Gut metagenome in CRC vs healthy adults, Shanghai, China
172 fecal metagenome samples from colorectal cancer patients and healthy controls in Shanghai, China, in a case-control study of gut microbial and fungal associations with colorectal cancer. machine-written summary
172 samples · 172 runs · CN · Adult · 2022 · 10.97 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,700 sample values (age, bmi, collection date, country, health condition, health condition detail, latitude, location locality) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 172 sample values (location site) · PMC10239823, PMC10436198, PMC11510655, PMC11995172, PMC12090783, PMC12283368, PMC12907713, PMC12992544, PMC13188911, PMC13281578, PMC13381771, PMC13383993, PMC13561539, PMC8813618 |
| ✓ Supplementary tables | 162 sample values (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 |
health condition: sample names and GMrepo disagree for 2 samples (e.g. healthy_control vs colorectal_cancer) — withheld.
The sources disagree on 2 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 (2)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN37757529 | health condition | healthy_control (sample names) | colorectal_cancer (GMrepo) | withheld: neither value published |
| SAMN37757530 | health condition | healthy_control (sample names) | colorectal_cancer (GMrepo) | withheld: neither value published |
Genera, mean relative abundance over 159 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 | 172 | 100% | ||||
| country | 172 | 100% | 172 | |||
| health_condition | 170 | 99% | 170 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 172 | 100% | 172 | |||
| collection_date | 172 | 100% | 172 | |||
| detailed_location | 172 | 100% | ||||
| health_condition_detail | 172 | 100% | 172 | |||
| location_locality | 172 | 100% | 172 | |||
| location_site | 172 | 100% | 172 | |||
| sex | 168 | 98% | 6 | 162 | ||
| bmi | 166 | 97% | 166 | |||
| latitude | 166 | 97% | 166 | |||
| location_region | 166 | 97% | 166 | |||
| longitude | 166 | 97% | 166 |
- Gut fungal landscape in colorectal cancer and its cross-kingdom interplay with gut microbial ecology. 2026 PMID 41704769 PMC12907713 own_data
- Enhanced microbiota-derived mucinases in colorectal cancer patients revealed by gut metagenome probing coupled with functional validation. 2026 PMID 41940696 PMC13188911 own_data
- Multi-kingdom microbiota analyses identify bacterial-fungal interactions and biomarkers of colorectal cancer across cohorts. 2022 PMID 35087227 PMC8813618 unsure
- Metagenomic analysis reveals gut plasmids as diagnosis markers for colorectal cancer. 2023 PMID 37283932 PMC10239823 unsure
- Taxonomic and functional profiling of fecal metagenomes for the early detection of colorectal cancer. 2023 PMID 37601681 PMC10436198 unsure
9 more
- Oral Microbial Translocation Genes in Gastrointestinal Cancers: Insights from Metagenomic Analysis. 2024 PMID 39458395 PMC11510655
- Transmission of antimicrobial resistance genes from the environment to human gut is more pronounced in colorectal cancer patients than in healthy subjects. 2025 PMID 40236771 PMC11995172
- Temporal network analysis of gut microbiota unveils aging trajectories associated with colon cancer. 2025 PMID 40298386 PMC12090783
- 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
- Distinct prophage infections in colorectal cancer-associated Bacteroides fragilis. 2026 PMID 41654659 PMC12992544
- Instance-based transfer learning enables cross-cohort early detection of colorectal cancer. 2026 PMID 42106361 PMC13381771
- Gut fungal signatures in colorectal cancer and their potential for supporting diagnosis: a multi-cohort metagenomic analysis. 2026 PMID 42271362 PMC13281578
- Metagenome analysis reveals multi-kingdom gut microbiota as diagnostic markers for colorectal cancer. 2026 PMID 42519695 PMC13383993
- Fedflow: cloud orchestration for federated learning with the FeatureCloud platform. 2026 PMID 42725323 PMC13561539
Archive description
Microbial DNA extracted from fecal sample from CRC patients and healthy subjects.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly 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 · “DNA extracted from stool samples of CRC”
- body site study.description · “DNA extracted from fecal sample from CRC”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage sample.attr.host_age · “65y (n=61/172)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN19290898 | age_at_collection_days | 17532.0 | R1 | 0.90 | sample.attr.host_age | 48y |
| SAMN19290898 | bmi | 24.19 | R1 | 0.90 | sample.attr.host_body_mass_index | 24.187 |
| SAMN19290898 | collection_date | 2019 | R1 | 0.90 | biosample.attribute:collection_date | 2019 |
| SAMN19290898 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Shanghai |
| SAMN19290898 | health_condition | colorectal_cancer | R1 | 0.70 | sample.name_rule:alias | CRC_1 |
| SAMN19290901 | health_condition | colorectal_cancer | R1 | 0.70 | sample.name_rule:library_name | CRC_4 |
| SAMN19290898 | health_condition_detail | CRC | R1 | 0.70 | sample.name_rule:alias | CRC_1 |
| SAMN19290901 | health_condition_detail | CRC | R1 | 0.70 | sample.name_rule:library_name | CRC_4 |
| SAMN37757529 | health_condition_detail | HS | R1 | 0.70 | sample.name_rule:isolate | HS_110 |
| SAMN19290898 | latitude | 31.1900 | R1 | 0.90 | biosample.attribute:lat_lon | 31.19 N 121.45 E |
| SAMN19290898 | location_locality | Shanghai | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Shanghai |
| SAMN19290898 | location_region | Shanghai Shi | R1 | 0.60 | biosample.attribute:lat_lon | 31.19 N 121.45 E |
| SAMN19290898 | location_site | Huzhou Central Hospital | R3 | 0.70 | paper.fulltext.methods | recruited from Huzhou Central Hospital between January 2022 and December 2023 |
| SAMN19290898 | longitude | 121.4500 | R1 | 0.90 | biosample.attribute:lat_lon | 31.19 N 121.45 E |
| SAMN37757529 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN19290899 | sex | male | R2 | 0.75 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!Sex] | Sex: male |
Sequencing
172 runs over 172 samples · mean 10.98 Gbp per run (median 10.97 Gbp, total 1,887.91 Gbp; 172 runs with a base count) · layout PAIRED 172 · platform ILLUMINA 172 · models Illumina NovaSeq 6000 (172) · 93% of runs with a Sandpiper profile · first public 2022-01-30 – 2023-10-12
Authors (48)
Chen Z first · Zhang Z · Nie BN · Huang W · Zhu Y · Zhang L · Xu M · Wang M · Yuan C · Liu N · Wang X · Tian J · Ba Q · Wang Z last · Yinhang W first · Xueli J · Zheng W · Xiaojian Y · Shu X · Qingjie Z · Ying L · Shuwen H last · Li Y first · Zhang H · Xiang B · Zhang Y · Zhang M last · Lu T · Dong B · Liu J · 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 · Weilguny L first · Probul N · Ren Y · Pons N · Baumbach J · Almeida M last
Downloads
PRJNA731589.csv.gz (6.2 KB) · parquet (79.1 KB) — all 172 samples, every field with route and confidence · PRJNA731589_determinations.csv.gz (16.0 KB) — 2,034 evidence rows