Gut metagenomes linked to colorectal cancer, Seattle, USA
198 gut shotgun metagenome samples from Seattle, Washington, USA, analyzed using gene-level clustering to identify bacterial genes and co-abundant gene clusters associated with colorectal cancer or health. machine-written summary
183 samples · 198 runs · US · Age unknown · 2025 · 1.06 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,647 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11464690 |
| ○ 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
18 of 29 people sampled more than once (172 samples; median 3, up to 35 per person). Schedule stated by the source: “Per-subject repeated fecal sampling with timepoint-labeled IDs (e.g., _t1, _t2); median 2 samples/subject, max 35”.
Genera, mean relative abundance over 178 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 | 183 | 100% | 183 | |||
| health_condition | 183 | 100% | 183 | |||
| subject_id | 183 | 100% | 183 | |||
| collection_date | 183 | 100% | 183 | |||
| detailed_location | 183 | 100% | ||||
| health_condition_detail | 183 | 100% | 183 | |||
| latitude | 183 | 100% | 183 | |||
| location_locality | 183 | 100% | 183 | |||
| location_region | 183 | 100% | 183 | |||
| longitude | 183 | 100% | 183 |
- Colorectal cancer-associated bacteria are broadly distributed in global microbiomes and drivers of precancerous change. 2024 PMID 39384807 PMC11464690 unsure
Archive description
The gut microbiome is implicated in the pathogenesis of colorectal cancer (CRC), but the full scope of this dialogue is unknown. Here we aimed to define the scale and membership of the body of CRC- and health-associated gut bacteria in global populations. We performed a microbiome-CRC correlation analysis of published ultra-deep shotgun metagenomic sequencing data from global microbiome surveys, utilizing a de novo (reference-agnostic) gene-level clustering approach to identify protein-coding co-abundant gene (CAGs) clusters. We link an unprecedented approximately 23-40 percent of gut bacteria to CRC or health, split nearly evenly as CRC- or health-associated. These microbes encode 2,319 CAGs encompassing 427,261 bacterial genes significantly enriched or depleted in CRC. We identified many microbes that had not previously been linked to CRC, thus expanding the scope of known unknowns of CRC-associated microbes. We performed an agnostic CAG-based screen of bacterial isolates and validated predicted effects of previously unimplicated bacteria in preclinical models, in which we observed differential induction of precancerous adenomas and field effects. Single-cell RNA sequencing disclosed microbiome-induced senescence-associated gene expression signatures in discrete colonic populations including fibroblasts. In organoid co-cultures, primary colon fibroblasts from mice with microbiomes promoted significantly greater growth than fibroblasts from microbiome-depleted mice. These results offer proof-of-principle for gene-level metagenomic analysis enabling discovery of microbiome links to health and demonstrate that the microbiome can drive precancer states, thereby potentially revealing novel cancer prevention opportunities.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “10090”
- host run.host_tax_id · “9606”
- host study.description · “validated predicted effects of previously unimplicated bacteria in preclinical models”
- body site study.description · “The gut microbiome is implicated”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN43512661 | collection_date | 2021-07-05 | R1 | 0.90 | biosample.attribute:collection_date | 2021-07-05 |
| SAMN43512661 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Washington, Seattle |
| SAMN43512661 | health_condition | colorectal_cancer | R1 | 0.85 | biosample.attribute:description | description: CRC |
| SAMN43512661 | health_condition_detail | CRC | R1 | 0.85 | biosample.attribute:description | description: CRC |
| SAMN43512661 | latitude | 47.6000 | R1 | 0.90 | biosample.attribute:lat_lon | 47.60 N 122.33 W |
| SAMN43512661 | location_locality | Seattle | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Washington, Seattle |
| SAMN43512661 | location_region | Washington | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Washington, Seattle |
| SAMN43512661 | longitude | -122.3300 | R1 | 0.90 | biosample.attribute:lat_lon | 47.60 N 122.33 W |
| SAMN43512661 | subject_id | 2_005 | R1 | 0.85 | sample.attr.personid | 2_005 |
Sequencing
198 runs over 183 samples · mean 1.14 Gbp per run (median 1.06 Gbp, total 226.70 Gbp; 198 runs with a base count) · layout PAIRED 157, SINGLE 41 · platform ILLUMINA 198 · models NextSeq 2000 (157), Illumina NovaSeq 6000 (26), Illumina MiniSeq (15) · 90% of runs with a Sandpiper profile · first public 2025-03-30
Authors (11)
Minot SS first · Li N · Srinivasan H · Ayers JL · Yu M · Koester ST · Stangis MM · Dominitz JA · Halberg RB · Grady WM · Dey N last
Downloads
PRJNA1157403.csv.gz (4.8 KB) · parquet (76.4 KB) — all 183 samples, every field with route and confidence · PRJNA1157403_determinations.csv.gz (10.1 KB) — 1,647 evidence rows