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Cohorts (90)
A cohort groups catalog studies that belong together: BioProjects linked to the same publication (registry paper links: a paper that describes the data of 2–4 catalog studies, or a paper citing 2–4 studies that were all submitted by the same centre) or listed in the same curated cohort record (the infant-extension cohort resolution, which also supplies the cohort name).
About this page
227 of the 2,798 catalog studies belong to one of these 90 cohorts; the rest are single-deposit studies. Each cohort page lists its studies with sample counts, the shared papers and a merged sample download. The grouping is deterministic and is recomputed at every release from registry_study_papers, study_paper_links and cohorts.csv; the list is in catalog_cohorts.csv.
| Cohort | Name | Studies | Samples | Subjects (ids) | Papers | Age categories | Countries | Conditions | Rule |
|---|---|---|---|---|---|---|---|---|---|
| PCFA365F25 | Gut micro-organisms associated with health, nutrition and dietary interventions. | 4 | 33,594 | 33,594 | 1 | adult:21,797 unknown:11,797 | US GB | shared paper, same submitting centre | |
| PC3E7773C6 | American Gut: an Open Platform for Citizen Science Microbiome Research. | 2 | 8,429 | 3,221 | 1 | adult:5,289 unknown:2,078 elderly:790 | US GB MX JP | other_disease ibs autoimmune_inflammatory | shared own-data paper |
| PC8BB8A8C5 | Variation in the metagenomic analysis of fecal microbiome composition calls for a standardized operating approach. | 4 | 3,148 | 556 | 1 | child:2,089 unknown:685 adult:371 | HK | other_infection obesity healthy_control | shared own-data paper |
| COH1259 | HELMi Helsinki infant/family microbiome cohort | 2 | 3,141 | 1,210 | 0 | infant:2,481 adult:572 neonate:87 | FI | healthy_control pregnancy_postpartum | curated cohort record |
| PCD38CDE9F | Shotgun metagenomic mapping of saliva reveals insights into diversity and function of the oral microbiome in pregnancy. | 2 | 3,048 | 236 | 1 | adult:3,047 adolescent:1 | DK SE | healthy_control allergy_or_atopy other_infection | shared paper, same submitting centre |
| PC6EF8199D | High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans. | 4 | 2,971 | 81 | 1 | adult:2,971 | US | healthy_control | shared paper, same submitting centre |
| PCA2CE0BD2 | Strains, functions and dynamics in the expanded Human Microbiome Project. | 2 | 2,385 | 294 | 1 | unknown:1,361 adult:1,024 | US | healthy_control | shared own-data paper |
| PC6C5AF0B3 | A microbiome-directed therapeutic food for children recovering from severe acute malnutrition. | 2 | 2,279 | 210 | 1 | infant:2,279 | BD | malnutrition | shared own-data paper |
| PC23997AE9 | Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data. | 2 | 2,193 | 267 | 1 | adult:1,444 unknown:748 neonate:1 | US | healthy_control other_disease allergy_or_atopy | shared paper, same submitting centre |
| PC8EEDC57A | Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide. | 4 | 1,962 | 1,015 | 8 | unknown:1,502 adult:275 elderly:185 | FR DE DK | cardiometabolic_other type2_diabetes healthy_control | shared own-data paper |
| PC8ADDAB0D | Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level. | 8 | 1,917 | 1,652 | 5 | adult:1,084 child:395 unknown:222 | US NL CN | healthy_control ulcerative_colitis crohns_disease | shared own-data paper |
| PCB0C53AB7 | Fecal Butyrate and Deoxycholic Acid Concentrations Correlate With Mortality in Patients With Liver Disease. | 6 | 1,334 | 684 | 3 | unknown:972 adult:322 elderly:40 | US | liver_disease other_disease other_infection | shared own-data paper |
| PCBD1F1D0E | Impact of co-amoxiclav versus amoxicillin on the gastrointestinal microbiota in sub-Saharan children hospitalized with pneumonia. | 2 | 1,313 | 0 | 1 | unknown:682 infant:631 | ZA UG ZM ZW | other_infection other_disease | shared own-data paper |
| PC6B662CD4 | Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis. | 6 | 1,282 | 484 | 3 | adult:1,251 unknown:31 | AU | ulcerative_colitis healthy_control | shared paper, same submitting centre |
| PC0AE02550 | Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn's disease. | 2 | 1,214 | 1,214 | 1 | unknown:654 elderly:332 adult:228 | JP | healthy_control other_cancer | shared paper, same submitting centre |
| PC22F6F435 | Gut Mycobiota Dysbiosis Is Associated with Melanoma and Response to Anti-PD-1 Therapy. | 2 | 1,087 | 1,007 | 1 | adult:948 elderly:78 adolescent:61 | PL | allergy_or_atopy cardiometabolic_other autoimmune_inflammatory | shared paper, same submitting centre |
| PCC578B58B | Early life microbial succession in the gut follows common patterns in humans across the globe. | 3 | 1,075 | 493 | 2 | infant:884 unknown:189 neonate:2 | IE ZA | healthy_control | shared own-data paper |
| PC0891C78E | Compositional and functional differences of gut microbiome and metabolome inform pathogenesis of cholestatic liver disease. | 2 | 1,048 | 1,048 | 1 | adult:1,048 | US | liver_disease healthy_control | shared paper, same submitting centre |
| PCAA48D8B6 | Alcohol-related liver disease disrupts bile acid homeostasis and gut microbial bile acid metabolism. | 4 | 1,025 | 528 | 1 | adult:894 unknown:131 | DK | liver_disease healthy_control | shared paper, same submitting centre |
| COH0025 | Benitez 2025 USA | 3 | 930 | 224 | 0 | infant:850 neonate:77 unknown:3 | US | healthy_control | curated cohort record |
| PC872D1D24 | Comparison of phage and plasmid populations in the gut microbiota between Parkinson's disease patients and controls. | 2 | 859 | 368 | 1 | elderly:469 adult:256 unknown:134 | US FI | neurological_psychiatric healthy_control autoimmune_inflammatory | shared own-data paper |
| PCEC05A34C | Microbial and Metabolic Gut Profiling across Seven Malignancies Identifies Fecal Faecalibacillus intestinalis and Formic Acid as Commonly Altered in Cancer Pati | 4 | 800 | 0 | 2 | adult:441 elderly:189 unknown:169 | PL | other_cancer healthy_control other_disease | shared own-data paper |
| PC8253142A | <i>Fusobacterium</i> species are distinctly associated with patients with Lynch syndrome colorectal cancer. | 3 | 744 | 714 | 1 | adult:460 elderly:283 adolescent:1 | JP IL | colorectal_cancer healthy_control colorectal_adenoma | shared own-data paper |
| PC853008D5 | Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers. | 2 | 724 | 300 | 1 | adult:659 elderly:43 child:14 | NL IN | healthy_control other_disease | shared own-data paper |
| PCB75F70FF | Microbial, functional, and virulence biomarkers associated with familial risk of Crohn's disease and ulcerative colitis. | 2 | 709 | 614 | 1 | adult:497 unknown:212 | ES | healthy_control ulcerative_colitis crohns_disease | shared paper, same submitting centre |
| PC80A309A5 | Risk assessment with gut microbiome and metabolite markers in NAFLD development. | 4 | 696 | 521 | 1 | adult:444 unknown:252 | CN | other_disease obesity cardiometabolic_other | shared own-data paper |
| PCEE88CED3 | Gut dysbiosis associates with cytokine production capacity in viral-suppressed people living with HIV. | 2 | 660 | 143 | 1 | adult:660 | NL | healthy_control other_infection | shared paper, same submitting centre |
| COH0002 | Stewart/Rose UK preterm infant cohort | 2 | 659 | 59 | 0 | infant:364 neonate:295 | GB | healthy_control nec preterm_nicu | curated cohort record |
| PC53F1ED9E | Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis. | 3 | 620 | 448 | 1 | adult:593 elderly:22 adolescent:5 | CN | healthy_control autoimmune_inflammatory liver_disease | shared own-data paper |
| PC5C212638 | Conjugated C-6 hydroxylated bile acids in serum relate to human metabolic health and gut Clostridia species. | 2 | 552 | 362 | 1 | adult:292 unknown:260 | DK ES CN | healthy_control type2_diabetes type1_diabetes | shared paper, same submitting centre |
| PC358DE082 | Alteration of Gut Microbiome in Patients With Schizophrenia Indicates Links Between Bacterial Tyrosine Biosynthesis and Cognitive Dysfunction. | 4 | 537 | 280 | 2 | adult:537 | DK | neurological_psychiatric healthy_control | shared own-data paper |
| PCB45D4DEF | Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response. | 4 | 526 | 45 | 2 | adult:318 elderly:166 unknown:42 | US IL | other_cancer | shared own-data paper |
| PC3AA85ED6 | Dynamic change patterns of the human gut microbiota-fluctuation, loss-acquisition, and turnover-and their underlying causes. | 2 | 516 | 93 | 1 | unknown:431 adult:85 | CN | healthy_control | shared own-data paper |
| COH0024 | MILK study | 2 | 507 | 330 | 0 | infant:334 unknown:173 | US | curated cohort record | |
| PCAAE9BDF6 | Age-dependent changes in the gut microbiota and serum metabolome correlate with renal function and human aging. | 2 | 481 | 458 | 1 | elderly:386 adult:95 | JP CN | healthy_control | shared own-data paper |
| PCB206D964 | Commensal-pathogen dynamics structure disease outcomes during Clostridioides difficile colonization. | 3 | 477 | 105 | 1 | adult:375 unknown:102 | US | healthy_control gi_infection_or_diarrhoea other_infection | shared own-data paper |
| PC911E0B92 | <i>L</i> <i>actococcus A</i> phages predict ACLF while <i>Enterococcus B</i> phages predict bacterial infection in decompens | 2 | 475 | 266 | 1 | adult:475 | HU IT DE ES | liver_disease | shared own-data paper |
| PC40A2CA2A | Two stable gut microbiome guilds predict liver tumor class and treatment responses. | 4 | 419 | 120 | 1 | unknown:254 adult:165 | CN TH | liver_disease healthy_control other_cancer | shared own-data paper |
| PC229809B3 | Data integration for prediction of weight loss in randomized controlled dietary trials. | 2 | 393 | 109 | 2 | adult:200 unknown:185 elderly:8 | DK | healthy_control | shared paper, same submitting centre |
| PC603FA30F | Drivers and determinants of strain dynamics following fecal microbiota transplantation. | 5 | 379 | 102 | 2 | adult:270 unknown:105 elderly:4 | NL AU | cardiometabolic_other other_infection healthy_control | shared own-data paper |
| PCD42C09F3 | Lifetime existence of a core of mutualistic symbionts and functionally uncoupled taxa in the gut of a Mediterranean cohort. | 2 | 363 | 30 | 1 | unknown:170 elderly:65 adult:63 | ES | healthy_control | shared paper, same submitting centre |
| COH0169 | Seong 2025 South Korea AD infant cohort | 2 | 351 | 13 | 0 | unknown:338 infant:13 | KR | allergy_or_atopy healthy_control | curated cohort record |
| COH0031 | MAMI | 2 | 328 | 85 | 0 | infant:236 neonate:33 unknown:32 | ES | healthy_control | curated cohort record |
| PCC8729007 | A faecal microbiota signature with high specificity for pancreatic cancer. | 2 | 320 | 224 | 2 | adult:198 elderly:122 | ES DE | other_cancer healthy_control obesity | shared paper, same submitting centre |
| PC1C11AE3F | Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactama | 2 | 299 | 22 | 1 | adult:299 | FR IN | healthy_control | shared own-data paper |
| PC31C440DD | Contributions of Human-Associated Archaeal Metabolites to Tumor Microenvironment and Carcinogenesis. | 2 | 284 | 237 | 2 | elderly:144 adult:140 | AT CN | colorectal_cancer healthy_control colorectal_adenoma | shared paper, same submitting centre |
| PC771EC102 | Alterations in the gut virome in patients with ankylosing spondylitis. | 2 | 284 | 257 | 1 | unknown:162 adult:117 adolescent:5 | CN | autoimmune_inflammatory healthy_control | shared paper, same submitting centre |
| PC4C98A4D5 | Microbial collagenase activity is linked to oral-gut translocation in advanced chronic liver disease. | 2 | 259 | 150 | 1 | adult:176 unknown:72 elderly:11 | GB | liver_disease healthy_control sepsis_or_infection | shared own-data paper |
| PC1299FA0E | A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog. | 2 | 254 | 204 | 1 | unknown:150 adult:104 | DK | healthy_control obesity liver_disease | shared paper, same submitting centre |
| PC4F054A8F | Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity. | 2 | 250 | 205 | 1 | adult:231 elderly:16 infant:2 | US | crohns_disease ulcerative_colitis healthy_control | shared own-data paper |
| PC82E2E8BF | Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurr | 2 | 239 | 78 | 1 | unknown:239 | NL | gi_infection_or_diarrhoea healthy_control | shared paper, same submitting centre |
| PCD94A585E | A metagenomic study of the gut microbiome in Behcet's disease. | 2 | 226 | 0 | 1 | adult:206 elderly:17 adolescent:3 | CN | autoimmune_inflammatory healthy_control other_disease | shared paper, same submitting centre |
| PC29EB869A | Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. | 2 | 222 | 222 | 1 | adult:140 elderly:81 unknown:1 | IT DE | healthy_control colorectal_cancer colorectal_adenoma | shared own-data paper |
| PCE1B28694 | Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts. | 2 | 221 | 221 | 2 | unknown:221 | US | healthy_control gi_infection_or_diarrhoea sepsis_or_infection | shared own-data paper |
| COH0009 | Brown 2018 USA | 2 | 218 | 35 | 0 | neonate:156 infant:62 | US | preterm_nicu nec healthy_control | curated cohort record |
| PC947CCD1D | Fecal microbiota transplantation from a healthy pouch donor for chronic pouchitis: a proof-of-concept study. | 2 | 218 | 1 | 1 | adult:218 | DK | other_disease ibd_or_gi_disease | shared paper, same submitting centre |
| PC9CF56EE2 | Structure of the Mucosal and Stool Microbiome in Lynch Syndrome. | 2 | 218 | 39 | 1 | unknown:131 adult:87 | US | colorectal_cancer | shared own-data paper |
| PC2D75A65D | BIOME-Preserve: A novel storage and transport medium for preserving anaerobic microbiota samples for culture recovery. | 2 | 217 | 4 | 1 | adult:119 unknown:98 | US | healthy_control | shared paper, same submitting centre |
| PC993EFD38 | Human gut microbiota community structures in urban and rural populations in Russia. | 2 | 217 | 142 | 1 | unknown:121 adult:73 adolescent:16 | RU | healthy_control | shared own-data paper |
| PC44DA07BB | Characterization of Antibiotic Administration Factors Associated with Microbiome Disruption and Subsequent Antibiotic-Resistant Infection and Colonization Event | 2 | 212 | 125 | 3 | unknown:139 adult:73 | US | other_disease | shared paper, same submitting centre |
| PC0E2F88BF | Metagenomic analyses of 7000 to 5500 years old coprolites excavated from the Torihama shell-mound site in the Japanese archipelago. | 2 | 200 | 196 | 1 | adult:196 unknown:4 | CN JP | cardiometabolic_other healthy_control | shared own-data paper |
| PC90AC732B | The NUTRIENT Trial (NUTRitional Intervention among myEloproliferative Neoplasms): Results from a Randomized Phase I Pilot Study for Feasibility and Adherence. | 2 | 189 | 123 | 1 | adult:145 elderly:44 | US | other_cancer healthy_control | shared paper, same submitting centre |
| PC1B96BD6F | Surgical Treatment for Colorectal Cancer Partially Restores Gut Microbiome and Metabolome Traits. | 2 | 182 | 75 | 1 | adult:102 unknown:68 elderly:12 | JP DE | colorectal_cancer | shared own-data paper |
| PC4380F38E | The gut metagenome harbors metabolic and antibiotic resistance signatures of moderate-to-severe asthma. | 2 | 173 | 95 | 1 | adult:95 unknown:78 | US | healthy_control allergy_or_atopy | shared own-data paper |
| PC2B20A1FF | A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy. | 3 | 159 | 106 | 1 | unknown:108 elderly:32 adult:19 | KR | other_cancer | shared paper, same submitting centre |
| PCDAD91996 | Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut. | 2 | 158 | 17 | 1 | unknown:158 | US | healthy_control ibd_unspecified | shared paper, same submitting centre |
| PC4B23511B | Clinical Impact of Microbiome Characteristics in Treatment-Naïve Extranodal NK/T-Cell Lymphoma Patients. | 2 | 149 | 41 | 1 | adult:110 elderly:39 | KR | other_cancer neurological_psychiatric | shared paper, same submitting centre |
| PC0B1F1273 | Antibiotic and antifungal use in pediatric leukemia and lymphoma patients are associated with increasing opportunistic pathogens and decreasing bacteria respons | 3 | 125 | 54 | 2 | unknown:67 child:58 | CA | other_cancer | shared own-data paper |
| PC9E76D6ED | Host-diet-gut microbiome interactions influence human energy balance: a randomized clinical trial. | 2 | 125 | 43 | 2 | unknown:125 | US | healthy_control | shared paper, same submitting centre |
| PC5EE030E3 | Anxiety associated with dietary intake and gut microbiome features in a cross-sectional cohort of sub-clinically anxious young women | 2 | 123 | 44 | 1 | adult:123 | GB | healthy_control | shared own-data paper |
| COH0039 | Kim 2022 South Korea | 2 | 116 | 0 | 0 | unknown:116 | KR | healthy_control | curated cohort record |
| PCF19105E6 | Gut microbiota and metabolic changes in children with idiopathic short stature. | 2 | 111 | 0 | 1 | child:93 adolescent:9 infant:9 | CN | other_disease healthy_control | shared own-data paper |
| PC292C0A5B | A plasmid network from the gut microbiome of semi-isolated human groups reveals unique and shared metabolic and virulence traits. | 3 | 110 | 110 | 2 | adult:80 unknown:15 elderly:10 | CM TZ BR IT | healthy_control | shared own-data paper |
| COH2292 | Peru Loreto LMIC infant stool cohort | 2 | 97 | 0 | 0 | unknown:97 | PE | curated cohort record | |
| PCD9E9C7D2 | Association between seizure reduction during ketogenic diet treatment of epilepsy and changes in circulatory metabolites and gut microbiota composition. | 2 | 94 | 46 | 2 | child:94 | SE | neurological_psychiatric healthy_control | shared paper, same submitting centre |
| PC652EB156 | Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis. | 2 | 81 | 32 | 1 | elderly:38 adult:37 unknown:6 | US | autoimmune_inflammatory | shared paper, same submitting centre |
| PCEA0988C4 | Bifidobacterium- and Escherichia-dominant ecological guilds shape altered microbial metabolic capacity of the gut microbiome in tuberculosis patients. | 2 | 80 | 70 | 1 | unknown:70 adult:10 | RU | healthy_control other_infection | shared own-data paper |
| PCA62A3345 | Potential biomarkers for human Ascending aortic aneurysm identified through metagenomic and metabolomic analyses: A case-control study. | 4 | 72 | 0 | 1 | adult:64 elderly:8 | CN | cardiometabolic_other healthy_control | shared paper, same submitting centre |
| COH0302 | Dalhousie pediatric leukemia/lymphoma gut microbiome cohort | 2 | 69 | 28 | 2 | unknown:69 | CA | other_cancer | curated cohort record |
| PCD24C3538 | Identification of Intestinal Microbial Community in Gallstone Patients with Metagenomic Next-Generation Sequencing. | 2 | 63 | 62 | 1 | adult:63 | CN | other_disease healthy_control | shared own-data paper |
| PC175C9147 | Glucuronidation metabolomic fingerprinting to map host-microbe metabolism. | 2 | 49 | 49 | 1 | infant:49 | US | healthy_control | shared paper, same submitting centre |
| PC2D89C0EC | Segmented filamentous bacteria are worldwide human gut commensals. | 2 | 44 | 1 | 1 | child:43 unknown:1 | US ML | crohns_disease healthy_control | shared own-data paper |
| PC5609EFEE | Comparison of gut viral communities between autism spectrum disorder and healthy children. | 2 | 44 | 0 | 1 | child:44 | CN | healthy_control neurological_psychiatric | shared own-data paper |
| PC4634A33C | Distinct characteristics of the gut virome in patients with osteoarthritis and gouty arthritis. | 2 | 36 | 26 | 1 | adult:36 | CN | autoimmune_inflammatory | shared paper, same submitting centre |
| COH0046 | Reyman 2022 Netherlands | 2 | 32 | 14 | 0 | neonate:20 unknown:10 infant:2 | NL | curated cohort record | |
| PCAE7A4E0D | Investigating the Human Intestinal DNA Virome and Predicting Disease-Associated Virus-Host Interactions in Severe Myalgic Encephalomyelitis/Chronic Fatigue Synd | 2 | 32 | 17 | 1 | unknown:32 | GB | healthy_control ibs other_disease | shared paper, same submitting centre |
| PCA393BFC8 | Uncovering the relationship between the human ocular surface microbiome and gut microbiome. | 2 | 21 | 0 | 1 | unknown:21 | CH | shared paper, same submitting centre | |
| PC6401D18E | Baseline human gut microbiota profile in healthy people and standard reporting template. | 2 | 19 | 18 | 1 | adult:19 | US | healthy_control | shared paper, same submitting centre |
| PC20D9D81E | Culture-based characterization of gut microbiota in inflammatory bowel disease. | 2 | 11 | 3 | 1 | adult:8 unknown:3 | KR | crohns_disease ulcerative_colitis healthy_control | shared paper, same submitting centre |
| PCE980011B | HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota. | 2 | 5 | 1 | 1 | adult:5 | KR | healthy_control | shared own-data paper |