CRC/adenoma vs control gut microbiome, case-control
124 stool samples from a case-control study comparing colorectal cancer, adenoma, and control patients. Note: archive record states Prague/Plzen, Czech Republic, while curated sample facts list Italy — this conflict is unresolved. machine-written summary
124 samples · 124 runs · Adult · 2025 · 3.65 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 182 sample values (collection date, health condition, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12283368 |
| ✓ Supplementary tables | 558 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 124 samples (e.g. IT vs CZ) — withheld.
The sources disagree on 124 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 124)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA115284983 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284984 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284985 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284986 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284987 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284988 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284989 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284990 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284991 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284992 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284993 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284994 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284995 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284996 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284997 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284998 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115284999 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285000 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285001 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285002 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285003 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285004 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285005 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285006 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285007 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285008 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285009 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285010 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285011 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285012 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285013 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285014 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285015 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285016 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285017 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285018 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285019 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285020 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285021 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
| SAMEA115285022 | country | IT (sequence archive) | CZ (supplementary table) | withheld: neither value published |
Genera, mean relative abundance over 116 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 | 124 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 124 | 100% | 29 | 95 | ||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 124 | 100% | 124 | |||
| collection_date | 124 | 100% | 124 | |||
| health_condition_detail | 124 | 100% | 29 | 95 | ||
| sex | 124 | 100% | 124 | |||
| bmi | 120 | 97% | 120 |
- 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 control, adenoma and CRC patients from hospitals in Prague and Plzen, Czech Republic. This cohort was established as part of the ONCOBIOME consortium in order to study the characteristics of the microbiome-CRC link in the different phases of the adenoma-carcinoma sequences, and their differentiation from healthy controls.
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 control,”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA115284983 | age_at_collection_days | 28124.0 | R2 | 0.85 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!Age] | 77 |
| SAMEA115284983 | bmi | 23.38 | R2 | 0.85 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!BMI] | 23.38435374 |
| SAMEA115284983 | collection_date | 2019 | R1 | 0.90 | biosample.attribute:collection_date | 2019 |
| SAMEA115284983 | health_condition | colorectal_cancer | R1 | 0.70 | sample.name_rule:sample_title | Sample_S24761_CC_CRC698_FE_DNA_DIA |
| SAMEA115284997 | health_condition | colorectal_cancer | R2 | 0.85 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!Study condition] | CRC |
| SAMEA115284983 | health_condition_detail | CRC | R1 | 0.70 | sample.name_rule:sample_title | Sample_S24761_CC_CRC698_FE_DNA_DIA |
| SAMEA115284997 | health_condition_detail | CRC | R2 | 0.85 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!Study condition] | CRC |
| SAMEA115284983 | sex | female | R2 | 0.85 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!Sex] | female |
Sequencing
124 runs over 124 samples · mean 4.87 Gbp per run (median 3.65 Gbp, total 603.83 Gbp; 124 runs with a base count) · layout PAIRED 124 · platform ILLUMINA 124 · models unspecified (124) · 94% of runs with a Sandpiper profile · first public 2025-01-24
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
PRJEB72525.csv.gz (4.6 KB) · parquet (75.5 KB) — all 124 samples, every field with route and confidence · PRJEB72525_determinations.csv.gz (7.3 KB) — 740 evidence rows