Integrated gut gene catalog, multi-country cross-sectional
260 gut metagenome samples from Spain, Denmark, and China, including individuals with type 2 diabetes, type 1 diabetes, and healthy controls, used to build an integrated reference gene catalog; cross-sectional design. machine-written summary
260 samples · 579 runs · ES, DK, CN · Age unknown · 2014 · 5.64 Gbp / sample · cohort Conjugated C-6 hydroxylated bile acids in serum re
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,393 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12041579, PMC13469089 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 725 sample values (bmi, health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
sex differs between samples of the same subject id (4 subjects, 11 samples) — sex withheld; subject ids shared by samples of both sexes (4 ids, 10 samples) — ids withheld.
The sources disagree on 15 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 (21)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA2338732 | sex | female (curatedMetagenomicData) | subject CD1: female in 4 samples, male in 1 sample | withheld: neither value published |
| SAMEA2338733 | sex | male (curatedMetagenomicData) | subject CD1: female in 4 samples, male in 1 sample | withheld: neither value published |
| SAMEA2338770 | sex | male (curatedMetagenomicData) | subject UC40: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA2338776 | sex | female (curatedMetagenomicData) | subject UC47: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMEA2338788 | sex | female (curatedMetagenomicData) | subject CD1: female in 4 samples, male in 1 sample | withheld: neither value published |
| SAMEA2338789 | sex | female (curatedMetagenomicData) | subject CD1: female in 4 samples, male in 1 sample | withheld: neither value published |
| SAMEA2338791 | sex | female (curatedMetagenomicData) | subject CD1: female in 4 samples, male in 1 sample | withheld: neither value published |
| SAMEA2338818 | sex | male (curatedMetagenomicData) | subject CD6: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA2338819 | sex | female (curatedMetagenomicData) | subject CD6: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA2338862 | sex | female (curatedMetagenomicData) | subject UC40: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA2338863 | sex | male (curatedMetagenomicData) | subject UC47: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMEA2338734 | subject id | CD2 | female (curatedMetagenomicData) | subject id withheld (samples of both sexes share it); sex kept |
| SAMEA2338735 | subject id | CD2 | male (curatedMetagenomicData) | subject id withheld (samples of both sexes share it); sex kept |
| SAMEA2338770 | subject id | UC40 | male (curatedMetagenomicData) | subject id withheld (samples of both sexes share it) |
| SAMEA2338776 | subject id | UC47 | female (curatedMetagenomicData) | subject id withheld (samples of both sexes share it) |
| SAMEA2338793 | subject id | CD2 | female (curatedMetagenomicData) | subject id withheld (samples of both sexes share it); sex kept |
| SAMEA2338794 | subject id | CD2 | male (curatedMetagenomicData) | subject id withheld (samples of both sexes share it); sex kept |
| SAMEA2338818 | subject id | CD6 | male (curatedMetagenomicData) | subject id withheld (samples of both sexes share it) |
| SAMEA2338819 | subject id | CD6 | female (curatedMetagenomicData) | subject id withheld (samples of both sexes share it) |
| SAMEA2338862 | subject id | UC40 | female (curatedMetagenomicData) | subject id withheld (samples of both sexes share it) |
| SAMEA2338863 | subject id | UC47 | male (curatedMetagenomicData) | subject id withheld (samples of both sexes share it) |
longitudinal — not resolved
14 of 70 people sampled more than once (37 samples; median 2, up to 5 per person).
Genera, mean relative abundance over 230 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 | 0 | 0% | ||||
| country | 260 | 100% | 260 | |||
| health_condition | 120 | 46% | 120 | |||
| subject_id | 93 | 36% | 93 | |||
| collection_date | 260 | 100% | 260 | |||
| detailed_location | 260 | 100% | ||||
| latitude | 260 | 100% | 260 | |||
| location_region | 260 | 100% | 260 | |||
| longitude | 260 | 100% | 260 | |||
| bmi | 248 | 95% | 248 | |||
| sex | 237 | 91% | 237 | |||
| health_condition_detail | 120 | 46% | 120 |
- An integrated catalog of reference genes in the human gut microbiome. 2014 PMID 24997786 own_data
- Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems. 2025 PMID 40301344 PMC12041579 own_data
- Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. 2015 PMID 26633628 PMC4681099 unsure
- Subspecies in the global human gut microbiome. 2017 PMID 29242367 PMC5740502 unsure
- Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy. 2019 PMID 31474368 PMC6736778 unsure
22 more
- Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance. 2020 PMID 31910889 PMC6947943
- Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion. 2020 PMID 31940321 PMC6961876
- MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota. 2020 PMID 31964767 PMC6977071
- Human Gut Microbiome Aging Clock Based on Taxonomic Profiling and Deep Learning. 2020 PMID 32534441 PMC7298543
- Assessment of fecal DNA extraction protocols for metagenomic studies. 2020 PMID 32657325 PMC7355182
- Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. 2020 PMID 33372654 PMC7861615
- Conjugated C-6 hydroxylated bile acids in serum relate to human metabolic health and gut Clostridia species. 2021 PMID 34168163 PMC8225906
- MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen. 2021 PMID 34592929 PMC8485520
- Characterizing Enterotypes in Human Metagenomics: A Viral Perspective. 2021 PMID 34659174 PMC8511818
- Identification and Characterization of Major Bile Acid 7α-Dehydroxylating Bacteria in the Human Gut. 2022 PMID 35736002 PMC9426597
- The microbiome's fiber degradation profile and its relationship with the host diet. 2022 PMID 36464700 PMC9721016
- Four functional profiles for fibre and mucin metabolism in the human gut microbiome. 2023 PMID 37858269 PMC10588041
- Isolation and characterization of a novel lytic Parabacteroides distasonis bacteriophage φPDS1 from the human gut. 2024 PMID 38178369 PMC10773633
- Changes in the type 2 diabetes gut mycobiome associate with metformin treatment across populations. 2024 PMID 38767350 PMC11237675
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. 2025 PMID 39947133 PMC12268991
- Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM). 2025 PMID 40424276 PMC12136445
- Microbiota-driven antitumour immunity mediated by dendritic cell migration. 2025 PMID 40659786 PMC12390848
- Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation. 2025 PMID 40681522 PMC12274573
- Megasphaera Elesdenii Dysregulates Colon Epithelial Homeostasis, Aggravates Colitis-Associated Tumorigenesis. 2025 PMID 40801433 PMC12591162
- Deciphering the personalized functional redundancy hierarchy in the gut microbiome. 2025 PMID 41345980 PMC12781464
- Fecal microbiome of patients with ulcerative colitis reflects their phenotype and inflammatory level. 2026 PMID 42156414 PMC13469089
- Global gut microbiome atlas identifies epidemiologic-stage-specific signatures in inflammatory bowel disease. 2026 PMID 42575094 PMC13589510
Archive description
The gut microbiota is key to human health and disease. Metagenome-wide association studies (MGWAS) that search for disease markers in the gut microbiota, species identification according to metagenomic linkage groups (MLGs) or metagenomic clusters (MGCs), and metatranscriptomics or metaproteomics studies, all depend on a reference gene catalog, which has only been available for individual cohorts or based on reference genome or protein sequences. Here we report a high-quality integrated reference gene catalog consisting 9,879,896 genes, using 6.4 TB sequencing data derived from 1267 published and unpublished human gut metagenomes from three continents. The catalog represents a comprehensive collection of common and rare species, genes and genetic variants, and suggests individuality in the human gut microbiota. Analyses of a group of Chinese and Danish samples using the catalog revealed country-specific signatures in nutrient and xenobiotic metabolism. Our data suggest that interventions on nutrition, pollution and epidemiology should be tailored to the gut microbiota of a given population or even personalized for an individual.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.80. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “reference genes in the human gut microbiome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA2338623 | bmi | 36.0 | R2 | 0.75 | external.cmd source | bmi: 36 |
| SAMEA2338623 | collection_date | 2008/2010 | R1 | 0.90 | biosample.attribute:collection_date | 2008/2010 |
| SAMEA2338623 | country | DK | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea_region | Denmark |
| SAMEA2338623 | health_condition | type2_diabetes | R2 | 0.75 | external.cmd source | disease: Type 2 Diabetes Mellitus |
| SAMEA2338623 | health_condition_detail | Type 2 Diabetes Mellitus | R2 | 0.75 | external.cmd source | disease: Type 2 Diabetes Mellitus |
| SAMEA2338623 | latitude | 55.6761 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.676097 12.568337 |
| SAMEA2338623 | location_region | Capital Region | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.676097 12.568337 |
| SAMEA2338623 | longitude | 12.5683 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.676097 12.568337 |
| SAMEA2338623 | sex | female | R2 | 0.75 | external.cmd source | sex: Female |
| SAMEA2338732 | subject_id | CD1 | R1 | 0.70 | sample.name_rule:alias | O2.CD1-0 |
Sequencing
579 runs over 260 samples · mean 2.54 Gbp per run (median 0.24 Gbp, total 1,471.59 Gbp; 579 runs with a base count) · layout SINGLE 292, PAIRED 287 · platform ILLUMINA 579 · models Illumina HiSeq 2000 (579) · 43% of runs with a Sandpiper profile · first public 2014-06-25
Authors (120)
Li J first · Jia H · Cai X · Zhong H · Feng Q · Sunagawa S · Arumugam M · Kultima JR · Prifti E · Nielsen T · Juncker AS · Manichanh C · Chen B · Zhang W · Levenez F · Wang J · Xu X · Xiao L · Liang S · Zhang D · Zhang Z · Chen W · Zhao H · Al-Aama JY · Edris S · Yang H · Hansen T · Nielsen HB · Brunak S · Kristiansen K · Guarner F · Pedersen O · Doré J · Ehrlich SD · MetaHIT Consortium · Bork P · Nayfach S first · Rodriguez-Mueller B · Garud N · Pollard KS last · Ormaasen I first · Rudi K · Diep DB · Snipen L last · Rhoades NS first · Cinco IR · Hendrickson SM · Prongay K · Haertel AJ · Flores GE · Slifka MK · Messaoudi I last · Van Syoc E first · Nixon MP · Silverman JD · Luo Y · Gonzalez FJ · Elbere I · Klovins J · Patterson AD · Rogers CJ · Ganda E last · Zhu C first · Wu L · Ning D · Tian R · Gao S · Zhang B · Zhao J · Zhang Y · Xiao N · Wang Y · Brown MR · Tu Q · Global Water Microbiome Consortium · Ju F · Wells GF · Guo J · He Z · Nielsen PH · Wang A · Chen T · He Q · Criddle CS · Wagner M · Tiedje JM · Curtis TP · Wen X · Yang Y · Alvarez-Cohen L · Stahl DA · Alvarez PJJ · Rittmann BE · Zhou J last · Maziers N first · Le Chatelier E · Plaza Oñate F · Fromentin S · Thirion F · Pons N · Borruel N · Casellas F · Torrejon A · Robles-Alonso V · Varela E · Derrien M · Veiga P · Oozeer R · Lombard V · Terrapon N · Henrissat B · Zhai J first · Li Y · Liu J · Su X · Cui R · Zheng D · Sun Y · Yu J · Dai C last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJEB5224.csv.gz (8.2 KB) · parquet (81.8 KB) — all 260 samples, every field with route and confidence · PRJEB5224_determinations.csv.gz (20.7 KB) — 2,118 evidence rows