Fecal metagenomics in CRC, polyps, controls, Spain
90 fecal samples from adults in San Sebastian, Basque Country, Spain, divided into colorectal cancer, polyps, and healthy control groups (30 each), analyzed by shotgun metagenomics in a case-control design. machine-written summary
90 samples · 90 runs · ES · Adult · 2023 · 8.30 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 780 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, location site) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10827328, PMC13188985, PMC13281578, PMC13383993, PMC13489618 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 120 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 84 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 | 90 | 100% | ||||
| country | 90 | 100% | 90 | |||
| health_condition | 90 | 100% | 30 | 60 | ||
| subject_id | 90 | 100% | 90 | |||
| collection_date | 90 | 100% | 90 | |||
| detailed_location | 90 | 100% | ||||
| health_condition_detail | 90 | 100% | 30 | 60 | ||
| latitude | 90 | 100% | 90 | |||
| location_locality | 90 | 100% | 90 | |||
| location_region | 90 | 100% | 90 | |||
| location_site | 90 | 100% | 90 | |||
| longitude | 90 | 100% | 90 |
- Identification of taxonomic changes in the fecal bacteriome associated with colorectal polyps and cancer: potential biomarkers for early diagnosis. 2023 PMID 38293554 PMC10827328 own_data
- StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution. 2026 PMID 42097292 PMC13188985 own_data
- Cross sectional analysis of gut microbiota of ALS patients with and without percutaneous endoscopic gastrostomy. 2026 PMID 42622006 PMC13489618 own_data
- Gut fungal signatures in colorectal cancer and their potential for supporting diagnosis: a multi-cohort metagenomic analysis. 2026 PMID 42271362 PMC13281578 unsure
- Metagenome analysis reveals multi-kingdom gut microbiota as diagnostic markers for colorectal cancer. 2026 PMID 42519695 PMC13383993 unsure
Archive description
Colorectal cancer (CRC) is a disease of worldwide concern, which has an increasingly established relationship with the intestinal microbiota. Most of the cases of sporadic CRC emerge in patients with polyps, which also are influenced by gut microbiota. In this study, we utilized shotgun metagenomics to analyze the taxonomic diversity of Bacteria present in fecal samples of control, polyps, and CRC patients. The samples were collected between 2017 and 2018 by the Biodonostia Health Research Institute - Donostia Hospital in the city of San Sebastian, Spain, following the 2003 European Guidelines and the 2006 National Strategy against Cancer. The population-based screening of CRC was approved by the Basque Autonomous Government and implemented in 2009. The screening is based on the detection of occult blood in feces (FOB) using a biennial quantitative fecal immunochemical test (FIT), targeting women and men between 50 and 69 years old and a colonoscopy under sedation for FIT positive cases. 90 samples were collected and further divided into three groups based on colonoscopy results: control group (n31-60 stool samples from individuals with colonoscopy showing no intestinal lesions, no history of diarrhea, and no history of previous intestinal infection), polyps group (n1-30 stool samples from individuals with colonoscopy showing polyps on the surface of the colon or rectum), and the CRC group, which consists of individuals with biopsies confirming malignancy of colon or rectum lesions (n61-90).
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids 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 study.title · “taxonomic changes in feces bacteriome associated with”
- body site study.description · “Colorectal cancer (CRC) is”
- body site study.description · “detection of occult blood in feces (FOB)”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “test (FIT), targeting women and men between”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN34351544 | collection_date | 2017/2018 | R1 | 0.90 | biosample.attribute:collection_date | 2017/2018 |
| SAMN34351544 | country | ES | R1 | 0.90 | sample.attr.geo_loc_name | Spain: Donostia University Hospital, San Sebastian, Basque Country |
| SAMN34351574 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:alias | Intestinal metagenome of healthy patient 31 |
| SAMN34351544 | health_condition | colorectal_adenoma | R2 | 0.75 | external.gmrepo source | phenotype: Intestinal Polyps |
| SAMN34351574 | health_condition_detail | healthy | R1 | 0.70 | sample.name_rule:alias | Intestinal metagenome of healthy patient 31 |
| SAMN34351544 | health_condition_detail | Intestinal Polyps | R2 | 0.75 | external.gmrepo source | phenotype: Intestinal Polyps |
| SAMN34351544 | latitude | 43.2921 | R1 | 0.90 | biosample.attribute:lat_lon | 43.292062 N 1.970451 W |
| SAMN34351544 | location_locality | San Sebastián | R1 | 0.85 | biosample.attribute:geo_loc_name | Spain: Donostia University Hospital, San Sebastian, Basque Country |
| SAMN34351544 | location_region | Basque Country | R1 | 0.85 | biosample.attribute:geo_loc_name | Spain: Donostia University Hospital, San Sebastian, Basque Country |
| SAMN34351544 | location_site | Donostia University Hospital | R1 | 0.85 | biosample.attribute:geo_loc_name | Spain: Donostia University Hospital, San Sebastian, Basque Country |
| SAMN34351544 | longitude | -1.9705 | R1 | 0.90 | biosample.attribute:lat_lon | 43.292062 N 1.970451 W |
| SAMN34351544 | subject_id | 1 | R1 | 0.70 | sample.name_rule:alias | Intestinal metagenome of patient 1 with polyps |
Sequencing
90 runs over 90 samples · mean 8.20 Gbp per run (median 8.30 Gbp, total 738.09 Gbp; 90 runs with a base count) · layout PAIRED 90 · platform ILLUMINA 90 · models Illumina MiSeq (90) · 93% of runs with a Sandpiper profile · first public 2023-05-05
Authors (51)
Grion BAR first · Fonseca PLC · Kato RB · García GJY · Vaz ABM · Jiménez BN · Dambolenea AL · Garcia-Etxebarria K · Brenig B · Azevedo V · Bujanda L · Banales JM · Góes-Neto A last · Hennecart B first · Belda E · de Lahondès R · Zucker JD · Prifti E last · Zhang Z first · Lu T · Dong B · Liu J · Zhang Y · Li S · Liu H · Li X · Guan T · Guo H · Yan Q · Lei Z · Yu X · Wang L · Kang J · Li L · Zhao D last · Wang X first · Wang J · Chen W · Sun J · Li J · Hu H last · de la Rubia Ortí JE first · Bargues-Navarro G · Sancho-Castillo S · Privado J · Benlloch García M · Sanchis Sanchis CE · Garcia Martinez L · Cuerda-Ballester M · Bolós PM · Roig FJ last
Downloads
PRJNA961076.csv.gz (3.4 KB) · parquet (74.7 KB) — all 90 samples, every field with route and confidence · PRJNA961076_determinations.csv.gz (7.5 KB) — 900 evidence rows