Gut metagenome in gastric cancer, case-control, China
154 fecal metagenome samples from a case-control study in China examining gut microbiota alterations associated with gastric cancer. machine-written summary
154 samples · 154 runs · CN · Adult · 2025 · 3.92 Gbp / sample
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what each source gave
| ✓ Sequence archive | 616 sample values (collection date, country, latitude, longitude) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
Genera, mean relative abundance over 152 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 | 154 | 100% | ||||
| country | 154 | 100% | 154 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 154 | 100% | 154 | |||
| latitude | 154 | 100% | 154 | |||
| longitude | 154 | 100% | 154 |
Archive description
Alterations in gut microbiota contribute to gastric cancer (GC) pathogenesis. We conducted deep metagenomic sequencing on fecal samples from a discovery cohort of 182 GC patients and 306 healthy controls, anlyzing microbial composition and networks, functions, predicted metabolomes, and cytokines across enterotypes. Four enterotypes were identified in the discovery cohort, among which pattern 4 emerged as a novel non-canonical type highly enriched in GC (71.4% vs. 13.8% in controls). Individuals with pattern 4 was featured by enrichment of Escherichia coli, Streptococcus spp. (e.g., S. parasanguinis, S. anginosus, S. salivarius), and Ligilactobacillus salivarius in gut microbiota, coupled with depletion of short-chain fatty acid (SCFA)-producing microbes. Functionally, it showed heightened xenobiotic and nitrogen metabolism but reduced C19-steroid biosynthesis and glycosaminoglycan degradation. Metabolome predictions revealed toxin accumulation and SCFA loss in their serum and feces, while immune profiling indicated broad immunosuppression with reduced cytokine levels. Integration of enterotyping markedly improved the case-control discrimination accuracy of random forest classifers in the discovery cohort (optimal area under the curve [AUC] = 0.971). Importantly, pattern 4 persisted in the validation cohort (40.0% of patients vs. 12.9% of controls), and the discovery-trained classifer maintained high diagnostic accuracy (AUC = 0.883). We identify a distinct GC-associated enterotype marked by multi-level dysregulation in taxonomy, function, metabolism, and immuniy, serving as a robust diagnostic biomarker and offering new insights into microbiota-mediated gastric carcinogenesis.
How this project entered the registry
Classified as human gut / stool / oral cavity / 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 · “Multi-kingdom gut microbiome for gastric”
- body site study.description · “Alterations in gut microbiota contribute to”
- body site study.description · “S. anginosus, S. salivarius ), and Ligilactobacillus”
- body site study.description · “loss in their serum and feces, while”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA120371873 | collection_date | 2024 | R1 | 0.90 | biosample.attribute:collection_date | 2024 |
| SAMEA120371873 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA120371873 | latitude | 39.0000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39 121 |
| SAMEA120371873 | longitude | 121.0000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39 121 |
Sequencing
154 runs over 154 samples · mean 4.24 Gbp per run (median 3.92 Gbp, total 653.07 Gbp; 154 runs with a base count) · layout PAIRED 154 · platform ILLUMINA 154 · models Illumina NovaSeq 6000 (154) · 99% of runs with a Sandpiper profile · first public 2025-10-23 – 2025-12-05
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJEB97759.csv.gz (4.0 KB) · parquet (74.8 KB) — all 154 samples, every field with route and confidence · PRJEB97759_determinations.csv.gz (3.4 KB) — 616 evidence rows