HMP Phase III gut metagenomes from healthy US adults
289 samples from healthy adult volunteers mainly residing in the USA, collected as part of the Human Microbiome Project Phase III whole-genome shotgun sequencing effort, including stool (gut) specimens; cross-sectional design. machine-written summary
289 samples · 312 runs · US · Adult · 2015 · 3.99 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 | 867 sample values (health condition, health condition detail, subject id) |
| ✓ Abstract / description | 289 sample values (country) |
| ○ Full text | read; no usable statement or table · PMC10059959, PMC10150486, PMC10258454, PMC10636326, PMC11786835, PMC5831082, PMC6047416, PMC8896461 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
26 of 61 people sampled more than once (54 samples; median 2, up to 3 per person). Schedule stated by the source: “Goal to capture 2nd and 3rd visits per individual, but no explicit visit dates/offsets given in dossier”.
Genera, mean relative abundance over 76 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 | 289 | 100% | ||||
| country | 289 | 100% | 289 | |||
| health_condition | 289 | 100% | 289 | |||
| subject_id | 289 | 100% | 289 | |||
| health_condition_detail | 289 | 100% | 289 |
- Strains, functions and dynamics in the expanded Human Microbiome Project. 2017 PMID 28953883 PMC5831082 own_data
- YAMP: a containerized workflow enabling reproducibility in metagenomics research. 2018 PMID 29917068 PMC6047416 own_data
- Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates. 2022 PMID 34987055 PMC8896461 own_data
- Evaluating the potential of assembler-binner combinations in recovering low-abundance and strain-resolved genomes from human metagenomes. 2025 PMID 39897886 PMC11786835 own_data
- Host genetic variation and its microbiome interactions within the Human Microbiome Project. 2018 PMID 29378630 PMC5789541 unsure
13 more
- Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome. 2019 PMID 30866812 PMC6417177
- Assessment of fecal DNA extraction protocols for metagenomic studies. 2020 PMID 32657325 PMC7355182
- Identification of Natural CRISPR Systems and Targets in the Human Microbiome. 2021 PMID 33217332 PMC7813156
- The human microbiome encodes resistance to the antidiabetic drug acarbose. 2021 PMID 34819672 PMC10258454
- 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
- 2 Hydroxybutyric Acid-Producing Bacteria in Gut Microbiome and Fusobacterium nucleatum Regulates 2 Hydroxybutyric Acid Level In Vivo. 2023 PMID 36984891 PMC10059959
- SNV-FEAST: microbial source tracking with single nucleotide variants. 2023 PMID 37121994 PMC10150486
- Bacterial indole-3-lactic acid affects epithelium-macrophage crosstalk to regulate intestinal homeostasis. 2023 PMID 37903267 PMC10636326
- Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota. 2024 PMID 38423015 PMC10939037
- Oral Microbial Translocation Genes in Gastrointestinal Cancers: Insights from Metagenomic Analysis. 2024 PMID 39458395 PMC11510655
- Gene-specific selective sweeps are pervasive across human gut microbiomes. 2026 PMID 41407853 PMC12916291
Archive description
The samples within this Bioproject represent the third phase (Phase III) of metagenomic sequencing (whole genome shotgun (WGS) sequencing) of microbial communities from specimens collected as a part of the NIH-supported Human Microbiome Project (HMP Consortium A framework for human microbiome research. Nature. 2012 Jun 13 486(7402):215-21. doi: 10.1038/nature11209). The sample collection represents a unique reference resource of microbiome samples from healthy adults largely residing in the USA at the time of sample collection. In the HMP Phase III component the goal has been to supplement previous WGS sequencing by generating additional sequence from as many of the specimens in the HMP collection as possible that had not been sequenced in the previous HMP Phase I and Phase II sequencing. In Phase III, a focus was placed on six of the 18 body sites: Stool (gut), Buccal mucosa (oral), Supragingival plaque (oral), Tongue dorsum (oral), Anterior nares (nasal), Posterior fornix (vaginal) and the goal was to further capture as many of the longitudinal samples (second and third visits by the same individual) as possible. From genomic DNA extracted from the collected specimens, WGS sequence was produced from libraries constructed from using a NexteraXT library construction protocol. All libraries were sequenced using a 100bp paired end approach using the Illumina HiSeq 2000 platform.
How this project entered the registry
Classified as human multiple sites / oral cavity / gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “Stool (gut), Buccal mucosa (oral)”
- body site sample.attr.isolation_source · “ORAL (n=172/289)”
- body site sample.attr.isolation_source · “GUT (n=89/289)”
- life stage study.description · “microbiome samples from healthy adults”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN03351441 | country | US | R4 | 0.50 | study.description | largely residing in the USA |
| SAMN03351441 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:description | Human Microbiome Phase 3 Metagenomic Environment |
| SAMN03351441 | health_condition_detail | Human Microbiome Phase 3 Metagenomic Environment | R1 | 0.85 | biosample.attribute:description | Human Microbiome Phase 3 Metagenomic Environment |
| SAMN03351441 | subject_id | 158155345 | R1 | 0.85 | biosample.attribute:source_material_id | 158155345 |
Sequencing
312 runs over 289 samples · mean 3.85 Gbp per run (median 3.91 Gbp, total 1,199.86 Gbp; 312 runs with a base count) · layout PAIRED 311, SINGLE 1 · platform ILLUMINA 312 · models Illumina HiSeq 2000 (312) · 86% of runs with a Sandpiper profile · first public 2015-04-03 – 2015-12-09
Authors (43)
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 · Piscotta FJ first · Whitfield ST · Nakashige TG · Estrela AB · Ali T · Brady SF last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Qin F first · Li J · Mao T · Feng S · Lai M last · Wang L first · Wang Q · Zhou Y last · Qayyum H first · Talib MS · Ali A · Kayani MUR last · Wolff R first · Garud NR last
Downloads
PRJNA275349.csv.gz (8.1 KB) · parquet (79.8 KB) — all 289 samples, every field with route and confidence · PRJNA275349_determinations.csv.gz (7.9 KB) — 1,156 evidence rows