Gut metagenome case-control study of CRC in US adults
897 gut metagenome samples from adults in the USA, part of a case-control study on the gut microbiome's association with colorectal cancer (CRC) and adenomas. machine-written summary
897 samples · 897 runs · US · Adult · 2025 · 6.15 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 4,485 sample values (collection date, country, latitude, location region, longitude) |
| ✓ Abstract / description | 897 sample values (health condition detail) |
| ✓ Full text | 897 sample values (subject id) · PMC12283368 |
| ✓ Supplementary tables | 3,587 sample values (age, bmi, health condition, sex) |
| – 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 |
Genera, mean relative abundance over 883 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 | 897 | 100% | ||||
| country | 897 | 100% | 897 | |||
| health_condition | 897 | 100% | 897 | |||
| subject_id | 897 | 100% | 897 | |||
| age_at_collection_days | 897 | 100% | 897 | |||
| collection_date | 897 | 100% | 897 | |||
| detailed_location | 897 | 100% | ||||
| health_condition_detail | 897 | 100% | 897 | |||
| latitude | 897 | 100% | 897 | |||
| location_region | 897 | 100% | 897 | |||
| longitude | 897 | 100% | 897 | |||
| sex | 897 | 100% | 897 | |||
| bmi | 896 | 100% | 896 |
- Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer. 2025 PMID 40461820 PMC12283368 unsure
Archive description
MicroN Study Prescient data
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site external_curation.infant_catalog · “body_site_call stool”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN47412685 | age_at_collection_days | 24106.5 | R2 | 0.75 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!Age] | 66 |
| SAMN47412685 | bmi | 29.28 | R2 | 0.75 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!BMI] | 29.28 |
| SAMN47412685 | collection_date | 2024-10-30 | R1 | 0.90 | biosample.attribute:collection_date | 2024-10-30 |
| SAMN47412685 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN47412685 | health_condition | colorectal_adenoma | R2 | 0.75 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!Study condition] | Adenoma |
| SAMN47412685 | health_condition_detail | mixed_case_control: CRC patients vs adenoma patients vs healthy controls | R4 | 0.40 | paper.abstract | 6 new cohorts (n = 1,625) providing |
| SAMN47412685 | latitude | 38.9800 | R1 | 0.90 | biosample.attribute:lat_lon | 38.98 N 77.11 W |
| SAMN47412685 | location_region | Maryland | R1 | 0.60 | biosample.attribute:lat_lon | 38.98 N 77.11 W |
| SAMN47412685 | longitude | -77.1100 | R1 | 0.90 | biosample.attribute:lat_lon | 38.98 N 77.11 W |
| SAMN47412685 | sex | female | R2 | 0.75 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!Sex] | female |
| SAMN47412685 | subject_id | SAMN47412685 | R3 | 0.70 | design.one_sample_per_subject:fulltext | Cohort 5 includes fecal samples from 448 healthy individuals, 435 patients with adenoma and 14 patients with CRC from NHSII. |
Sequencing
897 runs over 897 samples · mean 6.16 Gbp per run (median 6.15 Gbp, total 5,522.19 Gbp; 897 runs with a base count) · layout SINGLE 897 · platform ILLUMINA 897 · models Illumina HiSeq 4000 (897) · 98% of runs with a Sandpiper profile · first public 2025-03-18
Authors (40)
Piccinno G first · Thompson KN · Manghi P · Ghazi AR · Thomas AM · Blanco-Míguez A · Asnicar F · Mladenovic K · Pinto F · Armanini F · Punčochář M · Piperni E · Heidrich V · Fackelmann G · Ferrero G · Tarallo S · Nguyen LH · Yan Y · Keles NA · Tuna BG · Vymetalkova V · Trompetto M · Liska V · Hucl T · Vodicka P · Bencsiková B · Čarnogurská M · Popovici V · Marmorino F · Cremolini C · Pardini B · Cordero F · Song M · Chan AT · Derosa L · Zitvogel L · Huttenhower C · Naccarati A · Budinska E · Segata N last
Downloads
PRJNA1237248.csv.gz (28.2 KB) · parquet (113.3 KB) — all 897 samples, every field with route and confidence · PRJNA1237248_determinations.csv.gz (66.2 KB) — 9,866 evidence rows