{"filter":{"health_condition":"ulcerative_colitis"},"n_projects":102,"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":"PRJEB37731","age_categories":{"adolescent":1,"adult":2824},"countries":{"DK":2804,"SE":21},"first_public_year":"2020","gbp_per_sample_median":0.23,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"allergy_or_atopy":637,"autoimmune_inflammatory":23,"cardiometabolic_other":8,"healthy_control":1877,"neurological_psychiatric":54,"other_infection":210,"ulcerative_colitis":16},"intervention_design":"non_randomized_controlled","intervention_detail":"Hormonal contraceptives: combined oral contraceptive or levonorgestrel IUS vs non-hormonal methods","interventions":["drug_therapy"],"n_samples":2825,"papers":[{"doi":"10.1128/msphere.00448-20","pmcid":"PMC7677004","pmid":"33208514","title":"Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome."},{"doi":"10.3389/fcimb.2021.625229","pmcid":"PMC8018275","pmid":"33816334","title":"Dysbiosis of the Human Oral Microbiome During the Menstrual Cycle and Vulnerability to the External Exposures of Smoking and Dietary Sugar."},{"doi":"10.1093/humrep/deac094","pmcid":"PMC9247429","pmid":"35553675","title":"The healthy female microbiome across body sites: effect of hormonal contraceptives and the menstrual cycle."},{"doi":"10.3389/fcimb.2024.1324794","pmcid":"PMC11249552","pmid":"39015337","title":"Investigations of microbiota composition and neuroactive pathways in association with symptoms of stress and depression in a cohort of healthy women."},{"doi":"10.1186/s40168-024-01870-5","pmcid":"PMC11331738","pmid":"39160615","title":"Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes."}],"sample_intervention_arms":{},"sex":{"female":2825},"title":"Effects of the menstrual cycle and hormonal contraceptives on the human microbiome","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB37731","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB37731_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB37731.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB37731.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB37731.csv.gz"}},{"accession":"PRJNA1086048","age_categories":{"unknown":1154},"countries":{"HK":1154},"first_public_year":"2024","gbp_per_sample_median":7.24,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":174,"ulcerative_colitis":205},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":1154,"papers":[{"doi":"10.1038/s41591-024-03280-4","pmcid":"PMC11645270","pmid":"39367251","title":"Noninvasive, microbiome-based diagnosis of inflammatory bowel disease."}],"sample_intervention_arms":{},"sex":{},"title":"Metagenomic analysis of faecal microbiome as a tool for targeted non-invasive biomarkers for inflammatory bowel disease","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1086048","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1086048_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1086048.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1086048.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1086048.csv.gz"}},{"accession":"PRJEB110648","age_categories":{"unknown":1124},"countries":{"GB":1124},"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":373,"healthy_control":220,"ulcerative_colitis":531},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":1124,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Gut Virome Profiling in Ulcerative Colitis and Crohn's Disease","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB110648","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB110648_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB110648.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB110648.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB110648.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":"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 <i>Sutterella</i> 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":"PRJEB98069","age_categories":{"unknown":605},"countries":{"DK":605},"first_public_year":"2026","gbp_per_sample_median":3.01,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":605,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Distinct Microbial and Resistome Signatures Differentiate Healthy and Inflamed Ileal Pouches in Ulcerative Colitis Patients","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB98069","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB98069_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB98069.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB98069.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB98069.csv.gz"}},{"accession":"PRJEB50555","age_categories":{"adult":537},"countries":{"DE":22,"FR":76,"IL":73,"US":52},"first_public_year":"2022","gbp_per_sample_median":24.13,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":83,"healthy_control":56,"ulcerative_colitis":85},"intervention_design":"single_arm_before_after","intervention_detail":"Oral five-phage combination targeting IBD-associated Klebsiella pneumoniae in healthy volunteers","interventions":["phage_therapy"],"n_samples":537,"papers":[{"doi":"10.3390/microorganisms12102086","pmcid":"PMC11510655","pmid":"39458395","title":"Oral Microbial Translocation Genes in Gastrointestinal Cancers: Insights from Metagenomic Analysis."}],"sample_intervention_arms":{},"sex":{},"title":"Targeted suppression of human IBD-associated gut microbiota commensals for treatment of intestinal inflammation","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB50555","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB50555_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB50555.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB50555.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB50555.csv.gz"}},{"accession":"PRJNA945504","age_categories":{"unknown":482},"countries":{"KR":482},"first_public_year":"2023","gbp_per_sample_median":6.48,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":173,"healthy_control":50,"ulcerative_colitis":259},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":482,"papers":[{"doi":"10.1186/s12866-023-03084-5","pmcid":"PMC10640746","pmid":"37951857","title":"Diagnosis of Crohn's disease and ulcerative colitis using the microbiome."},{"doi":"10.1371/journal.pone.0340748","pmcid":"PMC13354076","pmid":"42430408","title":"Integrative metagenomics and structural bioinformatics identify explainable gut microbial variants associated with Crohn's disease."}],"sample_intervention_arms":{},"sex":{"female":144,"male":288},"title":"Diagnosis of Crohn's Disease and Ulcerative Colitis Using the Microbiome","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA945504","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA945504_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA945504.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA945504.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA945504.csv.gz"}},{"accession":"PRJEB81106","age_categories":{"unknown":450},"countries":{"DE":99,"IL":351},"first_public_year":"2024","gbp_per_sample_median":0.58,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":23,"healthy_control":25,"ulcerative_colitis":146},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":450,"papers":[{"doi":"10.1016/j.cell.2024.12.016","pmcid":null,"pmid":"39837331","title":"Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease."}],"sample_intervention_arms":{"diet_intervention":91,"fmt":47},"sex":{},"title":"Simultaneous metagenome-informed metaproteomics of the human gut microbiome, host and dietary exposome uncover functional interactomes in health & IBD","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB81106","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB81106_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB81106.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB81106.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB81106.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":"PRJEB26472","age_categories":{"adult":426},"countries":{},"first_public_year":"2018","gbp_per_sample_median":0.04,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":426},"intervention_design":"randomized_controlled_trial","intervention_detail":"FMT for active ulcerative colitis (FOCUS study)","interventions":["fmt"],"n_samples":426,"papers":[{"doi":"10.1016/j.chom.2020.03.006","pmcid":"PMC8647676","pmid":"32298656","title":"Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis."}],"sample_intervention_arms":{},"sex":{},"title":"Faecal cDNA Specific bacteria and metabolic pathways are associated with response to faecal microbiota transplantation in ulcerative colitis","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB26472","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB26472_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB26472.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB26472.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB26472.csv.gz"}},{"accession":"PRJNA1450848","age_categories":{"unknown":387},"countries":{"CN":387},"first_public_year":"2026","gbp_per_sample_median":9.81,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":56,"ulcerative_colitis":331},"intervention_design":"single_arm_before_after","intervention_detail":"FMT from non-urbanized donors for ulcerative colitis treatment","interventions":["fmt"],"n_samples":387,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Improved Efficacy of Fecal Microbiota Transplantation for Ulcerative Colitis with Non-urbanized Donors","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1450848","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1450848_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1450848.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1450848.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1450848.csv.gz"}},{"accession":"PRJEB38352","age_categories":{"unknown":382},"countries":{"US":382},"first_public_year":"2021","gbp_per_sample_median":8.68,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"crohns_disease":196,"ibd_unspecified":57,"ulcerative_colitis":129},"intervention_design":"observational_with_procedure","intervention_detail":"Ileocolonic resection or colectomy in IBD patients","interventions":["surgery"],"n_samples":382,"papers":[{"doi":"10.1093/ibd/izaa262","pmcid":"PMC8047854","pmid":"33026068","title":"Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity."}],"sample_intervention_arms":{"no_intervention":220,"surgery":105},"sex":{"female":157,"male":157},"title":"Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB38352","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB38352_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB38352.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB38352.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB38352.csv.gz"}},{"accession":"PRJNA1251707","age_categories":{"unknown":312},"countries":{"AU":312},"first_public_year":"2025","gbp_per_sample_median":5.3,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":28,"healthy_control":235,"ibd_unspecified":3,"ulcerative_colitis":46},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":312,"papers":[{"doi":"10.1101/2024.10.22.619608","pmcid":null,"pmid":null,"title":"A rational approach for the targeted discovery and characterisation of microbiome-derived therapeutics"}],"sample_intervention_arms":{},"sex":{},"title":"Metagenomes for rational identification of live biotherapeutics for the treatment of inflammatory bowel disease","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1251707","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1251707_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1251707.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1251707.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1251707.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":"PRJEB26357","age_categories":{"adult":284},"countries":{},"first_public_year":"2018","gbp_per_sample_median":1.71,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":284},"intervention_design":"randomized_controlled_trial","intervention_detail":"FMT (donor faecal microbiota) vs placebo in FOCUS trial for active UC","interventions":["fmt"],"n_samples":284,"papers":[{"doi":"10.1016/j.chom.2020.03.006","pmcid":"PMC8647676","pmid":"32298656","title":"Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis."},{"doi":"10.1038/s41467-024-53454-4","pmcid":"PMC11487140","pmid":"39420033","title":"The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission."},{"doi":"10.1038/s41586-024-08242-x","pmcid":"PMC12547691","pmid":"39604726","title":"Gut microbiota strain richness is species specific and affects engraftment."},{"doi":"10.1080/19490976.2025.2597628","pmcid":"PMC12710892","pmid":"41378445","title":"Cohort-specific determinants of donor strain engraftment following multi-donor faecal microbiota transplantation in two randomised clinical trials."}],"sample_intervention_arms":{},"sex":{},"title":"ShotGun BACTERIAL AND FUNCTIONAL DETERMINANTS OF OUTCOME IN FAECAL MICROBIOTA TRANSPLANTATION FOR ACTIVE ULCERATIVE COLITIS","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB26357","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB26357_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB26357.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB26357.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB26357.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":"PRJEB45397","age_categories":{"child":241},"countries":{"AU":241},"first_public_year":"2023","gbp_per_sample_median":3.52,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":90,"healthy_control":101,"ibd_unspecified":3,"ulcerative_colitis":46},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":241,"papers":[{"doi":"10.1016/j.xcrm.2023.101124","pmcid":"PMC10394256","pmid":"37467722","title":"Bacterial clade-specific analysis identifies distinct epithelial responses in inflammatory bowel disease."},{"doi":"10.1038/s41564-025-02154-w","pmcid":"PMC12578642","pmid":"41131367","title":"A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people."}],"sample_intervention_arms":{},"sex":{},"title":"Microbiome of Paediatric IBD Patients","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB45397","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB45397_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB45397.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB45397.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB45397.csv.gz"}},{"accession":"PRJNA436359","age_categories":{"child":241},"countries":{"US":241},"first_public_year":"2024","gbp_per_sample_median":1.12,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":241},"intervention_design":"observational_with_procedure","intervention_detail":"Conventional UC treatments (e.g. 5-ASA, corticosteroids) compared pre/post","interventions":["drug_therapy"],"n_samples":241,"papers":[{"doi":"10.1016/j.chom.2018.09.009","pmcid":"PMC6277984","pmid":"30308161","title":"Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course."},{"doi":"10.1038/s41467-018-07841-3","pmcid":"PMC6318335","pmid":"30604764","title":"Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response."},{"doi":"10.1038/s41564-022-01224-7","pmcid":"PMC9728153","pmid":"36138166","title":"Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine."},{"doi":"10.1002/ueg2.12485","pmcid":"PMC10859715","pmid":"38041519","title":"Gut microbiota signatures in inflammatory bowel disease."},{"doi":"10.1016/j.chom.2023.12.013","pmcid":"PMC10923022","pmid":"38215740","title":"Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course."}],"sample_intervention_arms":{},"sex":{},"title":"Gut microbial factors implicated in disease progression and treatment response in pediatric ulcerative colitis","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA436359","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA436359_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA436359.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA436359.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA436359.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":"PRJNA737472","age_categories":{"adult":224},"countries":{"US":224},"first_public_year":"2022","gbp_per_sample_median":15.09,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":true,"health_conditions":{"healthy_control":42,"ulcerative_colitis":182},"intervention_design":"randomized_controlled_trial","intervention_detail":"FMT with antibiotic pretreatment vs none; capsule vs enema maintenance, 2x2 factorial","interventions":["antibiotic","fmt"],"n_samples":224,"papers":[{"doi":"10.1038/s41598-022-09307-5","pmcid":"PMC8976058","pmid":"35365713","title":"Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis."},{"doi":"10.3389/fbinf.2022.867386","pmcid":"PMC9580935","pmid":"36304283","title":"Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts."},{"doi":"10.1038/s41598-024-62463-8","pmcid":"PMC11316000","pmid":"39122767","title":"Sustained mucosal colonization and fecal metabolic dysfunction by Bacteroides associates with fecal microbial transplant failure in ulcerative colitis patients."},{"doi":"10.1101/gr.279543.124","pmcid":"PMC12047655","pmid":"40210439","title":"Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC."},{"doi":"10.1016/s0016-5085(20)30716-2","pmcid":null,"pmid":null,"title":"36 ANTIBIOTIC PRETREATMENT PRIOR TO FECAL MICROBIOTA TRANSPLANTATION INCREASES RATES OF REMISSION IN PATIENTS WITH MILD TO MODERATE ULCERATIVE COLITIS: RESULTS FROM A PILOT RANDOMIZED CLINICAL TRIAL"}],"sample_intervention_arms":{"antibiotic":74,"fmt":155,"no_intervention":69},"sex":{"female":69,"male":113},"title":"Microbiome sequencing of ulcerative colitis patients receiving fecal microbiota transplantation","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA737472","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA737472_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA737472.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA737472.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA737472.csv.gz"}},{"accession":"PRJEB38528","age_categories":{"adult":223},"countries":{"SE":223},"first_public_year":"2020","gbp_per_sample_median":0.17,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"allergy_or_atopy":10,"autoimmune_inflammatory":15,"cardiometabolic_other":6,"crohns_disease":3,"neurological_psychiatric":21,"other_disease":3,"other_infection":6,"pregnancy_postpartum":16,"type1_diabetes":3,"ulcerative_colitis":2},"intervention_design":"observational_with_procedure","intervention_detail":"Cohort defined by planned C-section vs vaginal delivery; samples collected at delivery","interventions":[],"n_samples":223,"papers":[{"doi":"10.1128/spectrum.02733-21","pmcid":"PMC9045136","pmid":"35266820","title":"Evaluation of Modulatory Activities of Lactobacillus crispatus Strains in the Context of the Vaginal Microbiota."},{"doi":"10.1186/s12866-023-02764-6","pmcid":"PMC10024458","pmid":"36934229","title":"Is there a placental microbiota? A critical review and re-analysis of published placental microbiota datasets."},{"doi":"10.1038/s41598-026-54100-3","pmcid":"PMC13216312","pmid":"42203854","title":"Shotgun metagenomic mapping of saliva reveals insights into diversity and function of the oral microbiome in pregnancy."}],"sample_intervention_arms":{},"sex":{"female":223},"title":"Placenta biopsies, saliva samples, vaginal and rectal swabs collected at delivery for babies at term","trial_population_condition":"pregnancy_postpartum","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB38528","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB38528_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB38528.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB38528.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB38528.csv.gz"}},{"accession":"PRJEB58035","age_categories":{"adult":221},"countries":{"AU":221},"first_public_year":"2024","gbp_per_sample_median":11.58,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"ulcerative_colitis":221},"intervention_design":"randomized_controlled_trial","intervention_detail":"Oral lyophilized donor FMT vs placebo in ulcerative colitis patients","interventions":["fmt"],"n_samples":221,"papers":[{"doi":"10.1038/s41467-024-53454-4","pmcid":"PMC11487140","pmid":"39420033","title":"The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission."},{"doi":"10.1128/msystems.00991-25","pmcid":"PMC12542657","pmid":"40952001","title":"Bacterial taxonomic and functional changes following oral lyophilized donor fecal microbiota transplantation in patients with ulcerative colitis."}],"sample_intervention_arms":{"fmt":60,"placebo":75},"sex":{},"title":"Patient samples from lyophilised oral faecal microbiota transplantation for ulcerative colitis (LOTUS) study shotgun","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB58035","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB58035_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB58035.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB58035.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB58035.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":"PRJNA475599","age_categories":{"adult":215},"countries":{"US":215},"first_public_year":"2019","gbp_per_sample_median":0.8,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":true,"health_conditions":{"healthy_control":13,"ulcerative_colitis":202},"intervention_design":"randomized_controlled_trial","intervention_detail":"Colonoscopy FMT induction + 12wk daily encapsulated oral FMT vs sham","interventions":["fmt"],"n_samples":215,"papers":[{"doi":"10.1186/s12876-021-01856-9","pmcid":"PMC8268596","pmid":"34238227","title":"Daily, oral FMT for long-term maintenance therapy in ulcerative colitis: results of a single-center, prospective, randomized pilot study."},{"doi":"10.1128/mbio.00975-21","pmcid":"PMC8406238","pmid":"34281401","title":"Dynamic Colonization of Microbes and Their Functions after Fecal Microbiota Transplantation for Inflammatory Bowel Disease."}],"sample_intervention_arms":{"fmt":84,"no_intervention":41,"placebo":74},"sex":{},"title":"Fecal transplant for ulcerative colitis","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA475599","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA475599_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA475599.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA475599.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA475599.csv.gz"}},{"accession":"PRJNA1171764","age_categories":{"unknown":212},"countries":{"ES":212},"first_public_year":"2025","gbp_per_sample_median":3.74,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":77,"ulcerative_colitis":107},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":212,"papers":[{"doi":"10.1186/s40364-025-00802-1","pmcid":"PMC12172205","pmid":"40524271","title":"Microbiome multi-omics analysis reveals novel biomarkers and mechanisms linked with CD etiopathology."},{"doi":"10.1186/s40364-026-00950-y","pmcid":"PMC13352609","pmid":"42277905","title":"Microbial, functional, and virulence biomarkers associated with familial risk of Crohn's disease and ulcerative colitis."}],"sample_intervention_arms":{},"sex":{},"title":"Human gut metagenome of IBD patients and healthy controls","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1171764","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1171764_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1171764.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1171764.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1171764.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 <i>Akkermansia</i> 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":"PRJEB54606","age_categories":{"unknown":209},"countries":{"DK":209},"first_public_year":"2023","gbp_per_sample_median":2.48,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":209},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":209,"papers":[{"doi":"10.1093/ibd/izae179","pmcid":null,"pmid":"39150994","title":"The Composition of the Fecal and Mucosa-adherent Microbiota Varies Based on Age and Disease Activity in Ulcerative Colitis."}],"sample_intervention_arms":{},"sex":{},"title":"The fecal and mucosa adherent microbiome depends on age and disease severity in both composition and functional properties in ulcerative colitis","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB54606","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB54606_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB54606.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB54606.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB54606.csv.gz"}},{"accession":"PRJNA1071720","age_categories":{"unknown":209},"countries":{"NL":209},"first_public_year":"2024","gbp_per_sample_median":0.29,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":27,"ulcerative_colitis":182},"intervention_design":"randomized_controlled_trial","intervention_detail":"Budesonide or placebo pretreatment then 4 FMT infusions from selected donors","interventions":["drug_therapy","fmt"],"n_samples":209,"papers":[{"doi":"10.1093/ecco-jcc/jjae043","pmcid":"PMC11369067","pmid":"38572716","title":"Fecal Microbiota Transplantation engraftment after budesonide or placebo in patients with active ulcerative colitis using pre-selected donors: a randomized pilot study."},{"doi":"10.1093/ecco-jcc/jjae137","pmcid":"PMC11836888","pmid":"39225490","title":"Dynamics of Gut Microbiota After Fecal Microbiota Transplantation in Ulcerative Colitis: Success Linked to Control of Prevotellaceae."},{"doi":"10.1093/ismeco/ycaf119","pmcid":"PMC12378841","pmid":"40873786","title":"Ecological resilience in ulcerative colitis: microbial dynamics of donor and resident species in a longitudinal fecal microbiota transplantation study."},{"doi":"10.1038/s41467-026-73290-y","pmcid":"PMC13376552","pmid":"42151161","title":"Inorganic nitrogen metabolic reprogramming of the gut microbiome drives fecal microbiota transplantation in ulcerative colitis."}],"sample_intervention_arms":{},"sex":{},"title":"FECBUD Study Fecal Metagenomes","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1071720","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1071720_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1071720.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1071720.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1071720.csv.gz"}},{"accession":"PRJEB72371","age_categories":{"unknown":206},"countries":{"SE":206},"first_public_year":"2025","gbp_per_sample_median":13.84,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":64,"healthy_control":87,"ulcerative_colitis":55},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":206,"papers":[{"doi":"10.1038/s41598-025-18106-7","pmcid":"PMC12508173","pmid":"41062543","title":"Associations of the intestinal microbiota with plasma bile acids and inflammation markers in Crohn's disease and ulcerative colitis."}],"sample_intervention_arms":{},"sex":{},"title":"Multiomic analysis of Crohn's disease and Ulcerative colitis using machine learning models","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB72371","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB72371_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB72371.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB72371.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB72371.csv.gz"}},{"accession":"PRJNA844888","age_categories":{"unknown":188},"countries":{"US":188},"first_public_year":"2025","gbp_per_sample_median":7.79,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":188},"intervention_design":"randomized_controlled_trial","intervention_detail":"Encapsulated microbiota transplant therapy (MTP-101C) vs placebo capsules, 8 weeks, UC","interventions":["fmt"],"n_samples":188,"papers":[{"doi":"10.1093/ecco-jcc/jjae142","pmcid":"PMC12476944","pmid":"39240145","title":"Novel Microbial Engraftment Trajectories Following Microbiota Transplant Therapy in Ulcerative Colitis."}],"sample_intervention_arms":{"fmt":103},"sex":{},"title":"Vaughn UC IMT Study","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA844888","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA844888_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA844888.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA844888.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA844888.csv.gz"}},{"accession":"PRJNA532645","age_categories":{"adolescent":112,"adult":18,"child":51,"infant":5},"countries":{"CA":4,"FI":1,"IL":120,"IT":15},"first_public_year":"2019","gbp_per_sample_median":0.47,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":186},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":186,"papers":[{"doi":"10.1016/j.isci.2024.111442","pmcid":"PMC11650326","pmid":"39691780","title":"Gut-microbiota-based ensemble model predicts prognosis of pediatric inflammatory bowel disease."},{"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":{"antibiotic":78,"drug_therapy":108},"sex":{"female":98,"male":88},"title":"PRASCO gut microbiome profile of Pediatric Severe Acute Ulcerative Colitis patients under Antimicrobial treatment","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA532645","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA532645_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA532645.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA532645.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA532645.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":"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":"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":"PRJNA1283919","age_categories":{"adult":166},"countries":{"GB":166},"first_public_year":"2025","gbp_per_sample_median":6.46,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":34,"ulcerative_colitis":132},"intervention_design":"randomized_controlled_trial","intervention_detail":"Multidose FMT via nasogastric tube vs colonoscopy/enema in ulcerative colitis","interventions":["fmt"],"n_samples":166,"papers":[{"doi":"10.1093/ecco-jcc/jjag006","pmcid":"PMC13012878","pmid":"41587946","title":"Mechanistic insights into fecal microbiota transplantation for the treatment of ulcerative colitis: analysis of the STOP-Colitis trial."}],"sample_intervention_arms":{},"sex":{},"title":"STOP-COLITIS Metagenomic Sequencing Data","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1283919","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1283919_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1283919.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1283919.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1283919.csv.gz"}},{"accession":"PRJEB26473","age_categories":{"adult":160},"countries":{},"first_public_year":"2018","gbp_per_sample_median":0.06,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":160},"intervention_design":"randomized_controlled_trial","intervention_detail":"FMT vs placebo in active ulcerative colitis (FOCUS trial)","interventions":["fmt"],"n_samples":160,"papers":[{"doi":"10.1038/s41467-024-46983-5","pmcid":"PMC10965925","pmid":"38531874","title":"Profiling the colonic mucosal response to fecal microbiota transplantation identifies a role for GBP5 in colitis in humans and mice."},{"doi":"10.1016/j.chom.2020.03.006","pmcid":"PMC8647676","pmid":"32298656","title":"Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis."}],"sample_intervention_arms":{},"sex":{},"title":"biopsy cDNA Specific bacteria and metabolic pathways are associated with response to faecal microbiota transplantation in ulcerative colitis","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB26473","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB26473_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB26473.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB26473.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB26473.csv.gz"}},{"accession":"PRJEB26474","age_categories":{"adult":160},"countries":{},"first_public_year":"2018","gbp_per_sample_median":0.03,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":160},"intervention_design":"randomized_controlled_trial","intervention_detail":"FMT vs placebo in active ulcerative colitis (FOCUS trial)","interventions":["fmt"],"n_samples":160,"papers":[{"doi":"10.1016/j.chom.2020.03.006","pmcid":"PMC8647676","pmid":"32298656","title":"Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis."}],"sample_intervention_arms":{},"sex":{},"title":"biopsy DNA Specific bacteria and metabolic pathways are associated with response to faecal microbiota transplantation in ulcerative colitis","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB26474","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB26474_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB26474.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB26474.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB26474.csv.gz"}},{"accession":"PRJEB47061","age_categories":{"unknown":160},"countries":{"AT":160},"first_public_year":"2021","gbp_per_sample_median":6.26,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"ulcerative_colitis":122},"intervention_design":"unknown","intervention_detail":"FMT for ulcerative colitis; donor stool transplant","interventions":["antibiotic","bowel_preparation","fmt"],"n_samples":160,"papers":[{"doi":"10.1016/j.xcrm.2022.100711","pmcid":"PMC9418803","pmid":"35931074","title":"Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics."}],"sample_intervention_arms":{"fmt":122,"no_intervention":38},"sex":{},"title":"Fecal microbiota transplantation for treatment of ulcerative colitis","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB47061","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB47061_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB47061.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB47061.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB47061.csv.gz"}},{"accession":"PRJNA1265906","age_categories":{"adolescent":97,"adult":3,"child":32,"infant":1,"neonate":1},"countries":{"IL":134},"first_public_year":"2025","gbp_per_sample_median":0.94,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":61,"healthy_control":29,"ulcerative_colitis":44},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":134,"papers":[{"doi":"10.1186/s40168-026-02344-6","pmcid":"PMC13045140","pmid":"41742321","title":"Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum."}],"sample_intervention_arms":{},"sex":{},"title":"Gut microbiome in pediatric IBD patients","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1265906","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1265906_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1265906.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1265906.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1265906.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":"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 <i>Lachnospiraceae</i> 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":"PRJNA439152","age_categories":{"unknown":119},"countries":{"CN":119},"first_public_year":"2022","gbp_per_sample_median":0.06,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"ulcerative_colitis":119},"intervention_design":"non_randomized_controlled","intervention_detail":"5-aminosalicylic acid (5-ASA) treatment vs untreated UC patients","interventions":["drug_therapy"],"n_samples":119,"papers":[{"doi":"10.3389/fmicb.2018.01274","pmcid":"PMC6008376","pmid":"29951050","title":"5-Aminosalicylic Acid Alters the Gut Bacterial Microbiota in Patients With Ulcerative Colitis."}],"sample_intervention_arms":{"drug_therapy":19,"no_intervention":20},"sex":{},"title":"GUT BACTERIAL METAGENOME Metagenome","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA439152","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA439152_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA439152.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA439152.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA439152.csv.gz"}},{"accession":"PRJDB14272","age_categories":{"unknown":114},"countries":{"JP":114},"first_public_year":"2026","gbp_per_sample_median":0.16,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":114},"intervention_design":"single_arm_before_after","intervention_detail":"Antibiotic combination therapy for ulcerative colitis","interventions":["antibiotic"],"n_samples":114,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Metagenomic analysis of fecal samples obtained from ulcerative colitis patient in Japan","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB14272","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB14272_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB14272.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB14272.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB14272.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":"PRJNA701961","age_categories":{"unknown":109},"countries":{"CA":109},"first_public_year":"2021","gbp_per_sample_median":9.51,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":true,"health_conditions":{"gi_infection_or_diarrhoea":51,"healthy_control":29,"ulcerative_colitis":19},"intervention_design":"observational_with_procedure","intervention_detail":"FMT for recurrent C. difficile infection from healthy donors","interventions":["fmt"],"n_samples":109,"papers":[{"doi":"10.1186/s13059-023-02924-x","pmcid":"PMC10108530","pmid":"37069665","title":"Metabolic independence drives gut microbial colonization and resilience in health and disease."},{"doi":"10.1101/2021.03.02.433653","pmcid":null,"pmid":null,"title":"Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut"},{"doi":"10.1080/19490976.2022.2135963","pmcid":"PMC9621045","pmid":"36289064","title":"Functional profile of host microbiome indicates Clostridioides difficile infection."},{"doi":"10.1016/j.chom.2024.03.005","pmcid":"PMC11081829","pmid":"38565143","title":"A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota."},{"doi":"10.1093/bioinformatics/btae252","pmcid":"PMC11211831","pmid":"38940183","title":"Floria: fast and accurate strain haplotyping in metagenomes."}],"sample_intervention_arms":{"fmt":70,"no_intervention":39},"sex":{},"title":"Donor and recipient stool metagenomes from a fecal microbiota transplantation study","trial_population_condition":"gi_infection_or_diarrhoea","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA701961","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA701961_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA701961.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA701961.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA701961.csv.gz"}},{"accession":"PRJNA1004651","age_categories":{"adult":108},"countries":{"US":108},"first_public_year":"2023","gbp_per_sample_median":10.04,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":108},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":108,"papers":[{"doi":"10.1007/s00253-026-13948-1","pmcid":"PMC13631169","pmid":"42417977","title":"Metagenomics comparison identifies shared pathogenic microbiome in humans, pigs and chickens."}],"sample_intervention_arms":{},"sex":{},"title":"Human gut metagenome, whole genomic shotgun sequencing","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1004651","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1004651_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1004651.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1004651.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1004651.csv.gz"}},{"accession":"PRJNA1004560","age_categories":{"adolescent":60,"child":37},"countries":{"CA":97},"first_public_year":"2025","gbp_per_sample_median":13.48,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":27,"gi_infection_or_diarrhoea":21,"healthy_control":30,"other_disease":7,"ulcerative_colitis":12},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":97,"papers":[{"doi":"10.1080/19490976.2025.2539450","pmcid":"PMC12323425","pmid":"40754936","title":"The colonic mucosal virome in inflammatory bowel disease reveals Crassvirales depletion and disease-specific virome features."}],"sample_intervention_arms":{},"sex":{"female":51,"male":46},"title":"The colonic virome in inflammatory bowel disease","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1004560","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1004560_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1004560.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1004560.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1004560.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":"PRJNA1499619","age_categories":{"adult":92},"countries":{"CN":92},"first_public_year":"2026","gbp_per_sample_median":13.61,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":35,"ulcerative_colitis":57},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":92,"papers":[{"doi":"10.3389/fnut.2026.1942104","pmcid":"PMC13581694","pmid":"42755660","title":"Sarcopenia in patients with active ulcerative colitis: associations with serum metabolites and gut microbiota."}],"sample_intervention_arms":{},"sex":{},"title":"Gut microbial characteristics of hospitalized patients with active ulcerative colitis and sarcopenia","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1499619","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1499619_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1499619.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1499619.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1499619.csv.gz"}},{"accession":"PRJEB88212","age_categories":{"unknown":90},"countries":{"NO":90},"first_public_year":"2025","gbp_per_sample_median":4.54,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":32,"healthy_control":26,"ulcerative_colitis":32},"intervention_design":"single_arm_before_after","intervention_detail":"IBD treatment, faecal samples before and after","interventions":["drug_therapy"],"n_samples":90,"papers":[{"doi":"10.1186/s12866-026-05101-9","pmcid":"PMC13255511","pmid":"42045813","title":"Exploring alterations in the gut resistome in medically treated inflammatory bowel disease patients."}],"sample_intervention_arms":{},"sex":{},"title":"Shotgun microbiome sequencing of faecal contents from IBD patients, before and after treatment","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB88212","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB88212_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB88212.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB88212.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB88212.csv.gz"}},{"accession":"PRJEB46777","age_categories":{"adult":89},"countries":{"NL":89},"first_public_year":"2022","gbp_per_sample_median":5.36,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"randomized_controlled_trial","intervention_detail":"FMT via nasoduodenal tube vs autologous (control) in UC, double-blind RCT","interventions":["fmt"],"n_samples":89,"papers":[{"doi":"10.1053/j.gastro.2015.03.045","pmcid":null,"pmid":"25836986","title":"Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients With Ulcerative Colitis."},{"doi":"10.1038/s41591-022-01913-0","pmcid":"PMC9499871","pmid":"36109636","title":"Drivers and determinants of strain dynamics following fecal microbiota transplantation."},{"doi":"10.1186/s40168-023-01623-w","pmcid":"PMC10424414","pmid":"37580821","title":"Recipient-independent, high-accuracy FMT-response prediction and optimization in mice and humans."}],"sample_intervention_arms":{},"sex":{},"title":"Fecal Microbiota Transplantation for Ulcerative Colitis.","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB46777","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB46777_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB46777.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB46777.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB46777.csv.gz"}},{"accession":"PRJNA813736","age_categories":{"adult":87},"countries":{"IE":87},"first_public_year":"2022","gbp_per_sample_median":1.86,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":19,"healthy_control":48,"ulcerative_colitis":20},"intervention_design":"observational_with_procedure","intervention_detail":"Faecal microbiota transplant cohorts compared for plasmidome diversity restoration","interventions":["fmt"],"n_samples":87,"papers":[{"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":39,"male":41},"title":"Whole genome sequencing of the faecal microbiomes from healthy controls and patients with inflammatory bowel disease","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA813736","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA813736_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA813736.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA813736.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA813736.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":"PRJNA1043691","age_categories":{"child":84},"countries":{"SA":84},"first_public_year":"2024","gbp_per_sample_median":3.2,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":41,"ulcerative_colitis":43},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":84,"papers":[{"doi":"10.4103/sjg.sjg_221_24","pmcid":"PMC11804965","pmid":"39523762","title":"Gut fungal profile in new onset treatment-naïve ulcerative colitis in Saudi children."},{"doi":"10.4103/sjg.sjg_66_24","pmcid":"PMC11804967","pmid":"38708883","title":"Bacterial dysbiosis in newly diagnosed treatment naïve pediatric ulcerative colitis in Saudi Arabia."},{"doi":"10.4103/sjg.sjg_24_25","pmcid":"PMC12352812","pmid":"40223739","title":"Gut virome profile in new onset treatment naïve Saudi children with ulcerative colitis."}],"sample_intervention_arms":{},"sex":{},"title":"Microbiota Profile in Saudi Children with Ulcerative Colitis","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1043691","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1043691_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1043691.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1043691.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1043691.csv.gz"}},{"accession":"PRJNA905698","age_categories":{"unknown":84},"countries":{"US":84},"first_public_year":"2023","gbp_per_sample_median":0.78,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":24,"healthy_control":30,"ulcerative_colitis":30},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":84,"papers":[{"doi":"10.1126/sciadv.add8766","pmcid":"PMC10381928","pmid":"37506208","title":"Lectin-Seq: A method to profile lectin-microbe interactions in native communities."}],"sample_intervention_arms":{},"sex":{},"title":"Lectin-Seq: a method to profile lectin-microbe interactions in native communities","trial_population_condition":"healthy_control","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA905698","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA905698_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA905698.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA905698.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA905698.csv.gz"}},{"accession":"PRJNA1066476","age_categories":{"adult":83},"countries":{"CN":83},"first_public_year":"2024","gbp_per_sample_median":6.01,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"ulcerative_colitis":75},"intervention_design":"single_arm_before_after","intervention_detail":"Capsulized fecal microbiota transplantation in active ulcerative colitis patients","interventions":["fmt"],"n_samples":83,"papers":[{"doi":"10.3389/fcimb.2022.1086885","pmcid":"PMC9849685","pmid":"36683707","title":"Specific fungi associated with response to capsulized fecal microbiota transplantation in patients with active ulcerative colitis."},{"doi":"10.1128/spectrum.04152-22","pmcid":"PMC10269780","pmid":"37093057","title":"Capsulized Fecal Microbiota Transplantation Induces Remission in Patients with Ulcerative Colitis by Gut Microbial Colonization and Metabolite Regulation."}],"sample_intervention_arms":{"fmt":55,"no_intervention":28},"sex":{},"title":"Profiling the gut microbiome of patients with active ulcerative colitis received capsulized fecal microbiota transplantation","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1066476","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1066476_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1066476.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1066476.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1066476.csv.gz"}},{"accession":"PRJNA1173388","age_categories":{"unknown":82},"countries":{"SG":82},"first_public_year":"2025","gbp_per_sample_median":6.57,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":31,"healthy_control":22,"ulcerative_colitis":29},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":82,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Metagenomes from an inflammatory bowel disease cohort","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1173388","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1173388_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1173388.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1173388.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1173388.csv.gz"}},{"accession":"PRJNA564995","age_categories":{"child":82},"countries":{"US":82},"first_public_year":"2020","gbp_per_sample_median":0.53,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":32,"healthy_control":23,"ibd_unspecified":26,"ulcerative_colitis":1},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":82,"papers":[{"doi":"10.1093/ecco-jcc/jjaa094","pmcid":"PMC7648169","pmid":"32406906","title":"Dynamics of the Stool Virome in Very Early-Onset Inflammatory Bowel Disease."}],"sample_intervention_arms":{},"sex":{},"title":"Gut virome in VEO-IBD","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA564995","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA564995_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA564995.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA564995.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA564995.csv.gz"}},{"accession":"PRJNA429990","age_categories":{"unknown":81},"countries":{"CN":81},"first_public_year":"2018","gbp_per_sample_median":9.15,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":41,"healthy_control":15,"ulcerative_colitis":25},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":81,"papers":[{"doi":"10.1016/j.chom.2021.11.001","pmcid":"PMC8785648","pmid":"34822777","title":"Human gut bacterial metabolism drives Th17 activation and colitis."},{"doi":"10.1038/s41467-022-34405-3","pmcid":"PMC9649010","pmid":"36357393","title":"Faecal microbiome-based machine learning for multi-class disease diagnosis."},{"doi":"10.1016/j.ebiom.2024.105296","pmcid":"PMC11402190","pmid":"39216231","title":"Gut bacterial type III secretion systems aggravate colitis in mice and serve as biomarkers of Crohn's disease."},{"doi":"10.1038/s41591-024-03280-4","pmcid":"PMC11645270","pmid":"39367251","title":"Noninvasive, microbiome-based diagnosis of inflammatory bowel disease."},{"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":{},"title":"human gut metagenome Raw sequence reads","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA429990","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA429990_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA429990.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA429990.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA429990.csv.gz"}},{"accession":"PRJNA1064103","age_categories":{"unknown":80},"countries":{"US":80},"first_public_year":"2024","gbp_per_sample_median":0.55,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":50,"ulcerative_colitis":15},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":80,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Metagenomics of Colonoscopic Rinsates: Investigating Microbial Patterns in Inflammatory Bowel Disease","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1064103","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1064103_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1064103.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1064103.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1064103.csv.gz"}},{"accession":"PRJEB101774","age_categories":{"adult":79},"countries":{"DE":79},"first_public_year":"2025","gbp_per_sample_median":12.1,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":32,"ulcerative_colitis":26},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":79,"papers":[{"doi":"10.1038/s41598-026-63156-0","pmcid":"PMC13388663","pmid":"42481656","title":"Loss of TGR5-activating bile acids is associated with disease activity in inflammatory bowel disease."}],"sample_intervention_arms":{},"sex":{},"title":"Metagenomes and bile acid profiles in IBD","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB101774","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB101774_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB101774.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB101774.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB101774.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":"PRJNA1371390","age_categories":{"adult":73},"countries":{"KR":73},"first_public_year":"2026","gbp_per_sample_median":11.45,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":36,"ulcerative_colitis":37},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":73,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Human gut virome in ulcerative colitis","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1371390","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1371390_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1371390.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1371390.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1371390.csv.gz"}},{"accession":"PRJNA474024","age_categories":{"unknown":72},"countries":{"US":72},"first_public_year":"2019","gbp_per_sample_median":0.08,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ibd_unspecified":72},"intervention_design":"single_arm_before_after","intervention_detail":"Endoscopic FMT then oral capsule maintenance for 12 weeks","interventions":["fmt"],"n_samples":72,"papers":[{"doi":"10.1126/science.aau5238","pmcid":"PMC6543533","pmid":"30630933","title":"Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut."}],"sample_intervention_arms":{},"sex":{},"title":"Engraftment of Bacteroidetes species in a Fecal Microbiota Transplant study","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA474024","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA474024_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA474024.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA474024.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA474024.csv.gz"}},{"accession":"PRJNA647221","age_categories":{"adult":68},"countries":{},"first_public_year":"2024","gbp_per_sample_median":9.15,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":68},"intervention_design":"single_arm_before_after","intervention_detail":"Fecal microbiota transplantation in ulcerative colitis patients","interventions":["fmt"],"n_samples":68,"papers":[{"doi":"10.5009/gnl210369","pmcid":"PMC9474483","pmid":"35975640","title":"Exploration of Potential Gut Microbiota-Derived Biomarkers to Predict the Success of Fecal Microbiota Transplantation in Ulcerative Colitis: A Prospective Cohort in Korea."}],"sample_intervention_arms":{},"sex":{},"title":"Before and after fecal microbiota transplantation in ulcerative colitis patients","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA647221","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA647221_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA647221.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA647221.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA647221.csv.gz"}},{"accession":"PRJNA1220173","age_categories":{"unknown":65},"countries":{"CA":65},"first_public_year":"2025","gbp_per_sample_median":6.02,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":true,"health_conditions":{"healthy_control":4,"ulcerative_colitis":61},"intervention_design":"randomized_controlled_trial","intervention_detail":"FMT from single donor vs placebo in ulcerative colitis","interventions":["fmt"],"n_samples":65,"papers":[{"doi":"10.1038/s41467-025-58673-x","pmcid":"PMC11992129","pmid":"40216789","title":"Detecting microbial engraftment after FMT using placebo sequencing and culture enriched metagenomics to sort signals from noise."}],"sample_intervention_arms":{"fmt":12,"placebo":24},"sex":{},"title":"Detecting microbial engraftment after FMT in patients with ulcerative colitis","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1220173","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1220173_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1220173.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1220173.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1220173.csv.gz"}},{"accession":"PRJNA768409","age_categories":{"unknown":59},"countries":{"US":59},"first_public_year":"2021","gbp_per_sample_median":22.04,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"ulcerative_colitis":59},"intervention_design":"single_arm_before_after","intervention_detail":"Fecal microbiota transplantation, 2-donor preparation, sampled pre- and week 4 post-FMT","interventions":["fmt"],"n_samples":59,"papers":[{"doi":"10.1053/j.gastro.2021.09.061","pmcid":"PMC8678328","pmid":"34606847","title":"Transferable Immunoglobulin A-Coated Odoribacter splanchnicus in Responders to Fecal Microbiota Transplantation for Ulcerative Colitis Limits Colonic Inflammation."}],"sample_intervention_arms":{"fmt":19,"no_intervention":20},"sex":{},"title":"Metagenomic sequencing of UC patients subjected to FMT and FMT-donors","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA768409","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA768409_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA768409.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA768409.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA768409.csv.gz"}},{"accession":"PRJNA730677","age_categories":{"unknown":58},"countries":{"IL":58},"first_public_year":"2022","gbp_per_sample_median":5.5,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":27,"other_disease":10,"ulcerative_colitis":21},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":58,"papers":[{"doi":"10.1093/ecco-jcc/jjac071","pmcid":null,"pmid":"35560165","title":"Escherichia coli Strains from Patients with Inflammatory Bowel Diseases have Disease-specific Genomic Adaptations."}],"sample_intervention_arms":{},"sex":{},"title":"Genomic adaptations of Escherichia coli strains from patients with inflammatory bowel diseases","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA730677","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA730677_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA730677.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA730677.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA730677.csv.gz"}},{"accession":"PRJNA759642","age_categories":{"adolescent":18,"adult":32,"child":7},"countries":{"US":57},"first_public_year":"2021","gbp_per_sample_median":1.0,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":27,"ulcerative_colitis":8},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":57,"papers":[{"doi":"10.1038/s41598-022-07995-7","pmcid":"PMC9018687","pmid":"35440670","title":"16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis."},{"doi":"10.1016/j.isci.2024.111442","pmcid":"PMC11650326","pmid":"39691780","title":"Gut-microbiota-based ensemble model predicts prognosis of pediatric inflammatory bowel disease."},{"doi":"10.1016/j.xcrm.2025.102516","pmcid":"PMC12866134","pmid":"41421350","title":"Integrative multi-omics reveals microbial genomic variants driving altered host-microbe interactions in autism spectrum disorder."}],"sample_intervention_arms":{},"sex":{"female":17,"male":18},"title":"16s and shotgun sequencing from human faecal","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA759642","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA759642_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA759642.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA759642.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA759642.csv.gz"}},{"accession":"PRJNA763503","age_categories":{"unknown":56},"countries":{"RU":56},"first_public_year":"2021","gbp_per_sample_median":1.39,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":24,"healthy_control":5,"ulcerative_colitis":24},"intervention_design":"single_arm_before_after","intervention_detail":"FMT combined with anti-inflammatory therapy in CD/UC patients","interventions":["fmt"],"n_samples":56,"papers":[{"doi":"10.21203/rs.3.rs-999905/v1","pmcid":null,"pmid":null,"title":"Character of Microbial Engraftment Following the Fecal Microbiota Transplantation in Patients with Inflammatory Bowel Diseases"}],"sample_intervention_arms":{},"sex":{},"title":"Character of microbial engraftment following the fecal microbiota transplantation in patients with inflammatory bowel diseases","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA763503","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA763503_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA763503.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA763503.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA763503.csv.gz"}},{"accession":"PRJNA690735","age_categories":{"unknown":52},"countries":{"CA":52},"first_public_year":"2021","gbp_per_sample_median":13.74,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":20,"healthy_control":15,"ulcerative_colitis":17},"intervention_design":"randomized_controlled_trial","intervention_detail":"β-fructan (oligofructose) fiber supplementation in IBD RCT","interventions":["prebiotic_or_fibre"],"n_samples":52,"papers":[{"doi":"10.1053/j.gastro.2022.09.034","pmcid":null,"pmid":"36183751","title":"Unfermented ß-fructan Fibers Fuel Inflammation in Select Inflammatory Bowel Disease Patients."}],"sample_intervention_arms":{},"sex":{},"title":"Dietary Fibers Promote Inflammation in Inflammatory Bowel Diseases","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA690735","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA690735_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA690735.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA690735.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA690735.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":"PRJNA480674","age_categories":{"child":42},"countries":{"CA":42},"first_public_year":"2019","gbp_per_sample_median":0.2,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":27,"healthy_control":6,"ulcerative_colitis":9},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":42,"papers":[{"doi":"10.1186/s40168-018-0604-3","pmcid":"PMC6317230","pmid":"30606251","title":"Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases."}],"sample_intervention_arms":{},"sex":{},"title":"mmunoglobulin G Selectively Identifies Pathobionts in Pediatric Inflammatory Bowel Diseases","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA480674","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA480674_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA480674.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA480674.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA480674.csv.gz"}},{"accession":"PRJNA285502","age_categories":{"adult":41},"countries":{"US":41},"first_public_year":"2017","gbp_per_sample_median":4.25,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":41},"intervention_design":"single_arm_before_after","intervention_detail":"Single colonoscopic FMT administration in UC patients","interventions":["fmt"],"n_samples":41,"papers":[{"doi":"10.1371/journal.pone.0133925","pmcid":"PMC4544847","pmid":"26288277","title":"Low Level Engraftment and Improvement following a Single Colonoscopic Administration of Fecal Microbiota to Patients with Ulcerative Colitis."},{"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":{},"sex":{},"title":"Fecal microbiota transplantation (FMT) for ulcerative colitis","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA285502","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA285502_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA285502.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA285502.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA285502.csv.gz"}},{"accession":"PRJNA576887","age_categories":{"unknown":41},"countries":{"US":41},"first_public_year":"2020","gbp_per_sample_median":2.1,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":20,"ulcerative_colitis":21},"intervention_design":"none","intervention_detail":"Wrist actigraphy monitoring for 2 weeks to assess circadian rest-activity cycles; no therapeutic intervention given","interventions":[],"n_samples":41,"papers":[{"doi":"10.3389/fmed.2021.770491","pmcid":"PMC8900134","pmid":"35265631","title":"Disrupted Circadian Rest-Activity Cycles in Inflammatory Bowel Disease Are Associated With Aggressive Disease Phenotype, Subclinical Inflammation, and Dysbiosis."}],"sample_intervention_arms":{},"sex":{},"title":"Circadian Misalignment as a disease risk factor in Inflammatory Bowel Disease","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA576887","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA576887_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA576887.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA576887.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA576887.csv.gz"}},{"accession":"PRJNA983946","age_categories":{"adult":41},"countries":{"IN":41},"first_public_year":"2024","gbp_per_sample_median":13.38,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":14,"ulcerative_colitis":27},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":41,"papers":[],"sample_intervention_arms":{},"sex":{"male":41},"title":"Human gut metagenome of ulcerative colitis and healthy stool samples from Northern India","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA983946","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA983946_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA983946.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA983946.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA983946.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 <i>Akkermansia</i> 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":"PRJNA1302166","age_categories":{"unknown":38},"countries":{"IL":38},"first_public_year":"2026","gbp_per_sample_median":1.05,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":38,"papers":[{"doi":"10.1016/j.celrep.2026.117478","pmcid":null,"pmid":"42228562","title":"Antibiotic disruption of the gut microbiome triggers IBD-like proteolytic activity."}],"sample_intervention_arms":{},"sex":{},"title":"Metagenomic analysis of non-IBD, UC and pouchitis patients stool samples berfore and on antibiotics treatment","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1302166","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1302166_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1302166.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1302166.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1302166.csv.gz"}},{"accession":"PRJNA1160849","age_categories":{"child":37},"countries":{"CA":37},"first_public_year":"2025","gbp_per_sample_median":9.15,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":24,"ulcerative_colitis":8},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":37,"papers":[{"doi":"10.1152/ajpgi.00080.2026","pmcid":null,"pmid":"42531280","title":"Host-microbe interactions in the appendix of children with inflammatory bowel diseases."}],"sample_intervention_arms":{},"sex":{"female":8,"male":29},"title":"Metagenomic profiling on pediatric IBD patients from different anatomic sites","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1160849","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1160849_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1160849.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1160849.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1160849.csv.gz"}},{"accession":"PRJNA929645","age_categories":{"unknown":32},"countries":{},"first_public_year":"2024","gbp_per_sample_median":11.48,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":32},"intervention_design":"single_arm_before_after","intervention_detail":"Washed microbiota transplantation (WMT) in UC patients","interventions":["fmt"],"n_samples":32,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Microbiota Genome sequencing","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA929645","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA929645_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA929645.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA929645.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA929645.csv.gz"}},{"accession":"PRJEB50699","age_categories":{"unknown":31},"countries":{},"first_public_year":"2022","gbp_per_sample_median":15.45,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":31},"intervention_design":"randomized_controlled_trial","intervention_detail":"Lyophilised oral FMT donor samples, double-blind RCT in ulcerative colitis","interventions":["fmt"],"n_samples":31,"papers":[{"doi":"10.1128/msystems.00746-24","pmcid":"PMC11406951","pmid":"39136455","title":"Refining microbial community metabolic models derived from metagenomics using reference-based taxonomic profiling."},{"doi":"10.1371/journal.pcbi.1013470","pmcid":"PMC12507277","pmid":"40934284","title":"kMermaid: Ultrafast metagenomic read assignment to protein clusters by hashing of amino acid k-mer frequencies."},{"doi":"10.1038/s41467-024-53454-4","pmcid":"PMC11487140","pmid":"39420033","title":"The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission."},{"doi":"10.1128/msystems.00991-25","pmcid":"PMC12542657","pmid":"40952001","title":"Bacterial taxonomic and functional changes following oral lyophilized donor fecal microbiota transplantation in patients with ulcerative colitis."}],"sample_intervention_arms":{},"sex":{},"title":"Donor samples from Lyophilised oral faecal microbiota transplantation for ulcerative colitis (LOTUS) study shotgun","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB50699","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB50699_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB50699.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB50699.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB50699.csv.gz"}},{"accession":"PRJNA1241499","age_categories":{"adolescent":19,"child":11},"countries":{"US":30},"first_public_year":"2026","gbp_per_sample_median":7.2,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":10,"healthy_control":4,"other_disease":2,"ulcerative_colitis":13},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":30,"papers":[{"doi":"10.3390/biom15050746","pmcid":"PMC12109367","pmid":"40427639","title":"Multiomics-Based Profiling of the Fecal Microbiome Reveals Potential Disease-Specific Signatures in Pediatric IBD (PIBD)."}],"sample_intervention_arms":{},"sex":{"female":18,"male":12},"title":"Pediatric IBD Shotgun Metagenomics, Metatranscriptomics, and 16S rRNA","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1241499","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1241499_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1241499.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1241499.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1241499.csv.gz"}},{"accession":"PRJNA1088910","age_categories":{"unknown":28},"countries":{"KR":28},"first_public_year":"2024","gbp_per_sample_median":10.92,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":28,"papers":[{"doi":"10.1038/s41522-025-00686-x","pmcid":"PMC11993755","pmid":"40221450","title":"Refining microbiome diversity analysis by concatenating and integrating dual 16S rRNA amplicon reads."}],"sample_intervention_arms":{},"sex":{},"title":"Combined Analysis of Dual 16S rRNA Amplicon Sequences Through Concatenation of Paired-End Reads Enhances Microbiome Diversity and Functional profilinig_WMS","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1088910","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1088910_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1088910.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1088910.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1088910.csv.gz"}},{"accession":"PRJNA1333319","age_categories":{"unknown":27},"countries":{"DE":27},"first_public_year":"2026","gbp_per_sample_median":2.31,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_cancer":3,"healthy_control":3,"ulcerative_colitis":3},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":27,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Phage bacteria interaction networks differentiate ulcerative colitis and colorectal cancer from the healthy gut","trial_population_condition":"colorectal_cancer","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1333319","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1333319_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1333319.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1333319.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1333319.csv.gz"}},{"accession":"PRJNA1517182","age_categories":{"adult":27},"countries":{"CN":27},"first_public_year":"2026","gbp_per_sample_median":11.39,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":15,"ulcerative_colitis":12},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":27,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"Fecal metagenomic sequencing","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1517182","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1517182_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1517182.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1517182.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1517182.csv.gz"}},{"accession":"PRJEB44121","age_categories":{"infant":26},"countries":{"US":26},"first_public_year":"2021","gbp_per_sample_median":3.76,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"colorectal_adenoma":2,"colorectal_cancer":2,"crohns_disease":8,"ibd_unspecified":1,"other_disease":5,"ulcerative_colitis":8},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":26,"papers":[{"doi":"10.1126/sciimmunol.abn6660","pmcid":"PMC9416881","pmid":"35394816","title":"Human enteric viruses autonomously shape inflammatory bowel disease phenotype through divergent innate immunomodulation."}],"sample_intervention_arms":{},"sex":{"female":1},"title":"Human enteric viruses shape disease phenotype through divergent innate immunomodulation","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB44121","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB44121_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB44121.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB44121.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB44121.csv.gz"}},{"accession":"PRJEB46780","age_categories":{"unknown":26},"countries":{"AU":26},"first_public_year":"2022","gbp_per_sample_median":3.43,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"healthy_control":2},"intervention_design":"single_arm_before_after","intervention_detail":"Fecal microbiota transplantation for recurrent C. difficile infection or ulcerative colitis","interventions":["fmt"],"n_samples":26,"papers":[{"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":24},"sex":{},"title":"Fecal Microbiota Transplantation for Ulcerative Colitis and C. difficile Infection.","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB46780","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB46780_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB46780.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB46780.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB46780.csv.gz"}},{"accession":"PRJEB76677","age_categories":{"child":24},"countries":{"DE":24},"first_public_year":"2024","gbp_per_sample_median":5.63,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":7,"healthy_control":12,"ulcerative_colitis":5},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":24,"papers":[{"doi":"10.1152/ajpgi.00293.2016","pmcid":null,"pmid":"28039159","title":"Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis."}],"sample_intervention_arms":{},"sex":{},"title":"Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis.","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB76677","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB76677_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB76677.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB76677.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB76677.csv.gz"}},{"accession":"PRJNA391511","age_categories":{"child":24},"countries":{"US":24},"first_public_year":"2017","gbp_per_sample_median":0.11,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":24,"papers":[{"doi":"10.1097/mpg.0000000000002140","pmcid":"PMC6310095","pmid":"30169455","title":"Enteric Virome and Bacterial Microbiota in Children With Ulcerative Colitis and Crohn Disease."},{"doi":"10.3389/fmicb.2023.1078760","pmcid":"PMC9902911","pmid":"36760501","title":"Evaluation of computational phage detection tools for metagenomic datasets."}],"sample_intervention_arms":{},"sex":{},"title":"UCSF-BSRI IBD-Ulcerative colitis human fecal virome","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA391511","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA391511_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA391511.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA391511.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA391511.csv.gz"}},{"accession":"PRJNA398187","age_categories":{"unknown":22},"countries":{},"first_public_year":"2020","gbp_per_sample_median":4.43,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":3,"ulcerative_colitis":16},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":22,"papers":[{"doi":"10.1186/s12864-019-6427-1","pmcid":"PMC6967091","pmid":"31952477","title":"Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences."},{"doi":"10.1038/s41467-020-15342-5","pmcid":"PMC7089947","pmid":"32251296","title":"Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease."},{"doi":"10.3389/fmicb.2022.961020","pmcid":"PMC9614153","pmid":"36312950","title":"Strain level and comprehensive microbiome analysis in inflammatory bowel disease via multi-technology meta-analysis identifies key bacterial influencers of disease."},{"doi":"10.1080/19490976.2025.2450207","pmcid":"PMC11740686","pmid":"39812341","title":"Host-microbe multi-omics and succinotype profiling have prognostic value for future relapse in patients with inflammatory bowel disease."},{"doi":"10.1017/gmb.2025.10012","pmcid":"PMC12455517","pmid":"40994617","title":"Human DNA hijacking microbiota surveys: causes and consequences in colon related 16s rRNA amplicon sequencing."}],"sample_intervention_arms":{},"sex":{},"title":"Human gut metagenome Targeted loci environmental","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA398187","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA398187_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA398187.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA398187.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA398187.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":"PRJDB43252","age_categories":{"unknown":12},"countries":{"CN":12},"first_public_year":"2026","gbp_per_sample_median":7.36,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":3,"ulcerative_colitis":3},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":12,"papers":[{"doi":"10.3389/fmicb.2024.1375804","pmcid":"PMC10999624","pmid":"38591039","title":"Integrated 16S rRNA sequencing and metagenomics insights into microbial dysbiosis and distinct virulence factors in inflammatory bowel disease."}],"sample_intervention_arms":{},"sex":{},"title":"Integrated 16S rRNA sequencing and metagenomics insights into microbial dysbiosis and distinct virulence factors in inflammatory bowel disease (PRJCA023147)","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJDB43252","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB43252_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJDB43252.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJDB43252.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJDB43252.csv.gz"}},{"accession":"PRJNA438164","age_categories":{"child":12},"countries":{"US":12},"first_public_year":"2018","gbp_per_sample_median":0.35,"has_cases_and_healthy_controls":true,"has_treated_and_control_arms":true,"health_conditions":{"healthy_control":4,"ulcerative_colitis":8},"intervention_design":"single_arm_before_after","intervention_detail":"Fecal microbiota transplantation in pediatric ulcerative colitis","interventions":["fmt"],"n_samples":12,"papers":[{"doi":"10.1093/femsec/fiy133","pmcid":"PMC6454419","pmid":"30010747","title":"Gut microbial and metabolomic profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients."},{"doi":"10.1128/spectrum.02159-21","pmcid":"PMC9927247","pmid":"36472435","title":"A Matching Strategy To Guide Donor Selection for Ulcerative Colitis in Fecal Microbiota Transplantation: Meta-Analysis and Analytic Hierarchy Process."},{"doi":"10.1016/j.isci.2024.111442","pmcid":"PMC11650326","pmid":"39691780","title":"Gut-microbiota-based ensemble model predicts prognosis of pediatric inflammatory bowel disease."},{"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":4,"no_intervention":4,"placebo":4},"sex":{},"title":"Gut microbial profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA438164","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA438164_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA438164.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA438164.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA438164.csv.gz"}},{"accession":"PRJNA1521393","age_categories":{"adult":11},"countries":{"RU":11},"first_public_year":"2026","gbp_per_sample_median":0.29,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":true,"health_conditions":{"healthy_control":1,"ulcerative_colitis":9},"intervention_design":"single_arm_before_after","intervention_detail":"Sterile fecal filtrate transfer (filtrate FMT) from healthy donors to UC patients","interventions":["fmt"],"n_samples":11,"papers":[],"sample_intervention_arms":{"no_intervention":3,"other_intervention":6},"sex":{},"title":"First clinical cases of effective sterile fecal filtrate transfer for ulcerative colitis treatment: microbiome and virome shifts","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1521393","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1521393_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1521393.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1521393.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1521393.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":"PRJNA1009084","age_categories":{"unknown":9},"countries":{"US":9},"first_public_year":"2024","gbp_per_sample_median":0.56,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{},"intervention_design":"observational_with_procedure","intervention_detail":"","interventions":[],"n_samples":9,"papers":[{"doi":"10.1080/19490976.2024.2361493","pmcid":"PMC11225921","pmid":"38958039","title":"Disruption of intestinal oxygen balance in acute colitis alters the gut microbiome."}],"sample_intervention_arms":{},"sex":{},"title":"Disruption of intestinal oxygen balance in acute colitis alters the gut microbiome","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1009084","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1009084_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1009084.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1009084.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1009084.csv.gz"}},{"accession":"PRJNA732769","age_categories":{"adult":9},"countries":{"CA":9},"first_public_year":"2021","gbp_per_sample_median":0.09,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":5},"intervention_design":"non_randomized_controlled","intervention_detail":"Fecal VLP (phage) transplant from UC patients or healthy controls into HMA mice, +/- DSS colitis","interventions":["fmt","phage_therapy"],"n_samples":9,"papers":[{"doi":"10.1186/s40168-022-01275-2","pmcid":"PMC9264660","pmid":"35799219","title":"Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis."}],"sample_intervention_arms":{},"sex":{},"title":"The impact of bacteriophages on DSS-colitis and microbiota composition - VLP shotgun","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA732769","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA732769_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA732769.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA732769.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA732769.csv.gz"}},{"accession":"PRJNA975689","age_categories":{"adult":8},"countries":{"KR":8},"first_public_year":"2026","gbp_per_sample_median":12.02,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"crohns_disease":4,"ulcerative_colitis":4},"intervention_design":"none","intervention_detail":"","interventions":[],"n_samples":8,"papers":[{"doi":"10.3389/fmicb.2025.1538620","pmcid":"PMC11884817","pmid":"40051478","title":"Culture-based characterization of gut microbiota in inflammatory bowel disease."}],"sample_intervention_arms":{},"sex":{},"title":"Culturomics and metagenomics studies of gut microbial diversity in IBD patients","trial_population_condition":"ibd_unspecified","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA975689","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA975689_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA975689.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA975689.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA975689.csv.gz"}},{"accession":"PRJNA1480958","age_categories":{"unknown":7},"countries":{"CN":7},"first_public_year":"2026","gbp_per_sample_median":106.73,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":7},"intervention_design":"single_arm_before_after","intervention_detail":"Fecal microbiota transplantation, 3 FMTs in UC patients","interventions":["fmt"],"n_samples":7,"papers":[],"sample_intervention_arms":{},"sex":{},"title":"PacBio Long-reads Sequencing for FMT","trial_population_condition":"ulcerative_colitis","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJNA1480958","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1480958_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJNA1480958.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJNA1480958.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJNA1480958.csv.gz"}},{"accession":"PRJEB34939","age_categories":{"adult":5},"countries":{"SE":3},"first_public_year":"2019","gbp_per_sample_median":0.91,"has_cases_and_healthy_controls":false,"has_treated_and_control_arms":false,"health_conditions":{"ulcerative_colitis":5},"intervention_design":"unknown","intervention_detail":"","interventions":[],"n_samples":5,"papers":[{"doi":"10.1038/s42003-020-01214-7","pmcid":"PMC7474095","pmid":"32887924","title":"Genome sequence of segmented filamentous bacteria present in the human intestine."}],"sample_intervention_arms":{},"sex":{"male":5},"title":"Ileostomy content from a colectomised Swedish adult individual","trial_population_condition":"unknown","urls":{"ena":"https://www.ebi.ac.uk/ena/browser/view/PRJEB34939","evidence_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB34939_determinations.csv.gz","page":"https://olmlab.github.io/microbiome_repo/studies/PRJEB34939.html","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/PRJEB34939.csv","samples_full_csv_gz":"https://olmlab.github.io/microbiome_repo/data/studies/PRJEB34939.csv.gz"}}],"release":"R2026.25"}