CRC patients in Italy: microbiome case-control study
N=203 stool samples from colorectal cancer patients in Italy. Case-control design studying gut microbiome associations with CRC and adenoma progression as part of the ONCOBIOME consortium. machine-written summary
203 samples · 203 runs · Adult · 2025 · 3.74 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 203 sample values (collection date) |
| ✓ Abstract / description | 402 sample values (health condition, health condition detail) |
| ✓ Full text | 406 sample values (location locality, location site) · PMC12283368 |
| ✓ Supplementary tables | 613 sample values (age, bmi, health condition, health condition detail, sex) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
country: sequence archive and supplementary table disagree for 203 samples (e.g. IT vs CZ) — withheld.
The sources disagree on 203 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (40 of 203)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA115284779 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284780 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284781 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284782 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284783 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284784 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284785 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284786 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284787 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284788 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284789 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284790 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284791 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284792 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284793 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284794 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284795 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284796 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284797 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284798 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284799 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284800 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284801 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284802 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284803 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284804 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284805 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284806 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284807 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284808 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284809 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284810 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284811 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284812 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284813 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284814 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284815 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284816 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284817 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284818 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
Genera, mean relative abundance over 185 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 | 203 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 203 | 100% | 2 | 201 | ||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 203 | 100% | 203 | |||
| bmi | 203 | 100% | 203 | |||
| collection_date | 203 | 100% | 203 | |||
| detailed_location | 203 | 100% | ||||
| health_condition_detail | 203 | 100% | 2 | 201 | ||
| location_locality | 203 | 100% | 203 | |||
| location_site | 203 | 100% | 203 | |||
| sex | 203 | 100% | 203 |
- 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
Shotgun metagenomic stool samples from CRC patients enrolled at Masaryk Memorial Cancer Institute (Brno, Czech Republic) from 2015 to 2019. This cohort was established to study the microbiome-CRC link at different stages of the adenoma-carcinoma sequences as part of the ONCOBIOME consortium.
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 study.title · “Gut microbiome samples from”
- body site study.description · “Shotgun metagenomic stool samples from CRC”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA115284779 | age_at_collection_days | 21550.0 | R2 | 0.75 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!Age] | 59 |
| SAMEA115284779 | bmi | 40.0 | R2 | 0.75 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!BMI] | 40 |
| SAMEA115284779 | collection_date | 2019 | R1 | 0.90 | biosample.attribute:collection_date | 2019 |
| SAMEA115284800 | health_condition | colorectal_adenoma | R2 | 0.75 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!Study condition] | Adenoma |
| SAMEA115284779 | health_condition | colorectal_cancer | R4 | 0.50 | study.description | Shotgun metagenomic stool samples from CRC patients |
| SAMEA115284800 | health_condition_detail | Adenoma | R2 | 0.75 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!Study condition] | Adenoma |
| SAMEA115284779 | health_condition_detail | CRC patients enrolled at Masaryk Memorial Cancer Institute | R4 | 0.50 | study.description | CRC patients enrolled at Masaryk Memorial Cancer Institute |
| SAMEA115284779 | location_locality | Brno | R3 | 0.70 | paper.fulltext.methods | Masaryk Memorial Cancer Institute (Brno, Czech Republic) from 2015 |
| SAMEA115284779 | location_site | Masaryk Memorial Cancer Institute | R3 | 0.70 | paper.fulltext.methods | Patients were enrolled at Masaryk Memorial Cancer Institute |
| SAMEA115284779 | sex | female | R2 | 0.75 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!Sex] | female |
Sequencing
203 runs over 203 samples · mean 5.15 Gbp per run (median 3.74 Gbp, total 1,045.96 Gbp; 203 runs with a base count) · layout PAIRED 203 · platform ILLUMINA 203 · models unspecified (203) · 91% of runs with a Sandpiper profile · first public 2025-01-23 – 2025-02-21
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
Help complete this project
2 of the 4 core fields are below 50% coverage: country, subject_id. Share metadata
Downloads
PRJEB72524.csv.gz (6.8 KB) · parquet (78.6 KB) — all 203 samples, every field with route and confidence · PRJEB72524_determinations.csv.gz (11.3 KB) — 1,624 evidence rows