":"10.1016/j.chom.2024.10.006","pmcid":"PMC11629153","pmid":"39481388","title":"Longitudinal analysis of the gut microbiota during anti-PD-1 therapy reveals stable microbial features of response in melanoma patients."},{"doi":"10.1038/s41586-025-09249-8","pmcid":"PMC12390848","pmid":"40659786","title":"Microbiota-driven antitumour immunity mediated by dendritic cell migration."},{"doi":"10.1186/s40168-025-02249-w","pmcid":"PMC12590682","pmid":"41199348","title":"Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2."},{"doi":"10.34133/csbj.0065","pmcid":"PMC13173278","pmid":"42146906","title":"Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types."}],"sample_intervention_arms":{},"sex":{"female":20,"male":40},"title":"Gut microbiota composition of patients in MIMic cohort","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA928744","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA928744_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA928744.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA928744.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA928744.csv.gz"}},{"accession":"PRJNA698459","age_categories":{"adult":60,"elderly":9},"countries":{"DE":69},"first_public_year":"2021","gbp_per_sample_median":5.16,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":69},"intervention_design":"randomized_controlled_trial","intervention_detail":"5-day fast then modified DASH diet vs modified DASH diet alone","interventions":["diet_intervention"],"n_samples":69,"papers":[{"doi":"10.1038/s41467-021-22097-0","pmcid":"PMC8010079","pmid":"33785752","title":"Fasting alters the gut microbiome reducing blood pressure and body weight in metabolic syndrome patients."},{"doi":"10.1093/bioadv/vbad063","pmcid":"PMC10284677","pmid":"37359720","title":"LongDat: an R package for covariate-sensitive longitudinal analysis of high-dimensional data."}],"sample_intervention_arms":{"diet_intervention":69},"sex":{"female":54,"male":15},"title":"Fasting alters the gut microbiome with sustained blood pressure and body weight reduction in metabolic syndrome patients","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA698459","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA698459_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA698459.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA698459.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA698459.csv.gz"}},{"accession":"PRJNA1152927","age_categories":{"adult":36,"elderly":32},"countries":{"CN":68},"first_public_year":"2024","gbp_per_sample_median":11.76,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_infection":32},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":68,"papers":[{"doi":"10.1128/spectrum.02639-24","pmcid":"PMC11960049","pmid":"40062854","title":"Altered gut microbiota and metabolite profiles in community-acquired pneumonia: a metagenomic and metabolomic study."}],"sample_intervention_arms":{},"sex":{"female":34,"male":34},"title":"Alterations in the gut microbiota and metabolite profiles of patients with community-acquired pneumonia","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1152927","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1152927_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1152927.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1152927.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1152927.csv.gz"}},{"accession":"PRJNA905672","age_categories":{"adult":32,"elderly":34,"unknown":2},"countries":{"TN":68},"first_public_year":"2023","gbp_per_sample_median":0.24,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":35,"other_cancer":33},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":68,"papers":[{"doi":"10.3390/cimb45090477","pmcid":"PMC10527824","pmid":"37754261","title":"Colorectal Cancer Archaeome: A Metagenomic Exploration, Tunisia."}],"sample_intervention_arms":{},"sex":{"female":39,"male":29},"title":"Metagenomic data of gut microbiome from tunisian CRC patients","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA905672","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA905672_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA905672.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA905672.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA905672.csv.gz"}},{"accession":"PRJNA1438274","age_categories":{"adult":34,"elderly":32},"countries":{"US":66},"first_public_year":"2026","gbp_per_sample_median":39.41,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"gi_infection_or_diarrhoea":35,"healthy_control":12,"liver_disease":19},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":66,"papers":[{"doi":"10.1016/j.isci.2026.117312","pmcid":"PMC13524746","pmid":"42668680","title":"Proximity-ligation metagenomics reveals differential plasmid and chromosomal antimicrobial resistance gene carriage in disrupted gut ecosystems."}],"sample_intervention_arms":{},"sex":{"female":31,"male":22},"title":"Proximity-ligation metagenomics of rCDI and Cirrhosis Patients","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1438274","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1438274_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1438274.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1438274.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1438274.csv.gz"}},{"accession":"PRJNA1065874","age_categories":{"adult":36,"elderly":29},"countries":{"TW":65},"first_public_year":"2024","gbp_per_sample_median":7.12,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":32,"other_disease":33},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":65,"papers":[{"doi":"10.1186/s12866-024-03219-2","pmcid":"PMC11040827","pmid":"38658841","title":"Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study."}],"sample_intervention_arms":{},"sex":{"female":42,"male":23},"title":"Gut microbiome associated with gastric cancer and chronic gastritis","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1065874","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1065874_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1065874.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1065874.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1065874.csv.gz"}},{"accession":"PRJEB106095","age_categories":{"adult":50,"elderly":14},"countries":{},"first_public_year":"2026","gbp_per_sample_median":5.76,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":64,"papers":[],"sample_intervention_arms":{},"sex":{"female":37,"male":27},"title":"Hi-C and VLP sequencing data of SPMP cohort","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB106095","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB106095_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB106095.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB106095.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB106095.csv.gz"}},{"accession":"PRJNA1150764","age_categories":{"adult":62,"elderly":2},"countries":{"CN":64},"first_public_year":"2024","gbp_per_sample_median":0.21,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":64},"intervention_design":"non_randomized_controlled","intervention_detail":"Naoxintong capsule added to atorvastatin for hyperlipidemia","interventions":["drug_therapy"],"n_samples":64,"papers":[{"doi":"10.1016/j.phymed.2026.157799","pmcid":null,"pmid":"41544465","title":"Gut microbiome-metabolomics integration explores the adjunctive effect of Naoxintong capsule on atorvastatin in ameliorating hyperlipidemia: A randomized controlled pilot study."}],"sample_intervention_arms":{},"sex":{"female":32,"male":32},"title":"Integrated gut microbiome and metabolomics to the effects and mechanisms of the addition of Naoxintong capsule to atorvastatin in the treatment of hyperlipidemia","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1150764","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1150764_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1150764.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1150764.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1150764.csv.gz"}},{"accession":"PRJNA1248002","age_categories":{"elderly":64},"countries":{"US":64},"first_public_year":"2025","gbp_per_sample_median":2.4,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":64},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":64,"papers":[{"doi":"10.1158/1055-9965.epi-25-0157","pmcid":"PMC12316560","pmid":"40434915","title":"Comparing the Metagenomic Performance of Stools Collected from Custom Cards and 95% Ethanol in Epidemiologic Studies."}],"sample_intervention_arms":{},"sex":{"female":64},"title":"Comparison of 95% ethanol and cards for stool metagenomic studies","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1248002","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1248002_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1248002.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1248002.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1248002.csv.gz"}},{"accession":"PRJEB112132","age_categories":{"adult":34,"elderly":24,"unknown":4},"countries":{"ES":62},"first_public_year":"2026","gbp_per_sample_median":0.46,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":24,"other_infection":34},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":62,"papers":[],"sample_intervention_arms":{},"sex":{"female":33,"male":25},"title":"Family cohort with central areolar choroidal dystrophy","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB112132","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB112132_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB112132.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB112132.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB112132.csv.gz"}},{"accession":"PRJNA1263414","age_categories":{"adult":45,"elderly":17},"countries":{"RU":62},"first_public_year":"2025","gbp_per_sample_median":2.21,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":62},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":62,"papers":[{"doi":"10.1080/19490976.2026.2681788","pmcid":"PMC13274128","pmid":"42298353","title":"Gut microbial markers of immunotherapy response in melanoma: a cross-cohort analysis including the first Russian dataset."}],"sample_intervention_arms":{},"sex":{"female":37,"male":25},"title":"Human gut metagenome from melanoma patients","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1263414","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1263414_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1263414.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1263414.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1263414.csv.gz"}},{"accession":"PRJNA484031","age_categories":{"adult":43,"elderly":19},"countries":{"CN":62},"first_public_year":"2019","gbp_per_sample_median":8.68,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":62},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":62,"papers":[{"doi":"10.1177/2040622320904293","pmcid":"PMC7045296","pmid":"32153743","title":"Composition of fecal microbiota in low-set rectal cancer patients treated with FOLFOX."},{"doi":"10.1128/msphere.00816-23","pmcid":"PMC11036815","pmid":"38470044","title":"&lt;i&gt;Anaerostipes hadrus&lt;/i&gt;, a butyrate-producing bacterium capable of metabolizing 5-fluorouracil."}],"sample_intervention_arms":{},"sex":{"female":17,"male":45},"title":"Faeces Genome sequencing","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA484031","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA484031_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA484031.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA484031.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA484031.csv.gz"}},{"accession":"PRJNA498332","age_categories":{"adult":58,"elderly":4},"countries":{},"first_public_year":"2018","gbp_per_sample_median":0.8,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":31,"other_disease":29},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":62,"papers":[{"doi":"10.1073/pnas.2023202118","pmcid":"PMC8201803","pmid":"34083435","title":"A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases."}],"sample_intervention_arms":{},"sex":{"female":34,"male":27},"title":"Comparison of faecal virome composition in cystic fibrosis patients vs. a healthy cohort","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA498332","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA498332_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA498332.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA498332.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA498332.csv.gz"}},{"accession":"PRJNA553191","age_categories":{"adult":7,"elderly":49,"unknown":6},"countries":{"IT":62},"first_public_year":"2019","gbp_per_sample_median":5.35,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":62},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":62,"papers":[{"doi":"10.1128/msystems.00124-20","pmcid":"PMC7093822","pmid":"32209716","title":"Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation."},{"doi":"10.1128/msphere.00691-21","pmcid":"PMC8550338","pmid":"34494880","title":"The Human Gut Resistome up to Extreme Longevity."},{"doi":"10.1093/nargab/lqac070","pmcid":"PMC9492272","pmid":"36159175","title":"RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties."},{"doi":"10.1128/mbio.00052-23","pmcid":"PMC10294665","pmid":"37102874","title":"Aging-Associated Augmentation of Gut Microbiome Virulence Capability Drives Sepsis Severity."},{"doi":"10.1038/s41598-022-13313-y","pmcid":"PMC9163076","pmid":"35654877","title":"Metagenomic assembled plasmids of the human microbiome vary across disease cohorts."}],"sample_intervention_arms":{},"sex":{"female":40,"male":16},"title":"Shotgun metagenomics of human gut microbiota up to extreme longevity and the increasing role of xenobiotics degradation","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA553191","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA553191_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA553191.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA553191.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA553191.csv.gz"}},{"accession":"PRJEB110927","age_categories":{"adult":35,"elderly":18,"unknown":8},"countries":{"FR":61},"first_public_year":"2026","gbp_per_sample_median":6.83,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"randomized_controlled_trial","intervention_detail":"FOLFIRI + durvalumab with or without tremelimumab","interventions":["drug_therapy"],"n_samples":61,"papers":[{"doi":"10.1053/j.gastro.2024.10.020","pmcid":null,"pmid":"39454892","title":"Faecalibacteriumprausnitzii Is Associated With Clinical Response to Immune Checkpoint Inhibitors in Patients With Advanced Gastric Adenocarcinoma: Results of Microbiota Analysis of PRODIGE 59-FFCD 170"}],"sample_intervention_arms":{},"sex":{"female":22,"male":34},"title":"Durigast_F_prausnitzii_ICI_gastric_adenocarcinoma","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB110927","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB110927_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB110927.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB110927.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB110927.csv.gz"}},{"accession":"PRJNA1056258","age_categories":{"adult":43,"elderly":18},"countries":{"CA":61},"first_public_year":"2023","gbp_per_sample_median":0.19,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":61,"papers":[],"sample_intervention_arms":{},"sex":{"female":26,"male":35},"title":"The Role of Akkermansia muciniphila in Luminal Cholesterol Metabolism","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1056258","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1056258_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1056258.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1056258.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1056258.csv.gz"}},{"accession":"PRJNA649273","age_categories":{"adult":44,"elderly":15,"unknown":2},"countries":{"CA":61},"first_public_year":"2020","gbp_per_sample_median":6.64,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":25,"kidney_disease":36},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":61,"papers":[{"doi":"10.1186/s40168-023-01703-x","pmcid":"PMC10675928","pmid":"38007438","title":"Multi-site microbiota alteration is a hallmark of kidney stone formation."}],"sample_intervention_arms":{},"sex":{"female":23,"male":38},"title":"KiSMi Kidney stone patients - gut samples","trial_population_condition":"kidney_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA649273","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA649273_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA649273.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA649273.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA649273.csv.gz"}},{"accession":"PRJNA1138254","age_categories":{"adult":5,"elderly":55},"countries":{"GB":60},"first_public_year":"2024","gbp_per_sample_median":2.08,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ibd_unspecified":60},"intervention_design":"single_arm_before_after","intervention_detail":"Oral vancomycin 125mg QID for 4 weeks","interventions":["antibiotic"],"n_samples":60,"papers":[{"doi":"10.1093/ecco-jcc/jjae189","pmcid":"PMC11831226","pmid":"39673746","title":"Open Label Vancomycin in Primary Sclerosing Cholangitis-Inflammatory Bowel Disease: Improved Colonic Disease Activity and Associations With Changes in Host-Microbiome-Metabolomic Signatures."}],"sample_intervention_arms":{},"sex":{},"title":"PSC-Vanc Clinical Trial","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1138254","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1138254_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1138254.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1138254.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1138254.csv.gz"}},{"accession":"PRJNA1192958","age_categories":{"adult":55,"elderly":5},"countries":{"IN":60},"first_public_year":"2026","gbp_per_sample_median":0.31,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":33,"type2_diabetes":27},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":60,"papers":[],"sample_intervention_arms":{},"sex":{"female":20,"male":40},"title":"Human gut microbiome of healthy and T2D cohorts of India","trial_population_condition":"type2_diabetes","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1192958","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1192958_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1192958.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1192958.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1192958.csv.gz"}},{"accession":"PRJNA1258611","age_categories":{"elderly":60},"countries":{"CN":60},"first_public_year":"2025","gbp_per_sample_median":14.84,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"type2_diabetes":60},"intervention_design":"none","intervention_detail":"In vitro fecal fermentation comparing whole grain blend (black/red/brown rice) vs polished white rice","interventions":[],"n_samples":60,"papers":[{"doi":"10.3390/foods14152557","pmcid":"PMC12345654","pmid":"40807496","title":"Comparing a Whole Grain Blend with Polished White Rice for Starch Digestibility and Gut Microbiota Fermentation in Diabetic Patients: An In Vitro Study."}],"sample_intervention_arms":{"diet_intervention":40,"no_intervention":20},"sex":{},"title":"Comparing a Whole Grain Blend with Polished White Rice on Gut Microbiota Fermentation in Diabetic Patients","trial_population_condition":"type2_diabetes","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1258611","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1258611_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1258611.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1258611.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1258611.csv.gz"}},{"accession":"PRJNA1356513","age_categories":{"adult":58,"elderly":2},"countries":{"PR":60},"first_public_year":"2025","gbp_per_sample_median":1.36,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ibd_unspecified":58,"type2_diabetes":2},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":60,"papers":[{"doi":"10.1093/ibd/izag161","pmcid":null,"pmid":"42647084","title":"Diet quality, gut microbiome, and inflammatory signatures in Puerto Rican adults with Crohn disease: a multidimensional analysis."}],"sample_intervention_arms":{},"sex":{"female":28,"male":32},"title":"Dieta Anti-INflamatoria (DAIN) study","trial_population_condition":"crohns_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1356513","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1356513_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1356513.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1356513.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1356513.csv.gz"}},{"accession":"PRJNA1367514","age_categories":{"adult":48,"elderly":12},"countries":{"CN":60},"first_public_year":"2025","gbp_per_sample_median":6.8,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":30,"other_disease":30},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":60,"papers":[{"doi":"10.1038/s41467-025-68060-1","pmcid":"PMC12868900","pmid":"41457077","title":"Multi-omics analysis identifies a microbiota-bile acid-TLR signaling axis driving bladder injury in interstitial cystitis."}],"sample_intervention_arms":{},"sex":{"female":60},"title":"Shotgun metagenomic sequencing of fecal specimens from 30 paired human sample","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1367514","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1367514_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1367514.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1367514.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1367514.csv.gz"}},{"accession":"PRJNA686769","age_categories":{"adult":56,"elderly":4},"countries":{"CN":60},"first_public_year":"2025","gbp_per_sample_median":11.23,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":52,"healthy_control":8},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":60,"papers":[{"doi":"10.1136/ard-2024-225564","pmcid":null,"pmid":"39084885","title":"Rheumatoid arthritis patients harbour aberrant enteric bacteriophages with autoimmunity-provoking potential: a paired sibling study."}],"sample_intervention_arms":{},"sex":{},"title":"Altered enteric virome in rheumatoid arthritis","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA686769","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA686769_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA686769.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA686769.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA686769.csv.gz"}},{"accession":"PRJDB20343","age_categories":{"adult":15,"elderly":44},"countries":{"JP":59},"first_public_year":"2025","gbp_per_sample_median":6.74,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":59},"intervention_design":"single_arm_before_after","intervention_detail":"Antibiotic prophylaxis before/after colon cancer surgery","interventions":["antibiotic","surgery"],"n_samples":59,"papers":[{"doi":"10.1016/j.jgar.2025.12.014","pmcid":null,"pmid":"41455576","title":"Impact of antimicrobial prophylaxis in colorectal cancer surgery on the gut and oral microbiome and resistome: A prospective observational cohort study."}],"sample_intervention_arms":{"no_intervention":16},"sex":{"female":22,"male":37},"title":"Shotgun metagenome sequencing of oral and stool samples from colorectal cancer patients before and after administration of antibiotic prophylaxis for surgery","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB20343","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB20343_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB20343.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB20343.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB20343.csv.gz"}},{"accession":"PRJEB25514","age_categories":{"adult":17,"elderly":42},"countries":{"IT":59},"first_public_year":"2019","gbp_per_sample_median":5.48,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":59,"papers":[{"doi":"10.1128/msystems.00325-19","pmcid":"PMC6616150","pmid":"31289141","title":"A Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian Centenarians."},{"doi":"10.1080/19490976.2022.2107288","pmcid":"PMC9361766","pmid":"35939616","title":"The landscape in the gut microbiome of long-lived families reveals new insights on longevity and aging - relevant neural and immune function."},{"doi":"10.3389/fnagi.2022.820108","pmcid":"PMC9300991","pmid":"35875797","title":"Gut Microbiota Composition and Metabolic Potential of Long-Living People in China."},{"doi":"10.1080/19490976.2024.2393756","pmcid":"PMC11364081","pmid":"39197040","title":"Consistent signatures in the human gut microbiome of longevous populations."},{"doi":"10.1371/journal.pone.0305583","pmcid":"PMC11488730","pmid":"39423213","title":"Comprehensive gut microbiota composition and microbial interactions among the three age groups."}],"sample_intervention_arms":{},"sex":{"female":36,"male":23},"title":"A cross-sectional study of compositional and functional profiles of gut microbiota in Sardinian centenarians","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB25514","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB25514_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB25514.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB25514.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB25514.csv.gz"}},{"accession":"PRJEB62571","age_categories":{"adult":20,"child":15,"elderly":20,"infant":4},"countries":{"ES":59},"first_public_year":"2023","gbp_per_sample_median":1.17,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":59},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":59,"papers":[{"doi":"10.1038/s41598-026-35033-3","pmcid":"PMC12873169","pmid":"41513932","title":"Lifetime existence of a core of mutualistic symbionts and functionally uncoupled taxa in the gut of a Mediterranean cohort."}],"sample_intervention_arms":{},"sex":{"female":34,"male":25},"title":"Changes in the microbiota across life: the existence of a core of microbial taxa and decoupling taxa.","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB62571","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB62571_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB62571.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB62571.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB62571.csv.gz"}},{"accession":"PRJNA986283","age_categories":{"adult":26,"elderly":33},"countries":{"US":59},"first_public_year":"2023","gbp_per_sample_median":4.97,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_disease":59},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":59,"papers":[{"doi":"10.1038/s41467-023-42005-y","pmcid":"PMC10611739","pmid":"37891329","title":"Gut microbiota impacts bone via Bacteroides vulgatus-valeric acid-related pathways."}],"sample_intervention_arms":{},"sex":{"female":59},"title":"Understanding Gut Microbiome's Impact on Osteoporosis","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA986283","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA986283_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA986283.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA986283.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA986283.csv.gz"}},{"accession":"PRJNA715634","age_categories":{"adult":4,"elderly":1,"unknown":53},"countries":{"AU":58},"first_public_year":"2021","gbp_per_sample_median":3.69,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":58},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":58,"papers":[{"doi":"10.1038/s41396-021-00991-1","pmcid":"PMC8528831","pmid":"34035441","title":"Novel strain-level resolution of Crohn's disease mucosa-associated microbiota via an ex vivo combination of microbe culture and metagenomic sequencing."}],"sample_intervention_arms":{},"sex":{"female":3,"male":2},"title":"Novel Strain Level Resolution of Crohns Disease Mucosa-Associated Microbiota via an ex vivo Combination of Microbe Culture and Metagenomic Sequencing","trial_population_condition":"crohns_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA715634","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA715634_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA715634.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA715634.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA715634.csv.gz"}},{"accession":"PRJNA725020","age_categories":{"adult":52,"elderly":2,"unknown":4},"countries":{"US":58},"first_public_year":"2021","gbp_per_sample_median":14.71,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":58,"papers":[{"doi":"10.1186/s40168-023-01529-7","pmcid":"PMC10199544","pmid":"37210515","title":"Exposing new taxonomic variation with inflammation - a murine model-specific genome database for gut microbiome researchers."},{"doi":"10.1128/mbio.01511-23","pmcid":"PMC10653893","pmid":"37695138","title":"Targeted curation of the gut microbial gene content modulating human cardiovascular disease."}],"sample_intervention_arms":{},"sex":{"female":23,"male":31},"title":"Fecal Metagenomes","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA725020","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA725020_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA725020.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA725020.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA725020.csv.gz"}},{"accession":"PRJEB27005","age_categories":{"adult":48,"elderly":9},"countries":{"CM":40},"first_public_year":"2019","gbp_per_sample_median":5.09,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":57},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":57,"papers":[{"doi":"10.1371/journal.pone.0211139","pmcid":"PMC6364966","pmid":"30726303","title":"Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels."},{"doi":"10.1126/science.abm7759","pmcid":"PMC10777373","pmid":"36108023","title":"Codiversification of gut microbiota with humans."},{"doi":"10.1038/s43587-022-00306-9","pmcid":"PMC10154212","pmid":"37118093","title":"Toward an improved definition of a healthy microbiome for healthy aging."},{"doi":"10.1186/s40168-023-01614-x","pmcid":"PMC10436630","pmid":"37596617","title":"Statistical modeling of gut microbiota for personalized health status monitoring."},{"doi":"10.1038/s41598-024-82956-w","pmcid":"PMC11685674","pmid":"39738309","title":"DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction."}],"sample_intervention_arms":{},"sex":{"female":25,"male":32},"title":"Gut metagenomes of rural populations in Cameroon","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB27005","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB27005_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB27005.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB27005.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB27005.csv.gz"}},{"accession":"PRJNA1320802","age_categories":{"adult":56,"elderly":1},"countries":{"CN":57},"first_public_year":"2026","gbp_per_sample_median":12.98,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":31,"ibs":26},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":57,"papers":[{"doi":"10.1016/j.cmet.2026.03.003","pmcid":null,"pmid":"41928504","title":"Gut microbial metabolism via hippocampal indole-AhR signaling regulates emotional symptoms."}],"sample_intervention_arms":{},"sex":{"female":38,"male":19},"title":"A key microbiota triggering emotional disorders in IBS.","trial_population_condition":"ibs","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1320802","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1320802_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1320802.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1320802.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1320802.csv.gz"}},{"accession":"PRJNA565546","age_categories":{"elderly":57},"countries":{"CN":57},"first_public_year":"2019","gbp_per_sample_median":6.66,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":18,"other_disease":39},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":57,"papers":[{"doi":"10.3389/fcimb.2022.827575","pmcid":"PMC9008261","pmid":"35433497","title":"Gut Microbiome Signature Are Correlated With Bone Mineral Density Alterations in the Chinese Elders."}],"sample_intervention_arms":{},"sex":{"female":29,"male":28},"title":"fecal sample Raw sequence reads","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA565546","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA565546_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA565546.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA565546.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA565546.csv.gz"}},{"accession":"PRJNA833034","age_categories":{"adolescent":4,"adult":49,"child":1,"elderly":2},"countries":{"CN":56},"first_public_year":"2022","gbp_per_sample_median":6.5,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":56},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":56,"papers":[{"doi":"10.1002/advs.202400684","pmcid":"PMC11497089","pmid":"39225628","title":"Integrated Microbiome and Metabolome Analysis Reveals Hypothalamic-Comorbidities Related Signatures in Craniopharyngioma."}],"sample_intervention_arms":{},"sex":{"female":21,"male":35},"title":"Integrated metagenomics and metabolomics analysis illustrates the systemic impact of the gut microbiota in patients with craniopharyngioma","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA833034","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA833034_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA833034.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA833034.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA833034.csv.gz"}},{"accession":"PRJEB98485","age_categories":{"adult":36,"elderly":19},"countries":{"LV":55},"first_public_year":"2025","gbp_per_sample_median":6.96,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":true,"health_conditions":{"healthy_control":36,"neurological_psychiatric":4,"other_disease":15},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":55,"papers":[],"sample_intervention_arms":{"drug_therapy":12,"no_intervention":6},"sex":{"female":44,"male":11},"title":"Shotgun metagenomic sequencing of the gut microbiome reveals hormone‐specific taxonomic and functional shifts in PitNET patients","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB98485","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB98485_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB98485.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB98485.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB98485.csv.gz"}},{"accession":"PRJNA1294521","age_categories":{"adult":40,"elderly":15},"countries":{"US":55},"first_public_year":"2025","gbp_per_sample_median":0.07,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":55},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":55,"papers":[{"doi":"10.1080/19490976.2025.2608437","pmcid":"PMC12773562","pmid":"41481156","title":"Bile salt hydrolase activity as a rational target for MASLD therapy."}],"sample_intervention_arms":{},"sex":{"female":25,"male":30},"title":"16S sequencing of MASLD patient fecal samples","trial_population_condition":"liver_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1294521","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1294521_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1294521.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1294521.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1294521.csv.gz"}},{"accession":"PRJNA973824","age_categories":{"adult":31,"elderly":24},"countries":{"KZ":55},"first_public_year":"2024","gbp_per_sample_median":5.15,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":55,"papers":[{"doi":"10.1159/000536082","pmcid":"PMC11008724","pmid":"38246133","title":"The Trajectory of Successful Aging: Insights from Metagenome and Cytokine Profiling."},{"doi":"10.1038/s41598-025-02013-y","pmcid":"PMC12095471","pmid":"40399402","title":"Parity influences postpartum adaptations in the maternal gut microbiota."},{"doi":"10.3389/fnagi.2026.1745455","pmcid":"PMC13021664","pmid":"41907847","title":"Examination of shared gut microbiome signatures in aging and Parkinson's disease."}],"sample_intervention_arms":{},"sex":{},"title":"Immunoregulatory role of gut microbiome and mycobiome in aging","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA973824","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA973824_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA973824.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA973824.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA973824.csv.gz"}},{"accession":"PRJDB38277","age_categories":{"elderly":51},"countries":{},"first_public_year":"2025","gbp_per_sample_median":6.38,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":51,"papers":[{"doi":"10.3390/microorganisms13071657","pmcid":"PMC12298205","pmid":"40732166","title":"Healthy Ageing and Gut Microbiota: A Study on Longevity in Adults."}],"sample_intervention_arms":{},"sex":{},"title":"Characteristics of intestinal bacteria in long-lived elderly (PRJCA019954)","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB38277","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB38277_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB38277.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB38277.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB38277.csv.gz"}},{"accession":"PRJNA1030952","age_categories":{"adult":47,"elderly":4},"countries":{"JP":51},"first_public_year":"2023","gbp_per_sample_median":7.77,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":1,"crohns_disease":9,"healthy_control":10,"ibs":14,"other_cancer":6,"ulcerative_colitis":11},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":51,"papers":[{"doi":"10.1186/s40168-024-01903-z","pmcid":"PMC11446047","pmid":"39358771","title":"A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome."},{"doi":"10.1101/2025.06.16.659887","pmcid":null,"pmid":null,"title":"Biome-specific genome catalogues reveal functional potential of shallow sequencing"}],"sample_intervention_arms":{},"sex":{"female":28,"male":23},"title":"Single-cell and metagenome sequencing for human oral/gut microbiome","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1030952","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1030952_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1030952.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1030952.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1030952.csv.gz"}},{"accession":"PRJNA1111312","age_categories":{"adult":21,"elderly":30},"countries":{"FR":51},"first_public_year":"2024","gbp_per_sample_median":1.56,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"liver_disease":51},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":51,"papers":[{"doi":"10.1016/j.gastha.2024.07.020","pmcid":"PMC11785905","pmid":"39895875","title":"Shotgun Metagenomics Reveals Bacteroides stercoris as a Fecal Biomarker Depleted in Late-Stage Hepatocellular Carcinoma."}],"sample_intervention_arms":{},"sex":{"female":6,"male":45},"title":"Shotgun metagenomics reveals Bacteroides stercoris as a fecal biomarker depleted in late-stage hepatocellular carcinoma","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1111312","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1111312_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1111312.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1111312.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1111312.csv.gz"}},{"accession":"PRJNA1130699","age_categories":{"adult":19,"elderly":32},"countries":{"KR":51},"first_public_year":"2024","gbp_per_sample_median":17.72,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":51},"intervention_design":"observational_with_procedure","intervention_detail":"Anti-PD-L1/anti-PD-1 immune checkpoint blockade therapy","interventions":["drug_therapy"],"n_samples":51,"papers":[{"doi":"10.1038/s41467-024-55388-3","pmcid":"PMC11680825","pmid":"39730328","title":"A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy."}],"sample_intervention_arms":{"drug_therapy":51},"sex":{"female":12,"male":39},"title":"Whole metagenomic shotgun sequencing on fecal samples of NSCLC patients who received ICB treatment","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1130699","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1130699_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1130699.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1130699.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1130699.csv.gz"}},{"accession":"PRJDB14457","age_categories":{"adult":44,"elderly":6},"countries":{"JP":50},"first_public_year":"2025","gbp_per_sample_median":0.11,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":50},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":50,"papers":[{"doi":"10.3390/microorganisms10112169","pmcid":"PMC9697123","pmid":"36363762","title":"Identification of Human Gut Microbiome Associated with Enterolignan Production."},{"doi":"10.1038/s41598-025-04339-z","pmcid":"PMC12137908","pmid":"40467839","title":"NIBN Japan Microbiome Database, a database for exploring the correlations between human microbiome and health."}],"sample_intervention_arms":{},"sex":{"female":26,"male":24},"title":"Gut microbiota of healthy Japanese adult","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB14457","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB14457_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB14457.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB14457.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB14457.csv.gz"}},{"accession":"PRJNA705217","age_categories":{"adult":43,"elderly":7},"countries":{"US":50},"first_public_year":"2022","gbp_per_sample_median":1.34,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":21,"ibs":29},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":50,"papers":[{"doi":"10.1016/j.cgh.2024.06.028","pmcid":"PMC11707044","pmid":"38987012","title":"Transcriptomic and Metabolomic Correlates of Increased Colonic Permeability in Postinfection Irritable Bowel Syndrome."},{"doi":"10.1038/s41564-022-01103-1","pmcid":"PMC9081267","pmid":"35484230","title":"Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome."}],"sample_intervention_arms":{},"sex":{"female":36,"male":14},"title":"Gut metagenomes of patients with post-infection irritable bowel syndrome","trial_population_condition":"ibs","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA705217","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA705217_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA705217.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA705217.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA705217.csv.gz"}},{"accession":"PRJNA912151","age_categories":{"adult":43,"elderly":7},"countries":{"US":50},"first_public_year":"2022","gbp_per_sample_median":0.96,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":50,"papers":[{"doi":"10.3389/fnut.2022.1059163","pmcid":"PMC9852993","pmid":"36687728","title":"Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes."}],"sample_intervention_arms":{},"sex":{},"title":"Characterization of the gut microbiome in NH Bhutanese refugee adults","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA912151","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA912151_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA912151.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA912151.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA912151.csv.gz"}},{"accession":"PRJNA598446","age_categories":{"adult":24,"elderly":19,"unknown":6},"countries":{},"first_public_year":"2020","gbp_per_sample_median":6.09,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":49},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":49,"papers":[{"doi":"10.1038/s41467-020-18476-8","pmcid":"PMC7492273","pmid":"32934239","title":"A predictive index for health status using species-level gut microbiome profiling."},{"doi":"10.1186/s13073-021-00957-0","pmcid":"PMC8439035","pmid":"34517888","title":"Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis."}],"sample_intervention_arms":{},"sex":{"female":29,"male":14},"title":"A Predictive Index for Health Status Using Species-level Gut Microbiome Profiling","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA598446","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA598446_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA598446.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA598446.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA598446.csv.gz"}},{"accession":"PRJNA343008","age_categories":{"elderly":24,"infant":24},"countries":{"IE":48},"first_public_year":"2018","gbp_per_sample_median":0.66,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":48,"papers":[],"sample_intervention_arms":{},"sex":{"female":29,"male":18},"title":"feces metagenome Raw sequence reads","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA343008","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA343008_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA343008.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA343008.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA343008.csv.gz"}},{"accession":"PRJNA541981","age_categories":{"adult":15,"elderly":33},"countries":{"US":48},"first_public_year":"2019","gbp_per_sample_median":4.59,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":48},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":48,"papers":[{"doi":"10.1186/s13073-019-0672-4","pmcid":"PMC6785875","pmid":"31597568","title":"Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients."},{"doi":"10.1186/s13073-021-00974-z","pmcid":"PMC8513370","pmid":"34641962","title":"Bacteroides vulgatus and Bacteroides dorei predict immune-related adverse events in immune checkpoint blockade treatment of metastatic melanoma."},{"doi":"10.1084/jem.20200606","pmcid":"PMC7664509","pmid":"33175106","title":"Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers."},{"doi":"10.1172/jci.insight.140940","pmcid":"PMC7714408","pmid":"33268597","title":"Meta-analysis of the gut microbiota in predicting response to cancer immunotherapy in metastatic melanoma."},{"doi":"10.1158/1078-0432.ccr-20-4834","pmcid":"PMC9053858","pmid":"33593881","title":"A Uniform Computational Approach Improved on Existing Pipelines to Reveal Microbiome Biomarkers of Nonresponse to Immune Checkpoint Inhibitors."}],"sample_intervention_arms":{"drug_therapy":48},"sex":{"female":6,"male":42},"title":"Gut microbiome in melanoma patients","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA541981","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA541981_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA541981.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA541981.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA541981.csv.gz"}},{"accession":"PRJNA634145","age_categories":{"adult":45,"elderly":3},"countries":{"US":48},"first_public_year":"2021","gbp_per_sample_median":5.65,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":15,"other_disease":33},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":48,"papers":[{"doi":"10.1016/j.xjidi.2022.100115","pmcid":"PMC9214347","pmid":"35757783","title":"Multiomic Analysis of the Gut Microbiome in Psoriasis Reveals Distinct Host‒Microbe Associations."},{"doi":"10.1111/srt.13822","pmcid":"PMC11227279","pmid":"38970783","title":"Metagenomics reveals unique gut mycobiome biomarkers in psoriasis."},{"doi":"10.3389/fimmu.2025.1647466","pmcid":"PMC12540108","pmid":"41132660","title":"Lactobacillus plantarum-derived cytoplasmic membrane vesicles as novel anti-inflammatory nanotherapeutics for psoriasis management."}],"sample_intervention_arms":{},"sex":{"female":24,"male":24},"title":"human metagenome Raw sequence reads","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA634145","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA634145_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA634145.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA634145.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA634145.csv.gz"}},{"accession":"PRJNA788670","age_categories":{"adult":24,"elderly":24},"countries":{},"first_public_year":"2022","gbp_per_sample_median":4.18,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"obesity":48},"intervention_design":"randomized_controlled_trial","intervention_detail":"12 weeks HIIT vs MICT exercise training","interventions":["exercise"],"n_samples":48,"papers":[],"sample_intervention_arms":{"exercise":19,"no_intervention":29},"sex":{"female":16,"male":32},"title":"Effects of high-intensity interval training and moderate-intensity continuous training on gut microbiome in overweight and obese older adults","trial_population_condition":"obesity","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA788670","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA788670_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA788670.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA788670.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA788670.csv.gz"}},{"accession":"PRJNA845905","age_categories":{"adult":40,"elderly":8},"countries":{"US":48},"first_public_year":"2022","gbp_per_sample_median":1.91,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"transplant_or_immunocompromised":48},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":48,"papers":[{"doi":"10.3389/frtra.2023.1182534","pmcid":"PMC11235359","pmid":"38993864","title":"Reduced immunomodulatory metabolite concentrations in peri-transplant fecal samples from heart allograft recipients."},{"doi":"10.1371/journal.pone.0337727","pmcid":"PMC12788677","pmid":"41511994","title":"Fecal butyrate and deoxycholic acid quantitation for rapid assessment of the gut microbiome."},{"doi":"10.1073/pnas.2534432123","pmcid":"PMC13123906","pmid":"42012958","title":"The intestinal microbiota impacts nutritional immunity and resistance to &lt;i&gt;Acinetobacter baumannii&lt;/i&gt; pneumonia."}],"sample_intervention_arms":{},"sex":{"female":12,"male":36},"title":"Donor Specific Antibodies and the Microbiome in Heart Transplant Patients","trial_population_condition":"transplant_or_immunocompromised","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA845905","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA845905_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA845905.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA845905.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA845905.csv.gz"}},{"accession":"PRJEB49168","age_categories":{"adult":40,"elderly":5},"countries":{"SG":45},"first_public_year":"2021","gbp_per_sample_median":15.12,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":45},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":45,"papers":[{"doi":"10.1128/spectrum.00849-22","pmcid":"PMC9431525","pmid":"35699469","title":"Mutual Exclusion of Methanobrevibacter Species in the Human Gut Microbiota Facilitates Directed Cultivation of a Candidatus Methanobrevibacter Intestini Representative."},{"doi":"10.1038/s41467-022-33782-z","pmcid":"PMC9561172","pmid":"36229545","title":"Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians."},{"doi":"10.1128/spectrum.03969-23","pmcid":"PMC10986321","pmid":"38441466","title":"Comparison of &lt;i&gt;tet&lt;/i&gt;(X4)-containing contigs assembled from metagenomic sequencing data with plasmid sequences of isolates from a cohort of healthy subjects."},{"doi":"10.1186/s13059-024-03363-y","pmcid":"PMC11331721","pmid":"39160564","title":"Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes."},{"doi":"10.1101/2025.02.12.637485","pmcid":null,"pmid":null,"title":"From sporulation to village differentiation: the shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia"}],"sample_intervention_arms":{},"sex":{"female":28,"male":17},"title":"Singapore Platinum Metagenomes Project","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB49168","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB49168_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB49168.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB49168.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB49168.csv.gz"}},{"accession":"PRJEB57228","age_categories":{"adult":23,"elderly":21},"countries":{"DE":44},"first_public_year":"2024","gbp_per_sample_median":18.18,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":21,"neurological_psychiatric":23},"intervention_design":"single_arm_before_after","intervention_detail":"4-week high-fibre diet with lactulose prebiotic","interventions":["diet_intervention","prebiotic_or_fibre"],"n_samples":44,"papers":[{"doi":"10.1038/s41531-025-00885-5","pmcid":"PMC11968880","pmid":"40180909","title":"A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson's Disease."}],"sample_intervention_arms":{},"sex":{"female":22,"male":22},"title":"Dietary intervention of people with Parkinson's disease","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB57228","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB57228_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB57228.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB57228.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB57228.csv.gz"}},{"accession":"PRJNA1113191","age_categories":{"adult":31,"elderly":13},"countries":{"KR":44},"first_public_year":"2025","gbp_per_sample_median":10.73,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":44},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":44,"papers":[{"doi":"10.1038/s12276-026-01828-7","pmcid":"PMC13633279","pmid":"42722700","title":"Linking visceral fat accumulation to gut microbiota: key bacterial taxa and their roles in the glycogen synthesis pathway."}],"sample_intervention_arms":{},"sex":{"female":30,"male":14},"title":"Gut microbiome analysis of health screening participants at Seoul National University Hospital","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1113191","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1113191_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1113191.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1113191.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1113191.csv.gz"}},{"accession":"PRJNA397906","age_categories":{"adult":17,"elderly":22,"unknown":5},"countries":{"US":44},"first_public_year":"2017","gbp_per_sample_median":9.06,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":44},"intervention_design":"observational_with_procedure","intervention_detail":"Immune checkpoint inhibitor therapy in melanoma patients","interventions":["drug_therapy"],"n_samples":44,"papers":[{"doi":"10.1016/j.neo.2017.08.004","pmcid":"PMC5602478","pmid":"28923537","title":"Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients."},{"doi":"10.1093/g3journal/jkab046","pmcid":"PMC8049424","pmid":"33713107","title":"MetaPrism: A versatile toolkit for joint taxa/gene analysis of metagenomic sequencing data."},{"doi":"10.1016/j.xpro.2024.102847","pmcid":"PMC10837094","pmid":"38277270","title":"Protocol to identify fungal profile from fecal metagenomes in cancer patients prior to immunotherapy."},{"doi":"10.1016/j.slast.2025.100365","pmcid":null,"pmid":"41241214","title":"Technology-enabled integration of single-cell transcriptomics and microbiome data identifies RNA-targetable host-microbiota networks in colorectal adenoma."},{"doi":"10.1084/jem.20200606","pmcid":"PMC7664509","pmid":"33175106","title":"Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers."}],"sample_intervention_arms":{},"sex":{"female":9,"male":30},"title":"Metagenomic shotgun sequencing of gut microbiomes of melanoma patients receiving immune checkpoint inhibitor therapy","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA397906","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA397906_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA397906.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA397906.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA397906.csv.gz"}},{"accession":"PRJNA679346","age_categories":{"adult":3,"elderly":40},"countries":{"JP":43},"first_public_year":"2021","gbp_per_sample_median":21.28,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":21,"neurological_psychiatric":22},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":43,"papers":[{"doi":"10.1016/j.xcrm.2021.100398","pmcid":"PMC8484692","pmid":"34622235","title":"Identification of &lt;i&gt;Faecalibacterium prausnitzii&lt;/i&gt; strains for gut microbiome-based intervention in Alzheimer's-type dementia."},{"doi":"10.1186/s40168-026-02342-8","pmcid":"PMC13069797","pmid":"41782023","title":"Impacts of host genetics on gut microbiome composition in Alzheimer's disease."},{"doi":"10.20517/mrr.2024.35","pmcid":"PMC11684920","pmid":"39741952","title":"Secondary analysis reveals gut microbiota differences in patients with Parkinson's disease and/or cognitive impairment."}],"sample_intervention_arms":{},"sex":{"female":27,"male":16},"title":"Whole-metagenome shotgun sequencing of human feces","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA679346","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA679346_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA679346.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA679346.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA679346.csv.gz"}},{"accession":"PRJEB55787","age_categories":{"adult":36,"elderly":5},"countries":{"CH":41},"first_public_year":"2025","gbp_per_sample_median":10.76,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":20,"healthy_control":21},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":41,"papers":[{"doi":"10.1186/s12974-024-03109-4","pmcid":"PMC11077820","pmid":"38715051","title":"The gut microbiome and HLA-B27-associated anterior uveitis: a case-control study."}],"sample_intervention_arms":{},"sex":{"female":19,"male":22},"title":"Associations of the Intestinal Microbiome and HLA-B27-associated anterior uveitis","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB55787","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB55787_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB55787.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB55787.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB55787.csv.gz"}},{"accession":"PRJEB77410","age_categories":{"adult":23,"elderly":18},"countries":{"CO":41},"first_public_year":"2024","gbp_per_sample_median":7.3,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"gi_infection_or_diarrhoea":41},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":41,"papers":[{"doi":"10.1186/s13099-026-00809-5","pmcid":"PMC12980963","pmid":"41692795","title":"Contrasting the gut microbiome in Colombian patients with diarrhea: a comparative metagenomic study in hospitalization and emergency room services."}],"sample_intervention_arms":{},"sex":{"female":25,"male":13},"title":"Metagenome description of patients with diarrhea from hospitalization and emergency room services of Hospital Universitario Mayor Mederi","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB77410","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB77410_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB77410.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB77410.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB77410.csv.gz"}},{"accession":"PRJEB42151","age_categories":{"adult":36,"elderly":4},"countries":{"US":40},"first_public_year":"2020","gbp_per_sample_median":1.26,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":40},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":40,"papers":[{"doi":"10.1038/s41564-021-01050-3","pmcid":"PMC8852248","pmid":"35087228","title":"Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity."},{"doi":"10.20517/mrr.2024.09","pmcid":"PMC11480726","pmid":"39421249","title":"Pangenomic analysis identifies correlations between &lt;i&gt;Akkermansia&lt;/i&gt; species and subspecies and human health outcomes."}],"sample_intervention_arms":{},"sex":{"female":11,"male":29},"title":"Metaomics Reveals Microbiome Based Proteolysis as a Driver of Ulcerative Colitis Severity","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB42151","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB42151_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB42151.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB42151.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB42151.csv.gz"}},{"accession":"PRJNA1258750","age_categories":{"elderly":40},"countries":{"MY":40},"first_public_year":"2025","gbp_per_sample_median":10.75,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":40,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Whole genome sequencing of gut microbiota in cognitively frail and robust older adults from the AGELESS Cohort","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1258750","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1258750_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1258750.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1258750.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1258750.csv.gz"}},{"accession":"PRJNA1289665","age_categories":{"adult":39,"elderly":1},"countries":{"CN":40},"first_public_year":"2025","gbp_per_sample_median":12.49,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":40,"papers":[],"sample_intervention_arms":{},"sex":{"male":40},"title":"The human intestinal metagenome","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1289665","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1289665_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1289665.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1289665.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1289665.csv.gz"}},{"accession":"PRJNA314481","age_categories":{"adult":31,"elderly":9},"countries":{},"first_public_year":"2016","gbp_per_sample_median":0.71,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":10,"healthy_control":20,"other_cancer":10},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":40,"papers":[],"sample_intervention_arms":{},"sex":{"female":23,"male":17},"title":"Bacteria and human colon samples from human gut Metagenome","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA314481","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA314481_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA314481.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA314481.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA314481.csv.gz"}},{"accession":"PRJNA685581","age_categories":{"adult":35,"elderly":5},"countries":{"CN":40},"first_public_year":"2023","gbp_per_sample_median":12.21,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":31,"healthy_control":9},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":40,"papers":[{"doi":"10.3389/fmicb.2021.719599","pmcid":"PMC8600050","pmid":"34803940","title":"Glycan Biosynthesis Ability of Gut Microbiota Increased in Primary Hypertension Patients Taking Antihypertension Medications and Potentially Promoted by Macrophage-Adenosine Monophosphate-Activated Pr"}],"sample_intervention_arms":{},"sex":{"female":15,"male":23},"title":"hyptertensive gut metagenome in patients and mice","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA685581","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA685581_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA685581.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA685581.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA685581.csv.gz"}},{"accession":"PRJNA944152","age_categories":{"adult":15,"elderly":25},"countries":{"CA":25,"FR":15},"first_public_year":"2023","gbp_per_sample_median":2.71,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":40,"papers":[],"sample_intervention_arms":{},"sex":{"female":21,"male":19},"title":"sMadCam-1 associations with the gut microbiome in NSCLC cancer patients","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA944152","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA944152_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA944152.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA944152.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA944152.csv.gz"}},{"accession":"PRJEB97162","age_categories":{"adult":36,"elderly":3},"countries":{"CH":39},"first_public_year":"2025","gbp_per_sample_median":1.42,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"gi_infection_or_diarrhoea":39},"intervention_design":"single_arm_before_after","intervention_detail":"FMT capsules for recurrent C. difficile infection","interventions":["fmt"],"n_samples":39,"papers":[{"doi":"10.1101/2025.10.09.681403","pmcid":null,"pmid":null,"title":"Engraftment of donor phageome via fecal microbiota transplantation in recurrent  C. difficile  infection: a prospective observational study"}],"sample_intervention_arms":{"fmt":6,"no_intervention":33},"sex":{"female":6,"male":33},"title":"Engraftment of donor phageome via fecal microbiota transplantation in recurrent C. difficile infection","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB97162","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB97162_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB97162.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB97162.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB97162.csv.gz"}},{"accession":"PRJNA1475489","age_categories":{"adult":17,"elderly":22},"countries":{"US":39},"first_public_year":"2026","gbp_per_sample_median":0.16,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"allergy_or_atopy":2,"autoimmune_inflammatory":2,"colorectal_cancer":2,"healthy_control":19,"neurological_psychiatric":12,"type2_diabetes":2},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":39,"papers":[{"doi":"10.1080/29933935.2026.2679810","pmcid":"PMC13251516","pmid":"42282268","title":"Brain health and the gut microbiome (bMicrobiome Study): a proof-of-concept, feasibility study integrating shotgun metagenomics, metrology, and multidimensional phenotyping across the cognitive aging "}],"sample_intervention_arms":{},"sex":{"female":35,"male":4},"title":"Brain Health and the Gut Microbiome (bMicrobiome Study)","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1475489","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1475489_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1475489.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1475489.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1475489.csv.gz"}},{"accession":"PRJEB52923","age_categories":{"elderly":38},"countries":{"SE":38},"first_public_year":"2022","gbp_per_sample_median":7.44,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_disease":38},"intervention_design":"randomized_controlled_trial","intervention_detail":"Lactobacillus reuteri ATCC PTA 6475, daily supplementation, 1 year","interventions":["probiotic"],"n_samples":38,"papers":[{"doi":"10.1038/s41522-022-00348-2","pmcid":"PMC9581899","pmid":"36261538","title":"One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density."}],"sample_intervention_arms":{},"sex":{},"title":"One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB52923","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB52923_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB52923.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB52923.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB52923.csv.gz"}},{"accession":"PRJNA1028158","age_categories":{"adult":28,"elderly":10},"countries":{"CN":38},"first_public_year":"2023","gbp_per_sample_median":6.75,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":38},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":38,"papers":[{"doi":"10.1128/msystems.00805-24","pmcid":"PMC11915798","pmid":"40013792","title":"Multi-omics analysis reveals associations between gut microbiota and host transcriptome in colon cancer patients."}],"sample_intervention_arms":{},"sex":{"female":16,"male":22},"title":"Metagenomics-Seq of human intestinal mucosa","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1028158","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1028158_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1028158.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1028158.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1028158.csv.gz"}},{"accession":"PRJNA1056458","age_categories":{"adult":37,"elderly":1},"countries":{"IL":38},"first_public_year":"2024","gbp_per_sample_median":0.67,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":17,"healthy_control":21},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":38,"papers":[{"doi":"10.1038/s41467-024-48106-6","pmcid":"PMC11069498","pmid":"38704361","title":"Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort."}],"sample_intervention_arms":{},"sex":{"female":17,"male":21},"title":"Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort","trial_population_condition":"crohns_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1056458","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1056458_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1056458.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1056458.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1056458.csv.gz"}},{"accession":"PRJNA278393","age_categories":{"adolescent":4,"adult":32,"child":1,"elderly":1},"countries":{"IT":11,"TZ":27},"first_public_year":"2015","gbp_per_sample_median":1.31,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":38},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":38,"papers":[{"doi":"10.1016/j.cub.2015.04.055","pmcid":null,"pmid":"25981789","title":"Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota."},{"doi":"10.1073/pnas.2023202118","pmcid":"PMC8201803","pmid":"34083435","title":"A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases."},{"doi":"10.3389/fmicb.2016.01058","pmcid":"PMC4940381","pmid":"27462302","title":"Variations in the Post-weaning Human Gut Metagenome Profile As Result of Bifidobacterium Acquisition in the Western Microbiome."},{"doi":"10.1186/s12864-019-5883-y","pmcid":"PMC6570844","pmid":"31202277","title":"HumanMycobiomeScan: a new bioinformatics tool for the characterization of the fungal fraction in metagenomic samples."},{"doi":"10.1186/s12859-020-03703-2","pmcid":"PMC7430844","pmid":"32795263","title":"SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o."}],"sample_intervention_arms":{},"sex":{"female":16,"male":22},"title":"Metagenome sequencing of the Hadza hunter-gatherer gut microbiota.","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA278393","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA278393_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA278393.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA278393.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA278393.csv.gz"}},{"accession":"PRJNA573963","age_categories":{"elderly":38},"countries":{"US":38},"first_public_year":"2019","gbp_per_sample_median":6.43,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"neurological_psychiatric":38},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":38,"papers":[{"doi":"10.1101/783969","pmcid":null,"pmid":null,"title":"Antimicrobial resistance gene prevalence in a population of patients with advanced dementia is related to specific pathobionts"}],"sample_intervention_arms":{},"sex":{"female":33,"male":5},"title":"Gut Microbiome of Elderly Adults with Advanced Dementia","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA573963","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA573963_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA573963.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA573963.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA573963.csv.gz"}},{"accession":"PRJNA792726","age_categories":{"adult":33,"elderly":5},"countries":{"CN":38},"first_public_year":"2022","gbp_per_sample_median":12.44,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_infection":38},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":38,"papers":[{"doi":"10.1038/s41467-022-32991-w","pmcid":"PMC9446638","pmid":"36068270","title":"Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes."},{"doi":"10.1111/1462-2920.16201","pmcid":"PMC9538590","pmid":"36086955","title":"Untangling the link between the human gut microbiota composition and the severity of the symptoms of the COVID-19 infection."},{"doi":"10.1128/mbio.03519-22","pmcid":"PMC9973266","pmid":"36744910","title":"Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis."},{"doi":"10.1101/2022.09.18.508418","pmcid":null,"pmid":null,"title":"Guild-level microbiome signature associated with COVID-19 severity and prognosis"}],"sample_intervention_arms":{},"sex":{"female":10,"male":28},"title":"Integrated analysis of gut microbiome and host immune responses in COVID-19","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA792726","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA792726_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA792726.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA792726.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA792726.csv.gz"}},{"accession":"PRJNA929558","age_categories":{"adult":30,"elderly":8},"countries":{"US":38},"first_public_year":"2023","gbp_per_sample_median":0.42,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":38},"intervention_design":"single_arm_before_after","intervention_detail":"Sulfasalazine therapy in IBD-associated pSpA subjects","interventions":["drug_therapy"],"n_samples":38,"papers":[{"doi":"10.1016/j.xcrm.2024.101431","pmcid":"PMC10982976","pmid":"38378002","title":"The gut microbiome regulates the clinical efficacy of sulfasalazine therapy for IBD-associated spondyloarthritis."}],"sample_intervention_arms":{},"sex":{"female":20,"male":18},"title":"Sulfasalazine therapy for IBD-associated pSpA","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA929558","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA929558_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA929558.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA929558.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA929558.csv.gz"}},{"accession":"PRJNA299502","age_categories":{"adult":29,"elderly":5,"unknown":3},"countries":{"US":37},"first_public_year":"2015","gbp_per_sample_median":4.31,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":18,"type2_diabetes":19},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":37,"papers":[{"doi":"10.1016/j.cub.2015.10.060","pmcid":"PMC4703035","pmid":"26671671","title":"Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma."},{"doi":"10.1371/journal.pone.0226930","pmcid":"PMC6961876","pmid":"31940321","title":"Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion."},{"doi":"10.1186/s40168-021-01114-w","pmcid":"PMC8325300","pmid":"34330336","title":"HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data."},{"doi":"10.1038/s41467-024-47272-x","pmcid":"PMC11009399","pmid":"38605009","title":"Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases."},{"doi":"10.1016/j.chom.2025.09.014","pmcid":"PMC13059687","pmid":"41118772","title":"Gut bacteria metabolize natural and synthetic steroid hormones via the reductive OsrABC pathway."}],"sample_intervention_arms":{},"sex":{"female":23,"male":14},"title":"Human Gut Microbiome Metagenome","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA299502","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA299502_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA299502.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA299502.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA299502.csv.gz"}},{"accession":"PRJNA1416570","age_categories":{"adolescent":2,"adult":27,"child":1,"elderly":6},"countries":{"CN":36},"first_public_year":"2026","gbp_per_sample_median":10.18,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"transplant_or_immunocompromised":36},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":36,"papers":[{"doi":"10.1371/journal.pone.0343817","pmcid":"PMC12944773","pmid":"41746975","title":"Effects of tacrolimus treatment on the gut microbiota and metabolites in liver transplant recipients."}],"sample_intervention_arms":{},"sex":{"female":3,"male":33},"title":"gut microbiota and metabolites","trial_population_condition":"liver_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1416570","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1416570_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1416570.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1416570.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1416570.csv.gz"}},{"accession":"PRJNA809514","age_categories":{"adult":21,"elderly":15},"countries":{"CN":36},"first_public_year":"2022","gbp_per_sample_median":9.14,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"type2_diabetes":36},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":36,"papers":[{"doi":"10.3389/fmolb.2022.879294","pmcid":"PMC9240776","pmid":"35782875","title":"Polyethylene Glycol Loxenatide Injection (GLP-1) Protects Vascular Endothelial Cell Function in Middle-Aged and Elderly Patients With Type 2 Diabetes by Regulating Gut Microbiota."}],"sample_intervention_arms":{},"sex":{},"title":"Shorgun metagenomics of T2DM human gut microbes treated with GLP-1 drug","trial_population_condition":"type2_diabetes","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA809514","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA809514_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA809514.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA809514.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA809514.csv.gz"}},{"accession":"PRJEB68381","age_categories":{"adult":18,"elderly":17},"countries":{"DE":35},"first_public_year":"2023","gbp_per_sample_median":0.08,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":9,"neurological_psychiatric":1,"other_cancer":1,"other_disease":17,"type2_diabetes":7},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":35,"papers":[{"doi":"10.1136/gutjnl-2023-330987","pmcid":"PMC10894816","pmid":"38129103","title":"Gut microbiota predicts severity and reveals novel metabolic signatures in acute pancreatitis."}],"sample_intervention_arms":{},"sex":{"male":31},"title":"Pancreatitis - Microbiome As Predictor of Severity P-MAPS","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB68381","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB68381_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB68381.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB68381.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB68381.csv.gz"}},{"accession":"PRJNA479838","age_categories":{"adult":29,"elderly":6},"countries":{"CN":35},"first_public_year":"2018","gbp_per_sample_median":11.72,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":35},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":35,"papers":[{"doi":"10.7150/ijbs.37399","pmcid":"PMC6930378","pmid":"31892851","title":"Gut microbiome associated with APC gene mutation in patients with intestinal adenomatous polyps."}],"sample_intervention_arms":{},"sex":{"female":15,"male":20},"title":"human stool Raw sequence reads","trial_population_condition":"colorectal_adenoma","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA479838","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA479838_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA479838.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA479838.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA479838.csv.gz"}},{"accession":"PRJNA1091163","age_categories":{"adult":23,"elderly":9,"unknown":2},"countries":{"KZ":34},"first_public_year":"2024","gbp_per_sample_median":2.58,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":34,"papers":[{"doi":"10.1128/mra.00862-24","pmcid":"PMC11636347","pmid":"39498981","title":"Metagenomic analysis reveals higher Coriobacteriia abundance in mare's milk consumers."},{"doi":"10.1016/j.heliyon.2025.e41969","pmcid":"PMC11791146","pmid":"39906849","title":"Enterococcus dysbiosis as a mediator of vitamin D deficiency-associated memory impairments."},{"doi":"10.1186/s12967-026-08739-1","pmcid":"PMC13491917","pmid":"42618929","title":"Distinct gut microbiome profiles characterize obese and non-obese patients with atherosclerosis: a metagenomic analysis."}],"sample_intervention_arms":{},"sex":{"female":25,"male":7},"title":"Vitamin D","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1091163","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1091163_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1091163.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1091163.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1091163.csv.gz"}},{"accession":"PRJNA638403","age_categories":{"adult":32,"elderly":2},"countries":{"CN":34},"first_public_year":"2020","gbp_per_sample_median":7.87,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":34,"papers":[{"doi":"10.1038/s41396-021-01016-7","pmcid":"PMC8528855","pmid":"34079079","title":"Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers."},{"doi":"10.1128/msystems.00828-23","pmcid":"PMC10734426","pmid":"37905808","title":"Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach."},{"doi":"10.1186/s40168-025-02080-3","pmcid":"PMC11954268","pmid":"40158141","title":"Modeling microbiome-trait associations with taxonomy-adaptive neural networks."},{"doi":"10.1186/s12866-026-04902-2","pmcid":"PMC13067670","pmid":"41781883","title":"Metagenome-assembled genomes from the gut microbiome of spontaneous diabetic macaques provide insights into microbes associated with type 2 diabetes mellitus."}],"sample_intervention_arms":{},"sex":{"female":21,"male":13},"title":"Ecological and evolutionary alteration in the GD intestinal microbiome part05 Metagenome","trial_population_condition":"type2_diabetes","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA638403","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA638403_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA638403.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA638403.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA638403.csv.gz"}},{"accession":"PRJNA638405","age_categories":{"adult":30,"elderly":3,"unknown":1},"countries":{"CN":34},"first_public_year":"2020","gbp_per_sample_median":7.5,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":1},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":34,"papers":[{"doi":"10.1038/s41396-021-01016-7","pmcid":"PMC8528855","pmid":"34079079","title":"Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers."},{"doi":"10.1128/msystems.00828-23","pmcid":"PMC10734426","pmid":"37905808","title":"Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach."},{"doi":"10.1186/s40168-025-02080-3","pmcid":"PMC11954268","pmid":"40158141","title":"Modeling microbiome-trait associations with taxonomy-adaptive neural networks."}],"sample_intervention_arms":{},"sex":{"female":19,"male":14},"title":"Ecological and evolutionary alteration in the GD intestinal microbiome part07 Metagenome","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA638405","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA638405_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA638405.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA638405.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA638405.csv.gz"}},{"accession":"PRJNA656577","age_categories":{"adult":32,"elderly":2},"countries":{"US":34},"first_public_year":"2021","gbp_per_sample_median":4.55,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"autoimmune_inflammatory":34},"intervention_design":"single_arm_before_after","intervention_detail":"Methotrexate treatment in RA patients, pre- vs post-treatment microbiota","interventions":["drug_therapy"],"n_samples":34,"papers":[{"doi":"10.1016/j.chom.2020.12.008","pmcid":"PMC7954989","pmid":"33440172","title":"Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation."}],"sample_intervention_arms":{"drug_therapy":17,"no_intervention":17},"sex":{"female":24,"male":10},"title":"Effect of methotrexate on human gut microbiota","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA656577","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA656577_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA656577.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA656577.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA656577.csv.gz"}},{"accession":"PRJEB70916","age_categories":{"adult":26,"elderly":7},"countries":{"FR":33},"first_public_year":"2024","gbp_per_sample_median":3.07,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":19,"healthy_control":14},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":33,"papers":[{"doi":"10.3389/fonc.2023.1313735","pmcid":"PMC10876293","pmid":"38375206","title":"Loss of symbiotic and increase of virulent bacteria through microbial networks in Lynch syndrome colon carcinogenesis."},{"doi":"10.1186/s12967-026-08403-8","pmcid":"PMC13281578","pmid":"42271362","title":"Gut fungal signatures in colorectal cancer and their potential for supporting diagnosis: a multi-cohort metagenomic analysis."}],"sample_intervention_arms":{},"sex":{"female":17,"male":16},"title":"Whole Metagenome Sequencing of colo-rectal cancer in Lynch Syndrome Patients","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB70916","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB70916_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB70916.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB70916.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB70916.csv.gz"}},{"accession":"PRJNA628604","age_categories":{"adult":17,"elderly":10,"unknown":6},"countries":{"IL":33},"first_public_year":"2020","gbp_per_sample_median":4.31,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":true,"health_conditions":{"healthy_control":6,"other_infection":27},"intervention_design":"single_arm_before_after","intervention_detail":"Oral capsulized FMT for 2 days to eradicate CPE carriage","interventions":["fmt"],"n_samples":33,"papers":[{"doi":"10.1093/cid/ciaa737","pmcid":null,"pmid":"32511695","title":"Oral capsulized Fecal microbiota transplantation for eradication of carbapenemase-producing Enterobacteriaceae colonization with a metagenomic perspective."},{"doi":"10.1126/scitranslmed.abo2750","pmcid":"PMC10821315","pmid":"37910603","title":"Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement."},{"doi":"10.1186/s40168-025-02046-5","pmcid":"PMC12180181","pmid":"40542451","title":"Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation."}],"sample_intervention_arms":{"fmt":27,"no_intervention":6},"sex":{},"title":"Oral capsulized Fecal microbiota transplantation for eradication of carbapenemase-producing Enterobacteriaceae colonization with a metagenomic perspective","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA628604","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA628604_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA628604.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA628604.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA628604.csv.gz"}},{"accession":"PRJNA863406","age_categories":{"adult":32,"elderly":1},"countries":{"KR":33},"first_public_year":"2022","gbp_per_sample_median":0.02,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":33,"papers":[{"doi":"10.3389/fimmu.2023.1096565","pmcid":"PMC10152063","pmid":"37143677","title":"Identification of gut dysbiosis in axial spondyloarthritis patients and improvement of experimental ankylosing spondyloarthritis by microbiome-derived butyrate with immune-modulating function."}],"sample_intervention_arms":{},"sex":{"female":3,"male":30},"title":"Microbiome Analysis in spondyloarthritis patients","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA863406","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA863406_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA863406.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA863406.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA863406.csv.gz"}},{"accession":"PRJNA988170","age_categories":{"adult":31,"elderly":2},"countries":{"CN":33},"first_public_year":"2025","gbp_per_sample_median":7.84,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"observational_with_procedure","intervention_detail":"FMT enriched with F. prausnitzii; Fp strain/oleic acid in mouse AP models","interventions":[],"n_samples":33,"papers":[{"doi":"10.1038/s41522-025-00845-0","pmcid":"PMC12660694","pmid":"41271774","title":"Faecalibacterium prausnitzii alleviates experimental recurrent acute pancreatitis by producing oleic acid to regulate MAPK/NF-κB signaling and Th17/Treg balance."}],"sample_intervention_arms":{},"sex":{"female":9,"male":24},"title":"human gut metagenome Raw sequence reads","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA988170","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA988170_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA988170.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA988170.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA988170.csv.gz"}},{"accession":"PRJNA1469454","age_categories":{"adult":24,"elderly":8},"countries":{"RU":32},"first_public_year":"2026","gbp_per_sample_median":4.44,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":32},"intervention_design":"unknown","intervention_detail":"Immune checkpoint inhibitor immunotherapy, pre- vs 3-month post-treatment","interventions":["drug_therapy"],"n_samples":32,"papers":[],"sample_intervention_arms":{},"sex":{"female":18,"male":14},"title":"Human gut metagenome from melanoma patients collected at two timepoints","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1469454","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1469454_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1469454.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1469454.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1469454.csv.gz"}},{"accession":"PRJNA687957","age_categories":{"adult":13,"elderly":19},"countries":{"US":32},"first_public_year":"2021","gbp_per_sample_median":6.64,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":32},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":32,"papers":[{"doi":"10.1186/s13073-021-00957-0","pmcid":"PMC8439035","pmid":"34517888","title":"Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis."}],"sample_intervention_arms":{},"sex":{"female":21,"male":11},"title":"Gut Microbial Determinants of Clinically Important Improvement in Patients with Rheumatoid Arthritis","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA687957","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA687957_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA687957.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA687957.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA687957.csv.gz"}},{"accession":"PRJNA790678","age_categories":{"adult":10,"elderly":22},"countries":{"AU":32},"first_public_year":"2024","gbp_per_sample_median":7.91,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":20},"intervention_design":"observational_with_procedure","intervention_detail":"Colorectal resection with anastomosis; sampling around surgical site","interventions":["surgery"],"n_samples":32,"papers":[{"doi":"10.1111/ans.70499","pmcid":"PMC13129236","pmid":"41562240","title":"Dynamic 16S rRNA Sequencing of the Abdominal Wall Surgical Site Highlights Potential Pathways of Incisional Surgical Site Infection in Colorectal Surgery."}],"sample_intervention_arms":{},"sex":{"female":10,"male":22},"title":"Homo sapiens gastrointestinal mucosal associated microbiota Raw sequence reads","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA790678","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA790678_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA790678.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA790678.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA790678.csv.gz"}},{"accession":"PRJNA858062","age_categories":{"adult":31,"elderly":1},"countries":{"CN":32},"first_public_year":"2022","gbp_per_sample_median":13.62,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"autoimmune_inflammatory":16,"healthy_control":16},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":32,"papers":[{"doi":"10.1080/16078454.2023.2277501","pmcid":null,"pmid":"37921501","title":"Intestinal flora altered and correlated with interleukin-2/4 in patients with primary immune thrombocytopenia."},{"doi":"10.21203/rs.3.rs-1827887/v1","pmcid":null,"pmid":null,"title":"Altered intestinal flora in patients with primary immune thrombocytopenia"}],"sample_intervention_arms":{},"sex":{"female":20,"male":12},"title":"Homo sapiens Raw sequence reads","trial_population_condition":"autoimmune_inflammatory","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA858062","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA858062_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA858062.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA858062.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA858062.csv.gz"}},{"accession":"PRJNA626477","age_categories":{"adult":18,"elderly":12,"unknown":1},"countries":{"HU":31},"first_public_year":"2021","gbp_per_sample_median":6.12,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":31},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":31,"papers":[{"doi":"10.1038/s41396-021-00998-8","pmcid":"PMC8528809","pmid":"34002024","title":"Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients."},{"doi":"10.1371/journal.pone.0259898","pmcid":"PMC8601557","pmid":"34793492","title":"Gut microbiome functionality might be associated with exercise tolerance and recurrence of resected early-stage lung cancer patients."}],"sample_intervention_arms":{},"sex":{"female":12,"male":19},"title":"human gut microbiota Raw sequence reads with and without cancer cachexia","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA626477","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA626477_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA626477.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA626477.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA626477.csv.gz"}},{"accession":"PRJNA850128","age_categories":{"adult":15,"elderly":16},"countries":{},"first_public_year":"2023","gbp_per_sample_median":12.17,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_disease":31},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":31,"papers":[{"doi":"10.1002/jmv.28267","pmcid":null,"pmid":"36319439","title":"Gut microbiota dysbiosis is associated with sepsis-induced cardiomyopathy in patients: A case-control study."}],"sample_intervention_arms":{},"sex":{"female":11,"male":20},"title":"Gut microbiota dysbiosis is associated with sepsis-induced cardiomyopathy in patients","trial_population_condition":"sepsis_or_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA850128","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA850128_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA850128.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA850128.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA850128.csv.gz"}},{"accession":"PRJNA1263627","age_categories":{"adult":22,"elderly":8},"countries":{"SE":30},"first_public_year":"2025","gbp_per_sample_median":10.88,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_infection":30},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":30,"papers":[{"doi":"10.1186/s13099-026-00828-2","pmcid":"PMC13063484","pmid":"41913289","title":"Linking gut microbiome to HIV-1 reservoir size in people living with HIV."}],"sample_intervention_arms":{},"sex":{"female":12,"male":18},"title":"Linking Gut Microbiome to HIV-1 Reservoir Size in People Living with HIV","trial_population_condition":"transplant_or_immunocompromised","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1263627","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1263627_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1263627.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1263627.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1263627.csv.gz"}},{"accession":"PRJNA531273","age_categories":{"adult":21,"elderly":9},"countries":{"IN":30},"first_public_year":"2019","gbp_per_sample_median":1.14,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":30},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":30,"papers":[{"doi":"10.1128/msystems.00438-19","pmcid":"PMC7407896","pmid":"31719139","title":"Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India."},{"doi":"10.7554/elife.65088","pmcid":"PMC8096432","pmid":"33944776","title":"Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3."},{"doi":"10.3390/cancers14174214","pmcid":"PMC9454621","pmid":"36077748","title":"Meta-Analysis and Validation of a Colorectal Cancer Risk Prediction Model Using Deep Sequenced Fecal Metagenomes."},{"doi":"10.1038/s43587-022-00306-9","pmcid":"PMC10154212","pmid":"37118093","title":"Toward an improved definition of a healthy microbiome for healthy aging."},{"doi":"10.1007/s13205-023-03671-3","pmcid":"PMC10338424","pmid":"37457869","title":"Gut microbiota of healthy Asians and their discriminative features revealed by metagenomics approach."}],"sample_intervention_arms":{},"sex":{"female":12,"male":18},"title":"Association of Flavonifractor plautii, a flavonoid degrading bacterium, with the gut microbiome of colorectal cancer patients in India","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA531273","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA531273_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA531273.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA531273.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA531273.csv.gz"}},{"accession":"PRJNA914091","age_categories":{"adult":21,"elderly":9},"countries":{"ES":30},"first_public_year":"2023","gbp_per_sample_median":4.88,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":30},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":30,"papers":[{"doi":"10.3390/microorganisms11020402","pmcid":"PMC9964539","pmid":"36838367","title":"Evaluation of a Shotgun Metagenomics Approach for Detection of ESBL- and/or Carbapenemase-Producing Enterobacterales in Culture Negative Patients Recovered from Acute Leukemia."},{"doi":"10.1038/s41598-024-56054-w","pmcid":"PMC10920697","pmid":"38454103","title":"Study of the intestinal microbiota composition and the effect of treatment with intensive chemotherapy in patients recovered from acute leukemia."}],"sample_intervention_arms":{},"sex":{"female":20,"male":10},"title":"Evaluation of a shotgun metagenomics approach for detection of ESBL- and/or carbapenemase-producing Enterobacterales in culture negative patients recovered from acute leukemia","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA914091","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA914091_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA914091.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA914091.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA914091.csv.gz"}},{"accession":"PRJNA273574","age_categories":{"elderly":29},"countries":{"CH":29},"first_public_year":"2015","gbp_per_sample_median":0.0,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":29},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":29,"papers":[{"doi":"10.1371/journal.pone.0142793","pmcid":"PMC4641611","pmid":"26559530","title":"Design and Investigation of PolyFermS In Vitro Continuous Fermentation Models Inoculated with Immobilized Fecal Microbiota Mimicking the Elderly Colon."}],"sample_intervention_arms":{},"sex":{"female":29},"title":"Intestinal model Metagenome","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA273574","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA273574_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA273574.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA273574.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA273574.csv.gz"}},{"accession":"PRJNA939026","age_categories":{"adult":25,"elderly":3},"countries":{"IL":28},"first_public_year":"2023","gbp_per_sample_median":28.56,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":10,"other_disease":18},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":28,"papers":[{"doi":"10.1038/s41598-023-47723-3","pmcid":"PMC10673896","pmid":"38001152","title":"Gut microbial signatures are associated with Lynch syndrome (LS) and cancer history in Druze communities in Israel."},{"doi":"10.1016/j.isci.2024.110181","pmcid":"PMC11237946","pmid":"38993678","title":"&lt;i&gt;Fusobacterium&lt;/i&gt; species are distinctly associated with patients with Lynch syndrome colorectal cancer."}],"sample_intervention_arms":{},"sex":{"female":15,"male":13},"title":"Gut microbiota associated with Lynch syndrome in Druze communities in Israel","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA939026","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA939026_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA939026.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA939026.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA939026.csv.gz"}},{"accession":"PRJEB95899","age_categories":{"adult":16,"elderly":11},"countries":{"CO":27},"first_public_year":"2025","gbp_per_sample_median":7.3,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"gi_infection_or_diarrhoea":23,"healthy_control":4},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":27,"papers":[{"doi":"10.1186/s13099-026-00811-x","pmcid":"PMC12927239","pmid":"41725012","title":"Metagenomic analysis of the human gut virome reveals functional signatures and viral stability across hospitalized and non-hospitalized diarrheal and non-diarrheal individuals."}],"sample_intervention_arms":{},"sex":{"female":20,"male":7},"title":"Metagenomic Analysis of the Human Gut Virome Reveals Functional Signatures and Viral Stability in Diarrheal and Non-Diarrheal Individuals","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB95899","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB95899_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB95899.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB95899.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB95899.csv.gz"}},{"accession":"PRJNA996050","age_categories":{"adult":11,"elderly":16},"countries":{"NL":27},"first_public_year":"2023","gbp_per_sample_median":3.69,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":13,"other_cancer":14},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":27,"papers":[{"doi":"10.3389/fimmu.2023.1230306","pmcid":"PMC10667699","pmid":"38022530","title":"B cell immune profiles in dysbiotic vermiform appendixes of pancreatic cancer patients."}],"sample_intervention_arms":{},"sex":{"female":14,"male":13},"title":"Fecal metagenomic profiling of vermiform appendix from adult patients with pancreatic or colon cancer","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA996050","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA996050_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA996050.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA996050.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA996050.csv.gz"}},{"accession":"PRJNA703034","age_categories":{"adult":18,"elderly":8},"countries":{"US":26},"first_public_year":"2022","gbp_per_sample_median":1.51,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":26},"intervention_design":"single_arm_before_after","intervention_detail":"4 commonly used antibiotic regimens given to healthy volunteers","interventions":["antibiotic"],"n_samples":26,"papers":[{"doi":"10.1016/j.celrep.2022.110649","pmcid":"PMC9066705","pmid":"35417701","title":"Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults."}],"sample_intervention_arms":{},"sex":{},"title":"Metagenomics of Stool from ICU Patients","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA703034","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA703034_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA703034.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA703034.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA703034.csv.gz"}},{"accession":"PRJDB16532","age_categories":{"adult":13,"elderly":12},"countries":{"JP":25},"first_public_year":"2024","gbp_per_sample_median":20.18,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":8,"other_cancer":17},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":25,"papers":[{"doi":"10.1016/j.heliyon.2024.e38507","pmcid":"PMC11619966","pmid":"39640675","title":"Succinic semialdehyde derived from the gut microbiota can promote the proliferation of adult T-cell leukemia/lymphoma cells."}],"sample_intervention_arms":{},"sex":{"female":12,"male":13},"title":"Generic sample from human gut metagenome","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB16532","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB16532_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB16532.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB16532.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB16532.csv.gz"}},{"accession":"PRJEB13835","age_categories":{"elderly":23},"countries":{"CH":23},"first_public_year":"2017","gbp_per_sample_median":4.1,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":11,"other_disease":12},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":23,"papers":[{"doi":"10.1038/srep40826","pmcid":"PMC5240106","pmid":"28094305","title":"Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration."},{"doi":"10.1371/journal.pone.0258505","pmcid":"PMC8523055","pmid":"34662347","title":"The importance of age in compositional and functional profiling of the human intestinal microbiome."},{"doi":"10.1167/iovs.64.5.11","pmcid":"PMC10202153","pmid":"37195657","title":"Metagenomic Sequencing Analysis Identifies Cross-Cohort Gut Microbial Signatures Associated With Age-Related Macular Degeneration."}],"sample_intervention_arms":{"no_intervention":11},"sex":{},"title":"Age-related macular degeneration is associated with alterations in the gut microbiome","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB13835","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB13835_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB13835.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB13835.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB13835.csv.gz"}},{"accession":"PRJNA1222800","age_categories":{"adult":13,"elderly":10},"countries":{"US":23},"first_public_year":"2025","gbp_per_sample_median":14.36,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_cancer":23},"intervention_design":"single_arm_before_after","intervention_detail":"Nivolumab plus low-dose ipilimumab, phase II trial, 2 years","interventions":["drug_therapy"],"n_samples":23,"papers":[{"doi":"10.1038/s41467-025-59695-1","pmcid":"PMC12075640","pmid":"40360544","title":"Nivolumab plus low-dose ipilimumab in hypermutated HER2-negative metastatic breast cancer: a phase II trial (NIMBUS)."}],"sample_intervention_arms":{},"sex":{"female":23},"title":"Fecal metagenomes from patients with HER2-negative metastatic breast cancer","trial_population_condition":"other_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1222800","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1222800_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1222800.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1222800.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1222800.csv.gz"}},{"accession":"PRJNA1405914","age_categories":{"adult":22,"elderly":1},"countries":{"CN":23},"first_public_year":"2026","gbp_per_sample_median":0.13,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":11,"healthy_control":12},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":23,"papers":[],"sample_intervention_arms":{},"sex":{"female":11,"male":12},"title":"Gut microbiota-derived 5-hydroxyindoleacetic acid drives macrophage-dependent cardiac remodeling through the AHR-NFATC2-ITGA4 axis","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1405914","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1405914_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1405914.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1405914.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1405914.csv.gz"}},{"accession":"PRJNA414153","age_categories":{"adolescent":3,"adult":11,"child":4,"elderly":4,"infant":1},"countries":{},"first_public_year":"2017","gbp_per_sample_median":1.23,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":1,"gi_infection_or_diarrhoea":7,"other_disease":15},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":23,"papers":[],"sample_intervention_arms":{},"sex":{"female":6,"male":17},"title":"Human Appendix Microbiome","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA414153","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA414153_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA414153.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA414153.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA414153.csv.gz"}},{"accession":"PRJNA397219","age_categories":{"adult":12,"elderly":10},"countries":{"US":22},"first_public_year":"2017","gbp_per_sample_median":102.71,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":11,"healthy_control":11},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":22,"papers":[{"doi":"10.1016/j.ymeth.2018.04.024","pmcid":"PMC6191348","pmid":"29704665","title":"Synthesis of multi-omic data and community metabolic models reveals insights into the role of hydrogen sulfide in colon cancer."},{"doi":"10.1186/s13046-021-02239-4","pmcid":"PMC8857837","pmid":"35183223","title":"FOXQ1-mediated SIRT1 upregulation enhances stemness and radio-resistance of colorectal cancer cells and restores intestinal microbiota function by promoting β-catenin nuclear translocation."},{"doi":"10.1002/advs.202300107","pmcid":"PMC10477861","pmid":"37382183","title":"Efficient Mining of Anticancer Peptides from Gut Metagenome."},{"doi":"10.7717/peerj.20990","pmcid":"PMC13034871","pmid":"41918857","title":"MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes."},{"doi":"10.1186/s13099-022-00527-8","pmcid":"PMC9784093","pmid":"36564826","title":"Metagenomic analysis of the interaction between the gut microbiota and colorectal cancer: a paired-sample study based on the GMrepo database."}],"sample_intervention_arms":{},"sex":{"female":10,"male":12},"title":"Gut metagenomes of patients with colorectal cancer","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA397219","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA397219_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA397219.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA397219.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA397219.csv.gz"}},{"accession":"PRJNA736213","age_categories":{"adult":13,"elderly":9},"countries":{"IT":22},"first_public_year":"2021","gbp_per_sample_median":0.08,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":7,"neurological_psychiatric":15},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":22,"papers":[{"doi":"10.3390/biomedicines9070753","pmcid":"PMC8301418","pmid":"34209688","title":"The Gut Microbiota-Immunity Axis in ALS: A Role in Deciphering Disease Heterogeneity?"}],"sample_intervention_arms":{},"sex":{"female":7,"male":15},"title":"Profiling the gut microbiota of Amyotrophic Lateral Sclerosis (ALS) patients","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA736213","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA736213_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA736213.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA736213.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA736213.csv.gz"}},{"accession":"PRJNA970820","age_categories":{"adult":12,"elderly":9},"countries":{"US":21},"first_public_year":"2023","gbp_per_sample_median":3.36,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"liver_disease":21},"intervention_design":"observational_with_procedure","intervention_detail":"Liver transplantation cohort, stool sampled post-transplant","interventions":["surgery"],"n_samples":21,"papers":[{"doi":"10.1038/s41597-024-04153-8","pmcid":"PMC11717916","pmid":"39788961","title":"Deep sequencing-derived Metagenome Assembled Genomes from the gut microbiome of liver transplant patients."}],"sample_intervention_arms":{},"sex":{"female":10,"male":11},"title":"human gut metagenome Genome sequencing and assembly","trial_population_condition":"liver_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA970820","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA970820_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA970820.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA970820.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA970820.csv.gz"}},{"accession":"PRJNA1345179","age_categories":{"adult":17,"elderly":3},"countries":{"CN":20},"first_public_year":"2025","gbp_per_sample_median":7.35,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":13,"healthy_control":7},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":20,"papers":[{"doi":"10.1016/j.jare.2025.12.026","pmcid":"PMC13539226","pmid":"41429339","title":"Potential biomarkers for human Ascending aortic aneurysm identified through metagenomic and metabolomic analyses: A case-control study."}],"sample_intervention_arms":{},"sex":{"female":4,"male":16},"title":"Potential Biomarkers for Human Ascending Aortic Aneurysm Identified Through Metagenomic and Metabolomic Analyses: A case-control study(4)","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1345179","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1345179_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1345179.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1345179.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1345179.csv.gz"}},{"accession":"PRJNA943491","age_categories":{"adult":2,"elderly":18},"countries":{"SE":20},"first_public_year":"2023","gbp_per_sample_median":4.82,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":10,"other_cancer":10},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":20,"papers":[{"doi":"10.1002/cam4.6483","pmcid":"PMC10557870","pmid":"37641475","title":"Assessment of bacterial and viral gut communities in healthy and tumoral colorectal tissue using RNA and DNA deep sequencing."}],"sample_intervention_arms":{},"sex":{"female":14,"male":6},"title":"Colorectal RNA","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA943491","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA943491_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA943491.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA943491.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA943491.csv.gz"}},{"accession":"PRJNA806955","age_categories":{"adult":14,"elderly":5},"countries":{"CN":19},"first_public_year":"2022","gbp_per_sample_median":13.33,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":10,"neurological_psychiatric":9},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":19,"papers":[{"doi":"10.3389/fcimb.2022.829491","pmcid":"PMC8966894","pmid":"35372117","title":"Cerebral Intraparenchymal Hemorrhage Changes Patients' Gut Bacteria Composition and Function."}],"sample_intervention_arms":{},"sex":{"female":9,"male":10},"title":"metagenomics for IPH patients","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA806955","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA806955_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA806955.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA806955.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA806955.csv.gz"}},{"accession":"PRJNA984213","age_categories":{"elderly":19},"countries":{"IT":19},"first_public_year":"2023","gbp_per_sample_median":0.04,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":19},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":19,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Evaluation of the persistence of Bifidobacterium longum subsp. longum in the human gut across the entire life span","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA984213","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA984213_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA984213.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA984213.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA984213.csv.gz"}},{"accession":"PRJDB5860","age_categories":{"adult":15,"elderly":3},"countries":{"MN":18},"first_public_year":"2025","gbp_per_sample_median":5.61,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":9,"type2_diabetes":9},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":18,"papers":[{"doi":"10.3389/fmicb.2018.01345","pmcid":"PMC6024022","pmid":"29988433","title":"Urban Diets Linked to Gut Microbiome and Metabolome Alterations in Children: A Comparative Cross-Sectional Study in Thailand."},{"doi":"10.1007/s13205-020-02265-7","pmcid":"PMC7261292","pmid":"32537376","title":"Age-related changes in the gut microbiota and the core gut microbiome of healthy Thai humans."},{"doi":"10.1093/gigascience/giac077","pmcid":"PMC9366992","pmid":"35950838","title":"A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications."},{"doi":"10.3389/fmicb.2024.1355396","pmcid":"PMC11231203","pmid":"38983625","title":"Gut microbiome signatures associated with type 2 diabetes in obesity in Mongolia."}],"sample_intervention_arms":{},"sex":{"female":11,"male":7},"title":"Asian Microbiome Project","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB5860","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB5860_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB5860.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB5860.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB5860.csv.gz"}},{"accession":"PRJNA1345173","age_categories":{"adult":16,"elderly":2},"countries":{"CN":18},"first_public_year":"2025","gbp_per_sample_median":7.15,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":13,"healthy_control":5},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":18,"papers":[{"doi":"10.1016/j.jare.2025.12.026","pmcid":"PMC13539226","pmid":"41429339","title":"Potential biomarkers for human Ascending aortic aneurysm identified through metagenomic and metabolomic analyses: A case-control study."}],"sample_intervention_arms":{},"sex":{"female":5,"male":13},"title":"Potential Biomarkers for Human Ascending Aortic Aneurysm Identified Through Metagenomic and Metabolomic Analyses: A case-control study","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1345173","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1345173_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1345173.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1345173.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1345173.csv.gz"}},{"accession":"PRJNA1345176","age_categories":{"adult":17,"elderly":1},"countries":{"CN":18},"first_public_year":"2025","gbp_per_sample_median":7.27,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":8},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":18,"papers":[{"doi":"10.1016/j.jare.2025.12.026","pmcid":"PMC13539226","pmid":"41429339","title":"Potential biomarkers for human Ascending aortic aneurysm identified through metagenomic and metabolomic analyses: A case-control study."}],"sample_intervention_arms":{},"sex":{"female":2,"male":16},"title":"Potential Biomarkers for Human Ascending Aortic Aneurysm Identified Through Metagenomic and Metabolomic Analyses: A case-control study(3)","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1345176","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1345176_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1345176.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1345176.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1345176.csv.gz"}},{"accession":"PRJNA342339","age_categories":{"elderly":18},"countries":{"CH":18},"first_public_year":"2016","gbp_per_sample_median":0.0,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"healthy_control":18},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":18,"papers":[{"doi":"10.1186/s13099-016-0144-y","pmcid":"PMC5133761","pmid":"27980686","title":"Clostridium difficile colonization and antibiotics response in PolyFermS continuous model mimicking elderly intestinal fermentation."}],"sample_intervention_arms":{"antibiotic":6,"no_intervention":12},"sex":{"female":18},"title":"Metagenome of fermentation model samples inoculated with human feces","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA342339","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA342339_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA342339.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA342339.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA342339.csv.gz"}},{"accession":"PRJNA669585","age_categories":{"elderly":17},"countries":{"IT":17},"first_public_year":"2023","gbp_per_sample_median":0.02,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_disease":17},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":17,"papers":[{"doi":"10.3390/ijms21238946","pmcid":"PMC7728056","pmid":"33255677","title":"The Gut-Muscle Axis in Older Subjects with Low Muscle Mass and Performance: A Proof of Concept Study Exploring Fecal Microbiota Composition and Function with Shotgun Metagenomics Sequencing."}],"sample_intervention_arms":{},"sex":{},"title":"The gut-muscle axis in primary sarcopenia: a proof of concept study exploring human fecal microbiota composition and function with shotgun metagenomics sequencing","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA669585","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA669585_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA669585.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA669585.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA669585.csv.gz"}},{"accession":"PRJDB5180","age_categories":{"adult":9,"elderly":7},"countries":{"JP":16},"first_public_year":"2017","gbp_per_sample_median":0.0,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"liver_disease":16},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":16,"papers":[{"doi":"10.3389/fmicb.2017.00685","pmcid":"PMC5397476","pmid":"28473817","title":"Comprehensive Diagnosis of Bacterial Infection Associated with Acute Cholecystitis Using Metagenomic Approach."}],"sample_intervention_arms":{},"sex":{"female":9,"male":7},"title":"A metagenomic approach for acute cholecystitis patients enables pathogen detection and rapid diagnostics","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB5180","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB5180_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB5180.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB5180.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB5180.csv.gz"}},{"accession":"PRJNA1221292","age_categories":{"adult":5,"elderly":11},"countries":{"CN":16},"first_public_year":"2025","gbp_per_sample_median":6.64,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":8,"neurological_psychiatric":8},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":16,"papers":[{"doi":"10.3389/fnins.2025.1545690","pmcid":"PMC11880238","pmid":"40046438","title":"Plasma exosomal miRNA expression and gut microbiota dysbiosis are associated with cognitive impairment in Alzheimer's disease."}],"sample_intervention_arms":{},"sex":{"female":12,"male":4},"title":"Plasma Exosomal miRNA Expression and Gut Microbiota Dysbiosis Are Associated with Cognitive Impairment in Alzheimer's Disease.","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1221292","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1221292_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1221292.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1221292.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1221292.csv.gz"}},{"accession":"PRJNA1345175","age_categories":{"adult":14,"elderly":2},"countries":{"CN":16},"first_public_year":"2025","gbp_per_sample_median":7.22,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":8,"healthy_control":8},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":16,"papers":[{"doi":"10.1016/j.jare.2025.12.026","pmcid":"PMC13539226","pmid":"41429339","title":"Potential biomarkers for human Ascending aortic aneurysm identified through metagenomic and metabolomic analyses: A case-control study."}],"sample_intervention_arms":{},"sex":{"female":4,"male":12},"title":"Potential Biomarkers for Human Ascending Aortic Aneurysm Identified Through Metagenomic and Metabolomic Analyses: A case-control study(2)","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1345175","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1345175_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1345175.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1345175.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1345175.csv.gz"}},{"accession":"PRJNA1464200","age_categories":{"adult":11,"elderly":5},"countries":{"CN":16},"first_public_year":"2026","gbp_per_sample_median":11.27,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":16,"papers":[{"doi":"10.3389/fcimb.2026.1914654","pmcid":"PMC13558016","pmid":"42723989","title":"Brucellar spondylitis is associated with disturbance in gut microbiota and histamine metabolism associated inflammation."}],"sample_intervention_arms":{},"sex":{"female":5,"male":11},"title":"The human gut microbiota of patients with brucellosis spondylitis","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1464200","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1464200_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1464200.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1464200.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1464200.csv.gz"}},{"accession":"PRJNA600269","age_categories":{"adult":13,"elderly":3},"countries":{},"first_public_year":"2020","gbp_per_sample_median":2.8,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"observational_with_procedure","intervention_detail":"Stool sampling after colectomy/ileal pouch surgery in UC vs FAP","interventions":["surgery"],"n_samples":16,"papers":[{"doi":"10.1016/j.chom.2020.01.021","pmcid":"PMC8172352","pmid":"32101703","title":"Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation."},{"doi":"10.1128/msystems.00984-20","pmcid":"PMC8546988","pmid":"33653942","title":"Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn's Disease."}],"sample_intervention_arms":{},"sex":{"female":10,"male":6},"title":"Dysbiosis-induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation (shotgun metagenomics)","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA600269","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA600269_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA600269.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA600269.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA600269.csv.gz"}},{"accession":"PRJNA725613","age_categories":{"adult":12,"elderly":3,"unknown":1},"countries":{"CN":16},"first_public_year":"2021","gbp_per_sample_median":1.11,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":6,"colorectal_cancer":4,"other_disease":6},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":16,"papers":[{"doi":"10.3389/fmolb.2021.703638","pmcid":"PMC8299945","pmid":"34307461","title":"Exploring Gut Microbiota in Patients with Colorectal Disease Based on 16S rRNA Gene Amplicon and Shallow Metagenomic Sequencing."}],"sample_intervention_arms":{},"sex":{"female":7,"male":9},"title":"colorectal gut microbiota","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA725613","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA725613_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA725613.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA725613.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA725613.csv.gz"}},{"accession":"PRJNA297269","age_categories":{"elderly":15},"countries":{"IT":15},"first_public_year":"2016","gbp_per_sample_median":0.27,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":15,"papers":[{"doi":"10.1038/srep25945","pmcid":"PMC4863157","pmid":"27166072","title":"Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study."},{"doi":"10.1038/s41598-017-10734-y","pmcid":"PMC5593887","pmid":"28894183","title":"Gut microbiota composition is associated with polypharmacy in elderly hospitalized patients."},{"doi":"10.1007/s00248-018-1155-7","pmcid":"PMC6132499","pmid":"29445826","title":"Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes."},{"doi":"10.1186/s40168-020-00993-9","pmcid":"PMC7890817","pmid":"33597026","title":"PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data."},{"doi":"10.1080/19490976.2022.2135963","pmcid":"PMC9621045","pmid":"36289064","title":"Functional profile of host microbiome indicates Clostridioides difficile infection."}],"sample_intervention_arms":{},"sex":{},"title":"Fecal microbiota of hospitalised Elderlies with and without Peptoclostridium difficile infection metagenome","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA297269","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA297269_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA297269.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA297269.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA297269.csv.gz"}},{"accession":"PRJNA520777","age_categories":{"adult":10,"elderly":5},"countries":{},"first_public_year":"2020","gbp_per_sample_median":0.24,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"observational_with_procedure","intervention_detail":"Heart valvular replacement surgery; warfarin therapy dosing comparison (low vs high vs control responders)","interventions":["drug_therapy"],"n_samples":15,"papers":[{"doi":"10.21203/rs.3.rs-16493/v1","pmcid":null,"pmid":null,"title":"The gut microbiome affects the responses of heart valve replacement patients to the anticoagulant warfarin"}],"sample_intervention_arms":{"drug_therapy":15},"sex":{"female":12,"male":3},"title":"WGS sequencing of gut microbiome from patients receiving warfarin therapy","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA520777","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA520777_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA520777.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA520777.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA520777.csv.gz"}},{"accession":"PRJNA591064","age_categories":{"adult":9,"elderly":5},"countries":{},"first_public_year":"2020","gbp_per_sample_median":5.15,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":14,"papers":[{"doi":"10.3389/fcimb.2020.00190","pmcid":"PMC7233261","pmid":"32477962","title":"Gut Microbiota Composition Associated With Clostridium difficile-Positive Diarrhea and C. difficile Type in ICU Patients."},{"doi":"10.1080/19490976.2022.2135963","pmcid":"PMC9621045","pmid":"36289064","title":"Functional profile of host microbiome indicates Clostridioides difficile infection."}],"sample_intervention_arms":{},"sex":{"female":5,"male":9},"title":"Gut microbiota composition associated with Clostridium difficile-positive diarrhea and C. difficile type in ICU patients","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA591064","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA591064_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA591064.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA591064.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA591064.csv.gz"}},{"accession":"PRJNA362284","age_categories":{"adolescent":2,"adult":7,"child":1,"elderly":2,"unknown":1},"countries":{"JP":13},"first_public_year":"2019","gbp_per_sample_median":20.32,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":13,"papers":[{"doi":"10.1186/s40168-019-0737-z","pmcid":"PMC6712665","pmid":"31455406","title":"Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut."},{"doi":"10.1186/s13059-021-02566-x","pmcid":"PMC8862349","pmid":"35189932","title":"viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data."}],"sample_intervention_arms":{},"sex":{"female":6,"male":6},"title":"human gut metagenome PacBio Raw sequence reads","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA362284","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA362284_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA362284.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA362284.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA362284.csv.gz"}},{"accession":"PRJNA767321","age_categories":{"adult":10,"elderly":3},"countries":{"US":13},"first_public_year":"2021","gbp_per_sample_median":17.19,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":13},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":13,"papers":[],"sample_intervention_arms":{},"sex":{"female":8,"male":5},"title":"Human small intestine metagenomes from a pilot study on segmented filamentous bacteria","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA767321","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA767321_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA767321.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA767321.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA767321.csv.gz"}},{"accession":"PRJEB37898","age_categories":{"elderly":12},"countries":{"NL":12},"first_public_year":"2020","gbp_per_sample_median":0.75,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":12,"papers":[{"doi":"10.1186/s13073-021-00869-z","pmcid":"PMC8028076","pmid":"33827686","title":"Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home."}],"sample_intervention_arms":{},"sex":{},"title":"MDROs and gut microbiota in a nursing home","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB37898","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB37898_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB37898.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB37898.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB37898.csv.gz"}},{"accession":"PRJNA451097","age_categories":{"elderly":12},"countries":{"AT":12},"first_public_year":"2022","gbp_per_sample_median":12.7,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":6},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":12,"papers":[],"sample_intervention_arms":{},"sex":{"female":6,"male":6},"title":"Metagenome shotgun sequencing of human gut microbiota and metabolic syndrome","trial_population_condition":"cardiometabolic_other","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA451097","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA451097_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA451097.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA451097.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA451097.csv.gz"}},{"accession":"PRJNA666684","age_categories":{"adult":10,"elderly":2},"countries":{"CZ":12},"first_public_year":"2021","gbp_per_sample_median":111.01,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":6,"transplant_or_immunocompromised":6},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":12,"papers":[{"doi":"10.3389/fimmu.2021.671239","pmcid":"PMC8163231","pmid":"34054845","title":"Patients With Common Variable Immunodeficiency (CVID) Show Higher Gut Bacterial Diversity and Levels of Low-Abundance Genes Than the Healthy Housemates."}],"sample_intervention_arms":{},"sex":{"female":6,"male":6},"title":"A metagenomic study of CVID in humans","trial_population_condition":"transplant_or_immunocompromised","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA666684","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA666684_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA666684.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA666684.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA666684.csv.gz"}},{"accession":"PRJNA768833","age_categories":{"adult":8,"elderly":4},"countries":{"KE":12},"first_public_year":"2022","gbp_per_sample_median":11.56,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":12,"papers":[{"doi":"10.1016/s2666-5247(23)00137-4","pmcid":"PMC10393780","pmid":"37399829","title":"Evaluating the relationship between community water and sanitation access and the global burden of antibiotic resistance: an ecological study."}],"sample_intervention_arms":{},"sex":{"female":5,"male":7},"title":"Metagenomic Sequencing of Rural Kenyan Fecal Samples","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA768833","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA768833_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA768833.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA768833.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA768833.csv.gz"}},{"accession":"PRJEB86834","age_categories":{"adult":4,"elderly":3,"unknown":4},"countries":{"RU":11},"first_public_year":"2025","gbp_per_sample_median":10.23,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"other_infection":11},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":11,"papers":[{"doi":"10.1128/msphere.00139-26","pmcid":"PMC13317233","pmid":"42153646","title":"Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis."}],"sample_intervention_arms":{"antibiotic":4,"no_intervention":7},"sex":{"female":4,"male":5},"title":"Hi-C metagenomic reconstruction of bacterial and fungal microbiome colonizing gut-lung axis in severe-ill patients","trial_population_condition":"other_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB86834","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB86834_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB86834.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB86834.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB86834.csv.gz"}},{"accession":"PRJNA1260161","age_categories":{"adult":7,"elderly":3},"countries":{},"first_public_year":"2025","gbp_per_sample_median":6.57,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":10,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Homo sapiens1 Raw sequence reads","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1260161","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1260161_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1260161.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1260161.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1260161.csv.gz"}},{"accession":"PRJNA1285573","age_categories":{"adult":8,"elderly":2},"countries":{},"first_public_year":"2025","gbp_per_sample_median":6.4,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":10},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":10,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Homo sapiens1 Raw sequence reads","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1285573","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1285573_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1285573.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1285573.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1285573.csv.gz"}},{"accession":"PRJNA600008","age_categories":{"adult":8,"elderly":2},"countries":{},"first_public_year":"2020","gbp_per_sample_median":7.67,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":3,"ibd_unspecified":7},"intervention_design":"observational_with_procedure","intervention_detail":"colectomy with ileal pouch creation in UC/FAP patients","interventions":["surgery"],"n_samples":10,"papers":[{"doi":"10.1016/j.chom.2020.01.021","pmcid":"PMC8172352","pmid":"32101703","title":"Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation."}],"sample_intervention_arms":{},"sex":{"female":8,"male":2},"title":"Dysbiosis-induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA600008","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA600008_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA600008.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA600008.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA600008.csv.gz"}},{"accession":"PRJNA904560","age_categories":{"adult":9,"elderly":1},"countries":{"CN":10},"first_public_year":"2023","gbp_per_sample_median":11.05,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":5,"neurological_psychiatric":5},"intervention_design":"single_arm_before_after","intervention_detail":"FMT from ET patients to mice; L. plantarum L5 probiotic treatment in mice","interventions":["fmt","probiotic"],"n_samples":10,"papers":[{"doi":"10.1186/s40035-023-00391-9","pmcid":"PMC10717605","pmid":"38093327","title":"Supplementation with high-GABA-producing Lactobacillus plantarum L5 ameliorates essential tremor triggered by decreased gut bacteria-derived GABA."}],"sample_intervention_arms":{},"sex":{"female":1,"male":4},"title":"Essential tremor triggered by reduction of gut bacterial-derived GABA is ameliorated by supplementary of high GABA-producing Lactobacillus plantarum L5","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA904560","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA904560_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA904560.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA904560.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA904560.csv.gz"}},{"accession":"PRJEB33098","age_categories":{"adult":6,"elderly":2,"unknown":1},"countries":{"ES":9},"first_public_year":"2019","gbp_per_sample_median":9.51,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":6,"healthy_control":3},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":9,"papers":[{"doi":"10.1038/s41597-020-0427-5","pmcid":"PMC7075950","pmid":"32179734","title":"Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample."},{"doi":"10.1186/s13059-022-02743-6","pmcid":"PMC9454175","pmid":"36076275","title":"Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2."},{"doi":"10.1101/gr.277615.122","pmcid":"PMC10538363","pmid":"37253540","title":"Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT."}],"sample_intervention_arms":{},"sex":{"female":6,"male":3},"title":"Colonbiome pilot: 9 stools, sequenced by shotgun","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB33098","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB33098_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB33098.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB33098.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB33098.csv.gz"}},{"accession":"PRJNA1300398","age_categories":{"adult":7,"elderly":2},"countries":{"SE":9},"first_public_year":"2026","gbp_per_sample_median":9.45,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":4,"other_infection":5},"intervention_design":"single_arm_before_after","intervention_detail":"Dolutegravir (antiretroviral) treatment in people living with HIV","interventions":["drug_therapy"],"n_samples":9,"papers":[],"sample_intervention_arms":{},"sex":{"female":4,"male":3},"title":"Impact of dolutegravir on the gut microbiome and metabolic pathways in PLWH","trial_population_condition":"transplant_or_immunocompromised","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1300398","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1300398_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1300398.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1300398.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1300398.csv.gz"}},{"accession":"PRJNA298362","age_categories":{"elderly":9},"countries":{"US":9},"first_public_year":"2015","gbp_per_sample_median":12.75,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":9},"intervention_design":"single_arm_before_after","intervention_detail":"Probiotic consumption study in elderly subjects","interventions":["probiotic"],"n_samples":9,"papers":[{"doi":"10.1128/mbio.00231-15","pmcid":"PMC4453556","pmid":"25873374","title":"Functional dynamics of the gut microbiome in elderly people during probiotic consumption."}],"sample_intervention_arms":{},"sex":{},"title":"Functional dynamics of the elderly gut microbiome during probiotic consumption","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA298362","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA298362_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA298362.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA298362.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA298362.csv.gz"}},{"accession":"PRJNA1209849","age_categories":{"elderly":7},"countries":{"CN":7},"first_public_year":"2025","gbp_per_sample_median":8.25,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":7,"papers":[{"doi":"10.1111/acel.70166","pmcid":"PMC12419854","pmid":"40643197","title":"L-Tryptophan Produced by Bifidobacterium pseudocatenulatum NCU-08 Delays Aging in SAMP8 Mice by Activating the Sirt1/P53/P21/Rb Signaling Pathway."}],"sample_intervention_arms":{},"sex":{"female":7},"title":"Gut metagenomics Raw sequence reads","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1209849","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1209849_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1209849.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1209849.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1209849.csv.gz"}},{"accession":"PRJEB3085","age_categories":{"elderly":6},"countries":{"DE":6},"first_public_year":"2013","gbp_per_sample_median":0.0,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":6},"intervention_design":"single_arm_before_after","intervention_detail":"","interventions":[],"n_samples":6,"papers":[{"doi":"10.1136/gutjnl-2012-303184","pmcid":"PMC3812899","pmid":"23236009","title":"Gut microbiota disturbance during antibiotic therapy: a multi-omic approach."},{"doi":"10.3389/fmicb.2014.00335","pmcid":"PMC4163665","pmid":"25309515","title":"Structural and functional changes in the gut microbiota associated to Clostridium difficile infection."}],"sample_intervention_arms":{"antibiotic":6},"sex":{"male":6},"title":"Disturbance of the gut microbiota during antibiotic stress (therapy): a multi-omic approach","trial_population_condition":"other_disease","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB3085","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB3085_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB3085.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB3085.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB3085.csv.gz"}},{"accession":"PRJNA1521563","age_categories":{"adult":5,"elderly":1},"countries":{"HK":6},"first_public_year":"2026","gbp_per_sample_median":0.28,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"gi_infection_or_diarrhoea":6},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":6,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"A hospital cluster of human astrovirus MLB infection with a fatal case associated with Rotavirus C coinfection","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1521563","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1521563_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1521563.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1521563.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1521563.csv.gz"}},{"accession":"PRJNA308846","age_categories":{"elderly":6},"countries":{},"first_public_year":"2016","gbp_per_sample_median":5.74,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":6,"papers":[{"doi":"10.1371/journal.pone.0148028","pmcid":"PMC4746063","pmid":"26849217","title":"Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis."}],"sample_intervention_arms":{},"sex":{},"title":"Human Faecal Samples Raw sequence reads","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA308846","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA308846_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA308846.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA308846.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA308846.csv.gz"}},{"accession":"PRJNA312222","age_categories":{"adult":3,"elderly":1},"countries":{"US":4},"first_public_year":"2016","gbp_per_sample_median":358.16,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":2,"healthy_control":2},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":4,"papers":[{"doi":"10.3389/fmicb.2016.00783","pmcid":"PMC4880562","pmid":"27303377","title":"Capturing One of the Human Gut Microbiome's Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data."}],"sample_intervention_arms":{},"sex":{"female":2,"male":2},"title":"Genome reconstructions from human gut metagenomes","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA312222","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA312222_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA312222.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA312222.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA312222.csv.gz"}},{"accession":"PRJNA718195","age_categories":{"elderly":4},"countries":{"RU":4},"first_public_year":"2021","gbp_per_sample_median":35.95,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":4},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":4,"papers":[{"doi":"10.3389/fmicb.2021.770323","pmcid":"PMC8851603","pmid":"35185811","title":"Hi-C Metagenomics in the ICU: Exploring Clinically Relevant Features of Gut Microbiome in Chronically Critically Ill Patients."}],"sample_intervention_arms":{},"sex":{"female":2,"male":2},"title":"Hi-C metagenomics of gut microbiome in chronically critically ill patients","trial_population_condition":"sepsis_or_infection","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA718195","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA718195_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA718195.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA718195.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA718195.csv.gz"}},{"accession":"PRJNA1037706","age_categories":{"elderly":2},"countries":{"CN":2},"first_public_year":"2024","gbp_per_sample_median":0.21,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"other_infection":2},"intervention_design":"observational_with_procedure","intervention_detail":"Radical laparoscopic rectal cancer surgery, sampled post-operatively","interventions":["surgery"],"n_samples":2,"papers":[{"doi":"10.2147/idr.s452705","pmcid":"PMC11102091","pmid":"38766680","title":"Hypervirulent Klebsiella pneumoniae Mediated Hepatic Infarction Septic Shock After Rectal Cancer Surgery: A Case Report."}],"sample_intervention_arms":{},"sex":{},"title":"Hypervirulent Klebsiella pneumoniae mediated hepatic infarction septic shock after rectal cancer surgery","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1037706","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1037706_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1037706.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1037706.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1037706.csv.gz"}},{"accession":"PRJEB85717","age_categories":{"elderly":1},"countries":{"DE":1},"first_public_year":"2025","gbp_per_sample_median":3.45,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":1},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":1,"papers":[{"doi":"10.3390/ijms26104735","pmcid":"PMC12112180","pmid":"40429881","title":"Prognostic Value of a Multivariate Gut Microbiome Model for Progression from Normal Cognition to Mild Cognitive Impairment Within 4 Years."}],"sample_intervention_arms":{},"sex":{},"title":"Prognostic value of gut microbiome for progression from normal cognition to mild cognitive impairment within 4 years","trial_population_condition":"neurological_psychiatric","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB85717","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB85717_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB85717.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB85717.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB85717.csv.gz"}},{"accession":"PRJNA520743","age_categories":{"elderly":1},"countries":{},"first_public_year":"2020","gbp_per_sample_median":0.04,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"cardiometabolic_other":1},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":1,"papers":[{"doi":"10.1016/j.phrs.2020.104979","pmcid":null,"pmid":"32505835","title":"The gut microbes, Enterococcus and Escherichia-Shigella, affect the responses of heart valve replacement patients to the anticoagulant warfarin."}],"sample_intervention_arms":{},"sex":{"male":1},"title":"WGS sequencing of gut microbiome from patients receiving warfarin therapy（Supplementary）","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA520743","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA520743_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA520743.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA520743.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA520743.csv.gz"}}],"release":"R2026.25"}