HMP gut metagenome WGS, healthy adults, cross-sectional
Cross-sectional shotgun metagenomic sequencing of 2096 samples from healthy control subjects (735 adult, 1361 age unknown; country largely unreported) generated during the Human Microbiome Project production phase. machine-written summary
2,096 samples · 11,164 runs · US · Age unknown · 2010 · 10.91 Gbp / sample · cohort Strains, functions and dynamics in the expanded Hu
One study deposited as 2 BioProjects (2,385 catalog samples together): PRJNA275349 · PRJNA48479 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 4,192 sample values (sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10059959, PMC10134562, PMC10150486, PMC10258454, PMC10473153, PMC10566737, PMC10588041, PMC10939037, PMC11418011, PMC11510655, PMC11980382, PMC12336193, PMC12355549, PMC12570322, PMC12916291, PMC13269251, PMC4550057, PMC5244288, PMC5601332, PMC5740502, PMC5789541, PMC5831082, PMC5930361, PMC7157763, PMC7298543, PMC7355182, PMC7778953, PMC7790408, PMC7813156, PMC7854710, PMC8190618, PMC8201803, PMC8262883, PMC8326577, PMC8877467, PMC8913745, PMC9045136, PMC9096808, PMC9387673, PMC9426597, PMC9710629 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 4,188 sample values (age, bmi, country, health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3), GMrepo v3, mBodyMap, MicrobiomeDB (VEuPathDB) |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
133 of 206 people sampled more than once (368 samples; median 3, up to 8 per person).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 735 | 35% | ||||
| country | 760 | 36% | 760 | |||
| health_condition | 2,096 | 100% | 2,096 | |||
| subject_id | 2,096 | 100% | 2,096 | |||
| sex | 2,096 | 100% | 2,096 | |||
| age_at_collection_days | 744 | 35% | 744 | |||
| health_condition_detail | 441 | 21% | 441 | |||
| bmi | 147 | 7% | 147 |
- A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. 2021 PMID 34083435 PMC8201803 own_data
- Prevalence of Antibiotic Resistance Genes among Human Gut-Derived Bifidobacteria. 2017 PMID 27864179 PMC5244288 own_data
- The Sortase-Dependent Fimbriome of the Genus Bifidobacterium: Extracellular Structures with Potential To Modulate Microbe-Host Dialogue. 2017 PMID 28754709 PMC5601332 own_data
- Strains, functions and dynamics in the expanded Human Microbiome Project. 2017 PMID 28953883 PMC5831082 own_data
- A Gene Homologous to rRNA Methylase Genes Confers Erythromycin and Clindamycin Resistance in Bifidobacterium breve. 2018 PMID 29500262 PMC5930361 own_data
39 more
- Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes. 2021 PMID 33411719 PMC7790408
- Metagenomic characterization of sphingomyelinase C in the microbiome of humans and environments. 2022 PMID 36467737 PMC9710629
- Reference-guided assembly of metagenomes with MetaCompass. 2025 PMID 41015028 PMC12570322
- The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems 2025
- Structure and function of the healthy pre-adolescent pediatric gut microbiome. 2015 PMID 26306392 PMC4550057
- Subspecies in the global human gut microbiome. 2017 PMID 29242367 PMC5740502
- Host genetic variation and its microbiome interactions within the Human Microbiome Project. 2018 PMID 29378630 PMC5789541
- Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides. 2020 PMID 32265336 PMC7157763
- 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
- mMGE: a database for human metagenomic extrachromosomal mobile genetic elements. 2021 PMID 33074335 PMC7778953
- Identification of Natural CRISPR Systems and Targets in the Human Microbiome. 2021 PMID 33217332 PMC7813156
- Bacterial associations in the healthy human gut microbiome across populations. 2021 PMID 33531651 PMC7854710
- The structure and diversity of strain-level variation in vaginal bacteria. 2021 PMID 33656436 PMC8190618
- Human Gut Faecalibacterium prausnitzii Deploys a Highly Efficient Conserved System To Cross-Feed on β-Mannan-Derived Oligosaccharides. 2021 PMID 34061597 PMC8262883
- Linking Inflammatory Bowel Disease Symptoms to Changes in the Gut Microbiome Structure and Function. 2021 PMID 34349736 PMC8326577
- The human microbiome encodes resistance to the antidiabetic drug acarbose. 2021 PMID 34819672 PMC10258454
- Mycobiome-Host Coevolution? The Mycobiome of Ancestral Human Populations Seems to Be Different and Less Diverse Than Those of Extant Native and Urban-Industrialized Populations. 2022 PMID 35208912 PMC8877467
- Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria. 2022 PMID 35240043 PMC9096808
- Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation. 2022 PMID 35241796 PMC10473153
- Evaluation of Modulatory Activities of Lactobacillus crispatus Strains in the Context of the Vaginal Microbiota. 2022 PMID 35266820 PMC9045136
- Integrated metagenomics identifies a crucial role for trimethylamine-producing Lachnoclostridium in promoting atherosclerosis. 2022 PMID 35273169 PMC8913745
- Identification and Characterization of Major Bile Acid 7α-Dehydroxylating Bacteria in the Human Gut. 2022 PMID 35736002 PMC9426597
- Gut microbiota insights into human adaption to high-plateau diet. 2022 PMID 35989883 PMC9387673
- 2 Hydroxybutyric Acid-Producing Bacteria in Gut Microbiome and Fusobacterium nucleatum Regulates 2 Hydroxybutyric Acid Level In Vivo. 2023 PMID 36984891 PMC10059959
- A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome. 2023 PMID 37101246 PMC10134562
- SNV-FEAST: microbial source tracking with single nucleotide variants. 2023 PMID 37121994 PMC10150486
- Edible flora in pre-Columbian Caribbean coprolites: Expected and unexpected data. 2023 PMID 37819893 PMC10566737
- Four functional profiles for fibre and mucin metabolism in the human gut microbiome. 2023 PMID 37858269 PMC10588041
- Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota. 2024 PMID 38423015 PMC10939037
- The molecular basis of cereal mixed-linkage β-glucan utilization by the human gut bacterium Segatella copri. 2024 PMID 39122003 PMC11418011
- Oral Microbial Translocation Genes in Gastrointestinal Cancers: Insights from Metagenomic Analysis. 2024 PMID 39458395 PMC11510655
- The physical biogeography of <i>Fusobacterium nucleatum</i> in health and disease. 2025 PMID 40062772 PMC11980382
- Exploring fecal microbiota signatures associated with immune response and antibiotic impact in NSCLC: insights from metagenomic and machine learning approaches. 2025 PMID 40792105 PMC12336193
- Ancient microbial DNA and proteins preserve in concretions covering human remains. 2025 PMID 40822357 PMC12355549
- Gene-specific selective sweeps are pervasive across human gut microbiomes. 2026 PMID 41407853 PMC12916291
- Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals. 2026 PMID 42312244 PMC13269251
- Pan-microbiome analysis along the human respiratory axis reveals an ecological continuum in health and collapse in disease 2025
- High conservation of the dental plaque microbiome community across populations with differing subsistence strategies and levels of market integration 2022
Archive description
The HMP metagenomes production phase represents the shotgun sequencing of metagenomic DNA extracted from samples taken from multiple body sites across hundreds of human subjects. Coupled with the other data generated during the HMP project, these results will provide insights into the genes and pathways present in the human microbiome. We are learning more and more about the ways that human health is influenced by the complex and dynamic communities of microbes (the human microbiota) present on and within our bodies. Disruptions in these communities may trigger or influence the course of various disease states. Preliminary studies have shown this to be the case for certain diseases. The Human Microbiome Project expands on these studies to better understand, prevent and treat many human diseases.
How this project entered the registry
Classified as human multiple sites / oral cavity / gut / stool / nasal / nasopharyngeal shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host study.description · “human microbiome samples taken from multiple body sites”
- body site study.description · “samples taken from multiple body sites”
- body site sample.attr.isolation_source · “G_DNA_Tongue dorsum (n=1133/2096)”
- body site sample.attr.isolation_source · “G_DNA_Stool (n=441/2096)”
- body site sample.attr.isolation_source · “G_DNA_Anterior nares (n=255/2096)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN00032498 | age_at_collection_days | 10957.5 | R2 | 0.75 | external.cmd source | age: 30; age_unit: Year; age_group: Adult |
| SAMN00032523 | age_at_collection_days | 10957.5 | R2 | 0.75 | external.microbiomedb source | Age: 30 year |
| SAMN00032498 | bmi | 29.0 | R2 | 0.75 | external.cmd source | bmi: 29 |
| SAMN00032498 | country | US | R2 | 0.75 | external.cmd source | country: United States |
| SAMN00032523 | country | US | R2 | 0.75 | external.microbiomedb source | Country: United States of America |
| SAMN00031101 | health_condition | healthy_control | R2 | 0.70 | external.mbodymap source | phenotype: Healthy; disease: D006262 |
| SAMN00031533 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN00032498 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN00031533 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN00032498 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN00031101 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN00031101 | subject_id | 241691 | R1 | 0.85 | sample.attr.gap_subject_id | 241691 |
Sequencing
11,164 runs over 2,096 samples · mean 2.02 Gbp per run (median 0.58 Gbp, total 22,517.08 Gbp; 11,164 runs with a base count) · layout PAIRED 11,081, SINGLE 83 · platform ILLUMINA 11,089, LS454 75 · models Illumina HiSeq 2000 (9,416), Illumina Genome Analyzer II (1,671), 454 GS FLX Titanium (75), Illumina HiSeq 1000 (2) · 0% of runs with a Sandpiper profile · first public 2010-04-16 – 2015-03-12
Authors (120)
Nayfach S first · Rodriguez-Mueller B · Garud N · Pollard KS last · Lloyd-Price J first · Mahurkar A · Rahnavard G · Crabtree J · Orvis J · Hall AB · Brady A · Creasy HH · McCracken C · Giglio MG · McDonald D · Franzosa EA · Knight R · White O · Huttenhower C last · McCann A first · Ryan FJ · Stockdale SR · Dalmasso M · Blake T · Ryan CA · Stanton C · Mills S · Ross PR · Hill C last · Pasolli E first · Asnicar F · Manara S · Zolfo M · Karcher N · Armanini F · Beghini F · Manghi P · Tett A · Ghensi P · Collado MC · Rice BL · DuLong C · Morgan XC · Golden CD · Quince C · Segata N last · Elmassry MM first · Kim S · Busby B last · Tisza MJ first · Buck CB last · Piscotta FJ first · Whitfield ST · Nakashige TG · Estrela AB · Ali T · Brady SF last · Xie XH first · Huang YJ · Han GS · Yu ZG · Ma YL last · Tian Z first · Zhang X · Yao G · Jin J · Zhang T · Sun C · Wang Z · Zhang Q last · Wang L first · Wang Q · Zhou Y last · Nooij S first · Plomp N · Sanders IMJG · Schout L · van der Meulen AE · Terveer EM · Norman JM · Larralde MF · Vossen RHAM · Kloet SL · Faber KN · Harmsen HJM · Zeller GF · Kuijper EJ · Smits WK · Ducarmon QR last · Connolly JP first · Kelly L last · Han W first · Wang Y · Liu X · Sun T · Xu J last · Ngwese MM first · Adegbite BR · Zinsou JF · Fitzstevens JL · Schmidt VT · Moure PAN · Maloum MN · Tyakht AV · Huus KE · Youngblut ND · Kremsner PG · Adegnika AA · Ley RE last · Schroer HW first · Raygoza Garay JA · Christakis NA · Bosch DE last · Valguarnera E first · Tung J · Pak JJ · Russell SK · Hecht DW · Schwartz DJ · Wardenburg JB last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, country. Share metadata
Downloads
PRJNA48479.csv.gz (50.9 KB) · parquet (147.0 KB) — all 2,096 samples, every field with route and confidence · PRJNA48479_determinations.csv.gz (92.2 KB) — 8,380 evidence rows