{"base_url":"https://olmlab.github.io/microbiome_repo/","counts":{"age":{"adolescent":162,"adult":1347,"child":263,"elderly":402,"infant":311,"neonate":135},"conditions":{"allergy_or_atopy":49,"autoimmune_inflammatory":105,"cardiometabolic_other":103,"colorectal_adenoma":35,"colorectal_cancer":108,"crohns_disease":108,"gi_infection_or_diarrhoea":193,"healthy_control":1235,"ibd_or_gi_disease":14,"ibd_unspecified":86,"ibs":52,"intervention_cohort":14,"kidney_disease":27,"liver_disease":94,"malnutrition":26,"nec":13,"neurological_psychiatric":189,"obesity":117,"other_cancer":177,"other_disease":267,"other_infection":154,"pregnancy_postpartum":64,"preterm_nicu":83,"sepsis_or_infection":20,"transplant_or_immunocompromised":98,"type1_diabetes":24,"type2_diabetes":85,"ulcerative_colitis":102},"interventions":{"antibiotic":120,"bowel_preparation":10,"diet_intervention":152,"dietary_supplement":56,"drug_therapy":126,"exercise":16,"fmt":166,"live_biotherapeutic":13,"other_intervention":61,"phage_therapy":4,"prebiotic_or_fibre":66,"probiotic":100,"surgery":60,"synbiotic":18,"vaccine":18},"projects":2798},"description":"Evidence-linked metadata for public human gut shotgun metagenomes (all ages). A project = an INSDC BioProject; a sample = a BioSample (rarely a run).","endpoints":{"by_age":{"adolescent":"https://olmlab.github.io/microbiome_repo/api/by-age/adolescent.json","adult":"https://olmlab.github.io/microbiome_repo/api/by-age/adult.json","child":"https://olmlab.github.io/microbiome_repo/api/by-age/child.json","elderly":"https://olmlab.github.io/microbiome_repo/api/by-age/elderly.json","infant":"https://olmlab.github.io/microbiome_repo/api/by-age/infant.json","neonate":"https://olmlab.github.io/microbiome_repo/api/by-age/neonate.json"},"by_condition":{"allergy_or_atopy":"https://olmlab.github.io/microbiome_repo/api/by-condition/allergy_or_atopy.json","autoimmune_inflammatory":"https://olmlab.github.io/microbiome_repo/api/by-condition/autoimmune_inflammatory.json","cardiometabolic_other":"https://olmlab.github.io/microbiome_repo/api/by-condition/cardiometabolic_other.json","colorectal_adenoma":"https://olmlab.github.io/microbiome_repo/api/by-condition/colorectal_adenoma.json","colorectal_cancer":"https://olmlab.github.io/microbiome_repo/api/by-condition/colorectal_cancer.json","crohns_disease":"https://olmlab.github.io/microbiome_repo/api/by-condition/crohns_disease.json","gi_infection_or_diarrhoea":"https://olmlab.github.io/microbiome_repo/api/by-condition/gi_infection_or_diarrhoea.json","healthy_control":"https://olmlab.github.io/microbiome_repo/api/by-condition/healthy_control.json","ibd_or_gi_disease":"https://olmlab.github.io/microbiome_repo/api/by-condition/ibd_or_gi_disease.json","ibd_unspecified":"https://olmlab.github.io/microbiome_repo/api/by-condition/ibd_unspecified.json","ibs":"https://olmlab.github.io/microbiome_repo/api/by-condition/ibs.json","intervention_cohort":"https://olmlab.github.io/microbiome_repo/api/by-condition/intervention_cohort.json","kidney_disease":"https://olmlab.github.io/microbiome_repo/api/by-condition/kidney_disease.json","liver_disease":"https://olmlab.github.io/microbiome_repo/api/by-condition/liver_disease.json","malnutrition":"https://olmlab.github.io/microbiome_repo/api/by-condition/malnutrition.json","nec":"https://olmlab.github.io/microbiome_repo/api/by-condition/nec.json","neurological_psychiatric":"https://olmlab.github.io/microbiome_repo/api/by-condition/neurological_psychiatric.json","obesity":"https://olmlab.github.io/microbiome_repo/api/by-condition/obesity.json","other_cancer":"https://olmlab.github.io/microbiome_repo/api/by-condition/other_cancer.json","other_disease":"https://olmlab.github.io/microbiome_repo/api/by-condition/other_disease.json","other_infection":"https://olmlab.github.io/microbiome_repo/api/by-condition/other_infection.json","pregnancy_postpartum":"https://olmlab.github.io/microbiome_repo/api/by-condition/pregnancy_postpartum.json","preterm_nicu":"https://olmlab.github.io/microbiome_repo/api/by-condition/preterm_nicu.json","sepsis_or_infection":"https://olmlab.github.io/microbiome_repo/api/by-condition/sepsis_or_infection.json","transplant_or_immunocompromised":"https://olmlab.github.io/microbiome_repo/api/by-condition/transplant_or_immunocompromised.json","type1_diabetes":"https://olmlab.github.io/microbiome_repo/api/by-condition/type1_diabetes.json","type2_diabetes":"https://olmlab.github.io/microbiome_repo/api/by-condition/type2_diabetes.json","ulcerative_colitis":"https://olmlab.github.io/microbiome_repo/api/by-condition/ulcerative_colitis.json"},"by_intervention":{"antibiotic":"https://olmlab.github.io/microbiome_repo/api/by-intervention/antibiotic.json","bowel_preparation":"https://olmlab.github.io/microbiome_repo/api/by-intervention/bowel_preparation.json","diet_intervention":"https://olmlab.github.io/microbiome_repo/api/by-intervention/diet_intervention.json","dietary_supplement":"https://olmlab.github.io/microbiome_repo/api/by-intervention/dietary_supplement.json","drug_therapy":"https://olmlab.github.io/microbiome_repo/api/by-intervention/drug_therapy.json","exercise":"https://olmlab.github.io/microbiome_repo/api/by-intervention/exercise.json","fmt":"https://olmlab.github.io/microbiome_repo/api/by-intervention/fmt.json","live_biotherapeutic":"https://olmlab.github.io/microbiome_repo/api/by-intervention/live_biotherapeutic.json","other_intervention":"https://olmlab.github.io/microbiome_repo/api/by-intervention/other_intervention.json","phage_therapy":"https://olmlab.github.io/microbiome_repo/api/by-intervention/phage_therapy.json","prebiotic_or_fibre":"https://olmlab.github.io/microbiome_repo/api/by-intervention/prebiotic_or_fibre.json","probiotic":"https://olmlab.github.io/microbiome_repo/api/by-intervention/probiotic.json","surgery":"https://olmlab.github.io/microbiome_repo/api/by-intervention/surgery.json","synbiotic":"https://olmlab.github.io/microbiome_repo/api/by-intervention/synbiotic.json","vaccine":"https://olmlab.github.io/microbiome_repo/api/by-intervention/vaccine.json"},"projects":"https://olmlab.github.io/microbiome_repo/api/projects.json","samples_csv":"https://olmlab.github.io/microbiome_repo/api/samples/<ACCESSION>.csv","vocabularies":"https://olmlab.github.io/microbiome_repo/api/vocabularies.json","wide_parquet":"https://olmlab.github.io/microbiome_repo/data/gut_sample_metadata_wide.parquet"},"how_to_search":["Pick the most specific slice: api/by-intervention/<code>.json, api/by-condition/<code>.json or api/by-age/<category>.json (codes in api/vocabularies.json).","Filter its projects on the other keys (health_conditions counts, interventions, intervention_design, has_cases_and_healthy_controls, has_treated_and_control_arms, n_samples, countries).","For each candidate open urls.samples_csv to see the samples, their arms (intervention column), conditions and sequencing depth (seq_gbp).","Cite the project page (urls.page) and the ENA accession; values carry evidence on the project page."],"name":"Microbiome Repo","package_version":"1.20.0","project_keys":{"accession":"BioProject accession","age_categories":"life stage -> number of samples","countries":"country -> number of samples","gbp_per_sample_median":"median sequencing depth per sample (Gbp)","has_cases_and_healthy_controls":">= 3 healthy_control samples and >= 3 samples with a disease code","has_treated_and_control_arms":">= 3 samples in an active arm and >= 3 placebo / no_intervention samples (archive attributes)","health_conditions":"code -> number of samples","intervention_design":"randomized_controlled_trial | non_randomized_controlled | crossover | single_arm_before_after | observational_with_procedure | none | unknown","intervention_detail":"short free text naming agent / regimen","interventions":"interventions the study ADMINISTERED (study level, from abstract / description; [] = none stated)","n_samples":"curated catalog samples","papers":"up to 5 linked papers","sample_intervention_arms":"code -> number of samples whose own archive record states the arm (placebo / no_intervention = controls / baselines)","sex":"sex -> number of samples","title":"project title","trial_population_condition":"underlying condition of the trial population","urls":"page, samples_csv (plain CSV), samples_full_csv_gz, evidence_csv_gz, ena"},"release":"R2026.25","sample_columns":{"age_at_collection_days":"","age_category":"","antibiotic_exposure":"","body_site_class":"","collection_date":"","country":"","health_condition":"","health_condition_detail":"","intervention":"","intervention_detail":"","n_runs":"","sample_key":"","seq_gbp":"","sex":"","study_accession":"","subject_id":"","timepoint_label":""}}