Gut metagenome/metatranscriptome in US men cohort
1307 stool samples from healthy adult men in a USA subcohort of the Health Professionals Follow-up Study, profiled by metagenomic and metatranscriptomic sequencing for taxonomic and functional composition; cross-sectional design. machine-written summary
1,307 samples · 2,598 runs · US · Adult · 2017 · 2.78 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 5,228 sample values (collection date, country, subject id, timepoint) |
| ✓ Abstract / description | 379 sample values (health condition) |
| ○ Full text | read; no usable statement or table · PMC10607447, PMC10948025, PMC11338639, PMC11496760, PMC11585353, PMC11614764, PMC12358190, PMC12721379, PMC12775044, PMC13548641, PMC6016839, PMC6557121, PMC6759757, PMC6764417, PMC6821265, PMC7060530, PMC7384232, PMC7615765, PMC8201803, PMC8564485, PMC8966171 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 4,091 sample values (antibiotic exposure, health condition, health condition detail, sex) · from BugSigDB, curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
301 of 308 people sampled more than once (1,300 samples; median 4, up to 8 per person). Schedule stated by the source: “Up to four stool samples per subject: one set ~48 hours apart, second set ~6 months later”.
Genera, mean relative abundance over 1,267 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 | 1,307 | 100% | ||||
| country | 1,307 | 100% | 1,307 | |||
| health_condition | 1,307 | 100% | 928 | 379 | ||
| subject_id | 1,307 | 100% | 1,307 | |||
| antibiotic_exposure | 1,307 | 100% | 1,307 | |||
| collection_date | 1,307 | 100% | 1,307 | |||
| timepoint_label | 1,307 | 100% | 1,307 | |||
| health_condition_detail | 928 | 71% | 928 | |||
| sex | 928 | 71% | 928 |
- A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. 2021 PMID 34083435 PMC8201803 own_data
- Stability of the human faecal microbiome in a cohort of adult men. 2018 PMID 29335554 PMC6016839 own_data
- Metatranscriptome of human faecal microbial communities in a cohort of adult men. 2018 PMID 29335555 PMC6557121 own_data
- MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome. 2019 PMID 31116375 PMC6821265 own_data
- Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes. 2019 PMID 31402174 PMC6764417 own_data
32 more
- Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly. 2019 PMID 31551328 PMC6759757
- Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men. 2020 PMID 31972239 PMC7384232
- Dietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome. 2022 PMID 35350985 PMC8966171
- Mapping the T cell repertoire to a complex gut bacterial community. 2023 PMID 37587342 PMC10948025
- Genomes of a Novel Group of Phages That Use Alternative Genetic Code Found in Human Gut Viromes. 2023 PMID 37894982 PMC10607447
- Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans. 2024 PMID 38484069 PMC7615765
- Phylogenetic diversity of putative nickel-containing carbon monoxide dehydrogenase-encoding prokaryotes in the human gut microbiome. 2024 PMID 39166974 PMC11338639
- Microbiome-based correction for random errors in nutrient profiles derived from self-reported dietary assessments. 2024 PMID 39438479 PMC11496760
- Metatranscriptomics-guided discovery and characterization of a polyphenol-metabolizing gut microbial enzyme. 2024 PMID 39471822 PMC11585353
- Phylogenetic diversity of the carbon monoxide-utilizing prokaryotes and their divergent carbon monoxide metabolisms in the human gut microbiome 2023
- Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children. 2020 PMID 32143621 PMC7060530
- The human gut archaeome: identification of diverse haloarchaea in Korean subjects. 2020 PMID 32753050 PMC7409454
- Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease. 2021 PMID 33769280 PMC8062136
- Dispersal strategies shape persistence and evolution of human gut bacteria. 2021 PMID 34111423 PMC8288446
- The Capacity to Produce Hydrogen Sulfide (H2S) via Cysteine Degradation Is Ubiquitous in the Human Gut Microbiome. 2021 PMID 34745023 PMC8564485
- The human microbiome encodes resistance to the antidiabetic drug acarbose. 2021 PMID 34819672 PMC10258454
- Identification and Characterization of Major Bile Acid 7α-Dehydroxylating Bacteria in the Human Gut. 2022 PMID 35736002 PMC9426597
- Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions. 2023 PMID 37553697 PMC10408196
- <i>Anaerostipes hadrus</i>, a butyrate-producing bacterium capable of metabolizing 5-fluorouracil. 2024 PMID 38470044 PMC11036815
- Transient colonizing microbes promote gut dysbiosis and functional impairment. 2024 PMID 39245657 PMC11381545
- Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts. 2024 PMID 39558133 PMC11602726
- Characteristics of putative keystones in the healthy adult human gut microbiota as determined by correlation network analysis. 2024 PMID 39633812 PMC11614764
- Discovery of robust and highly specific microbiome signatures of non-alcoholic fatty liver disease. 2025 PMID 39810263 PMC11730835
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. 2025 PMID 39947133 PMC12268991
- The prototypic crAssphage is a linear phage-plasmid. 2025 PMID 40730160 PMC12358190
- Systematically investigating and identifying bacteriocins in the human gut microbiome. 2025 PMID 40902606 PMC12648112
- Bioactive Plasmid- and Phage-Encoded Antimicrobial Peptides (AMPs) in the Human Gut: A Metatranscriptome-Virome Profiling Reveals Exploratory Links to Metabolic Human Diseases. 2025 PMID 41315055 PMC12775044
- Metatranscriptomic-driven insights into mucosal glycan degradation by the human gut microbiota. 2025 PMID 41342600 PMC12721379
- Temporal dynamics of gut biosynthetic gene clusters link persistent colonization and engraftment in fecal microbiota transplantation. 2026 PMID 41741396 PMC12940132
- CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data. 2026 PMID 42103726 PMC13377033
- Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals. 2026 PMID 42312244 PMC13269251
- Circulating imidazole propionate and coronary heart disease risk: interplay between histidine intake, fiber, and gut microbiome. 2026 PMID 42332773 PMC13548641
Archive description
We conducted metagenomic and metatranscriptomic sequencing of the human gut microbiome among 308 participants enrolled in a subcohort of men nested within the Health Professionals Follow-up Study. Using a previously validated self-sampling stool collection method (PMID24843156), participants provided up to four stool samples – one set of samples collected approximately 48 hours apart followed by a second set approximately 6 months later. DNA extracted from 929 stool samples and RNA extracted from 378 stool samples was reverse-transcribed to cDNA and sequenced using the Illumina HiSeq platform. Raw data were filtered to remove low quality and human reads. Metagenomic and metatranscriptomic read data were then profiled for functional and taxonomic composition using the HUMAnN2 and MetaPhlAn2 platforms respectively.
How this project entered the registry
Classified as human gut / stool mixed assays of adult by sonnet_x2 with confidence 0.75. Assay mixed.
- host run.host_tax_id · “9606”
- host study.description · “human gut microbiome among 308 participants”
- body site study.description · “stool collection method”
- life stage study.description · “men nested within the Health Professionals Follow-up Study”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN06164391 | antibiotic_exposure | no | R2 | 0.60 | external.bugsigdb source | Antibiotics exclusion: 3 months |
| SAMN06164391 | collection_date | 2012 | R1 | 0.90 | biosample.attribute:collection_date | 2012 |
| SAMN06164391 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN06164391 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN06164458 | health_condition | healthy_control | R4 | 0.50 | paper.abstract | healthy human faeces |
| SAMN06164391 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN06164391 | sex | male | R2 | 0.75 | external.cmd source | sex: Male |
| SAMN06164391 | subject_id | 10042055 | R1 | 0.85 | sample.attr.host_subject_id | 10042055 |
| SAMN06164391 | timepoint_label | SF05 | R1 | 0.85 | sample.attr.sample_timepoints | SF05 |
Sequencing
2,598 runs over 1,307 samples · mean 1.37 Gbp per run (median 1.10 Gbp, total 3,568.73 Gbp; 2,598 runs with a base count) · layout SINGLE 1,307, PAIRED 1,291 · platform ILLUMINA 2,598 · models Illumina HiSeq 2000 (2,598) · 87% of runs with a Sandpiper profile · first public 2017-01-15 – 2018-01-13
Authors (21)
Tisza MJ first · Buck CB last · Bauchinger F first · Berry D last · Garcia-Guevara F first · Resink T · Clasen F · Uhlén M · Achour A · Shoaie S last · Goulet L first · Plaza Oñate F · Famechon A · Quinquis B · Belda E · Prifti E · Le Chatelier E · Gautreau G last · Katayama YA first · Kamikawa R · Yoshida T last
Downloads
PRJNA354235.csv.gz (32.9 KB) · parquet (118.4 KB) — all 1,307 samples, every field with route and confidence · PRJNA354235_determinations.csv.gz (67.9 KB) — 9,698 evidence rows