American Gut Project: crowdsourced human gut microbiome cohort
Cross-sectional study of 7024 samples (fecal, oral, skin, other sites) from citizen-science participants mainly in the USA, UK, Spain, and Japan, examining gut microbiome associations with diet, lifestyle, and health conditions including IBS, autoimmune/inflammatory, and neurological/psychiatric disorders. machine-written summary
7,353 samples · 13,995 runs · US, GB, MX · Infant / toddler · 2015 · 0.12 Gbp / sample · cohort American Gut: an Open Platform for Citizen Science
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 72,402 sample values (age, antibiotic exposure, bmi, collection date, country, delivery mode, diet, health condition) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10767325, PMC11494892, PMC5954204, PMC7516180, PMC9403272 |
| ✓ Supplementary tables | 5 sample values (delivery mode, feeding mode) |
| ✓ External resources | 838 sample values (age, bmi, health condition, health condition detail, sex) · from Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
antibiotic exposure: sequence archive and Meta2DB disagree for 190 samples (e.g. yes vs no) — withheld; health condition: sequence archive and Meta2DB disagree for 16 samples (e.g. cardiometabolic_other vs healthy_control) — withheld; sex differs between samples of the same subject id (1 subjects, 2 samples) — sex withheld; subject ids shared by samples of both sexes (1 ids, 2 samples) — ids withheld.
The sources disagree on 201 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (40 of 210)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA104162691 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA104162694 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA104162699 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA104187335 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA104187683 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA104206829 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA104601397 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA104601420 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA104601468 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA104602939 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA104702067 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA104702277 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA3901127 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA3901273 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA4036687 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA6674234 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA6674386 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA6674411 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA6674774 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA6675893 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061543 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061551 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061555 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061557 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061559 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061561 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061567 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061568 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061569 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061584 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061589 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061608 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061616 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061624 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061701 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061714 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061750 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061763 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061796 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
| SAMEA8061805 | antibiotic exposure | yes (sequence archive) | no (Meta2DB) | withheld: neither value published |
longitudinal
139 of 3,133 people sampled more than once (394 samples; median 2, up to 34 per person) · follow-up median 4 mo (max 17 mo) · median interval between samples 9 d (time from collection dates).
Each row is one person (36 shown of 139); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 888 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 5,275 | 72% | ||||
| country | 6,173 | 84% | 6,173 | |||
| health_condition | 3,118 | 42% | 2,752 | 366 | ||
| subject_id | 3,504 | 48% | 3,504 | |||
| antibiotic_exposure | 6,837 | 93% | 6,837 | |||
| diet | 6,696 | 91% | 6,696 | |||
| health_condition_detail | 6,635 | 90% | 6,574 | 61 | ||
| smoking_status | 6,506 | 88% | 6,506 | |||
| bmi | 6,502 | 88% | 6,482 | 20 | ||
| sex | 5,760 | 78% | 5,623 | 137 | ||
| delivery_mode | 5,466 | 74% | 5,465 | 1 | ||
| age_at_collection_days | 5,272 | 72% | 5,018 | 254 | ||
| probiotic_exposure | 4,849 | 66% | 4,849 | |||
| collection_date | 4,593 | 62% | 4,593 | |||
| medication | 1,330 | 18% | 1,330 | |||
| feeding_mode | 4 | 0% | 4 |
- Multi-population cohort meta-analysis of human intestinal microbiota in early life reveals the existence of infant community state types (ICSTs). PMID 33005310 PMC7516180 curated
- Genomic reconstruction of short-chain fatty acid production by the human gut microbiota. PMID 36032669 PMC9403272 curated
- Heterogeneity of gut microbiome compositions in the third decade of life in Japanese women: insights from a comparative analysis. PMID 38188664 PMC10767325 curated
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892 curated
- American Gut: an Open Platform for Citizen Science Microbiome Research. 2018 PMID 29795809 PMC5954204 own_data
Archive description
The American Gut project is the largest crowdsourced citizen science project to date. Fecal, oral, skin, and other body site samples collected from thousands of participants represent the largest human microbiome cohort in existence. Detailed health and lifestyle and diet data associated with each sample is enabling us to deeply examine associations between the human microbiome and factors such as diet (from vegan to near carnivore and everything in between), season, amount of sleep, and disease states such as IBD, diabetes, or autism spectrum disorder-as well as many other factors not listed here. The American Gut project also encompasses the British Gut and Australian Gut projects, widening the cohort beyond North America. As the project continues to grow, we will be able to identify significant associations that would not be possible with smaller, geographically and health/disease status-limited cohorts.
How this project entered the registry
Classified as human gut / stool / oral cavity / skin / nasal / nasopharyngeal / other human site mixed assays of infant / toddler and adult and elderly by opus_adjudicated with confidence 0.40. Assay mixed.
- host run.host_tax_id · “9606”
- host study.description · “largest human microbiome cohort in existence”
- body site study.description · “Fecal, oral, skin, and other body site samples”
- body site run.scientific_name · “human nasopharyngeal metagenome”
- life stage sample.attr.age_years · “20s (n=204/1036)”
- life stage sample.attr.age_years · “72.2 (n=117/1036)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104162391 | age_at_collection_days | 9862 | R1 | 0.90 | sample.attr.age_years | 27 |
| SAMEA104187471 | age_at_collection_days | 365 | R1 | 0.85 | biosample_attr | 1 |
| SAMEA8061553 | age_at_collection_days | 18664.28 | R1 | 0.85 | biosample.attribute:age years | age years: 51.1 |
| SAMEA8234772 | age_at_collection_days | 6939.8 | R1 | 0.85 | biosample.attribute:age_corrected | age_corrected: 19 |
| SAMEA8061648 | age_at_collection_days | 16071.0 | R2 | 0.70 | external.meta2db source | host_age: 44 |
| SAMEA104162391 | antibiotic_exposure | no | R1 | 0.85 | biosample_attr | I have not taken antibiotics in the past year. |
| SAMEA8061524 | antibiotic_exposure | yes | R1 | 0.85 | biosample.attribute:antibiotic_history | antibiotic_history: Week |
| SAMEA104162391 | bmi | 20.6 | R1 | 0.90 | biosample.attribute:bmi_corrected | bmi_corrected: 20.60 |
| SAMEA104459038 | bmi | 22.86 | R1 | 0.90 | biosample.attribute:bmi | bmi: 22.86 |
| SAMEA111459046 | bmi | 31.2 | R1 | 0.90 | biosample.attribute:host_body_mass_index | host_body_mass_index: 31.2 |
| SAMEA6674170 | bmi | 33.84 | R2 | 0.70 | external.meta2db source | host_body_mass_index: 33.84 kilogram per meter squared |
| SAMEA104162391 | collection_date | 2017-01-21 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 01/21/2017 |
| SAMEA6674170 | collection_date | 2017-07-26 | R1 | 0.85 | biosample.attribute:collection_date_only | collection_date_only: 2017-07-26 |
| SAMEA104162391 | country | US | R1 | 0.90 | biosample_attr | USA |
| SAMEA104206669 | country | US | R1 | 0.80 | biosample.attribute:country_residence | country_residence: United States |
| SAMEA8061524 | country | US | R1 | 0.90 | sample.attr.country_of_birth | United States |
| SAMEA104162391 | delivery_mode | vaginal | R1 | 0.90 | biosample_attr | false |
| SAMEA3608272 | delivery_mode | vaginal | R2 | 0.75 | paper.supp.table | Delivery=vaginal |
| SAMEA104162395 | diet | omnivore | R1 | 0.85 | biosample.attribute:diet_type | diet_type: Omnivore |
| SAMEA8061524 | diet | other_diet | R1 | 0.85 | biosample.attribute:diet type | diet type: Omnivore but do not eat red meat |
| SAMEA92737168 | feeding_mode | exclusive_breast | R2 | 0.75 | paper.supp.table | Feeding=Breast_Milk |
| SAMEA104162391 | health_condition | neurological_psychiatric | R1 | 0.75 | biosample.attribute:mental_illness | mental_illness: true |
| SAMEA104162521 | health_condition | other_disease | R1 | 0.60 | biosample.attribute:skin_condition | skin_condition: Diagnosed by a medical professional (doctor, physician assistant) |
| SAMEA104187314 | health_condition | ibs | R1 | 0.80 | biosample.attribute:ibs | ibs: Diagnosed by a medical professional (doctor, physician assistant) |
| SAMEA104187317 | health_condition | other_disease | R1 | 0.60 | biosample.attribute:clinical_condition | clinical_condition: Diagnosed by a medical professional (doctor, physician assistant) |
| SAMEA104187340 | health_condition | autoimmune_inflammatory | R1 | 0.60 | biosample.attribute:autoimmune | autoimmune: Diagnosed by an alternative medicine practitioner |
| SAMEA104187387 | health_condition | ulcerative_colitis | R1 | 0.80 | biosample.attribute:ibd_diagnosis_refined | ibd_diagnosis_refined: Ulcerative colitis |
| SAMEA104187412 | health_condition | liver_disease | R1 | 0.80 | biosample.attribute:liver_disease | liver_disease: Diagnosed by a medical professional (doctor, physician assistant) |
| SAMEA104187414 | health_condition | other_disease | R1 | 0.60 | biosample.attribute:lung_disease | lung_disease: Diagnosed by a medical professional (doctor, physician assistant) |
| SAMEA104187442 | health_condition | ibd_unspecified | R1 | 0.75 | biosample.attribute:ibd | ibd: Diagnosed by a medical professional (doctor, physician assistant) |
| SAMEA104187451 | health_condition | other_cancer | R1 | 0.85 | biosample.attribute:cancer | cancer: Diagnosed by a medical professional (doctor, physician assistant) |
| SAMEA104187520 | health_condition | cardiometabolic_other | R1 | 0.80 | biosample.attribute:cardiovascular_disease | cardiovascular_disease: Diagnosed by a medical professional (doctor, physician assistant) |
| SAMEA104187615 | health_condition | neurological_psychiatric | R1 | 0.85 | biosample.attribute:epilepsy_or_seizure_disorder | epilepsy_or_seizure_disorder: Diagnosed by a medical professional (doctor, physician assistant) |
| SAMEA111459102 | health_condition | type2_diabetes | R1 | 0.80 | biosample.attribute:diabetes | diabetes: Diagnosed by a medical professional (doctor, physician assistant) |
| SAMEA123192736 | health_condition | kidney_disease | R1 | 0.80 | biosample.attribute:kidney_disease | kidney_disease: Diagnosed by a medical professional (doctor, physician assistant) |
| SAMEA123258081 | health_condition | other_cancer | R1 | 0.85 | biosample.attribute:cancer_treatment | Surgery only |
| SAMEA14415988 | health_condition | gi_infection_or_diarrhoea | R1 | 0.85 | biosample.attribute:cdiff | cdiff: Diagnosed by a medical professional (doctor, physician assistant) |
| SAMEA6675804 | health_condition | type2_diabetes | R1 | 0.80 | biosample.attribute:diabetes_type | diabetes_type: Type II diabetes |
| SAMEA8061541 | health_condition | other_cancer | R1 | 0.75 | biosample.attribute:cancer treatment | cancer treatment: Surgery only |
| SAMEA9464318 | health_condition | neurological_psychiatric | R1 | 0.75 | biosample.attribute:add_adhd | add_adhd: Diagnosed by a medical professional (doctor, physician assistant) |
Sequencing
13,995 runs over 7,353 samples · mean 0.80 Gbp per run (median 0.23 Gbp, total 11,220.71 Gbp; 13,995 runs with a base count) · layout PAIRED 10,007, SINGLE 3,988 · platform ILLUMINA 13,995 · models Illumina NovaSeq 6000 (9,336), Illumina MiSeq (2,795), Illumina HiSeq 2500 (1,577), Illumina HiSeq 4000 (287) · 9% of runs with a Sandpiper profile · first public 2015-10-15 – 2026-08-01
Authors (23)
Mancabelli L first · Tarracchini C · Milani C · Lugli GA · Fontana F · Turroni F · van Sinderen D · Ventura M last · Frolova MS first · Suvorova IA · Iablokov SN · Petrov SN · Rodionov DA last · LE TM first · Nguyen HDT · Lee OE · Lee D · Choi Y · Chong GO · Cho J · Park NJ · Han HS · Seo I last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJEB11419.csv.gz (542.6 KB) · parquet (1.2 MB) — all 7,353 samples, every field with route and confidence · PRJEB11419_determinations.csv.gz (961.5 KB) — 73,245 evidence rows