Gut metagenome in hepatocellular carcinoma patients, Amiens
51 fecal samples from HCC patients at Amiens University Hospital, France, studied via shotgun metagenomics to assess gut microbiota changes across liver cancer stages; case-control design. machine-written summary
51 samples · 51 runs · FR · Adult · 2024 · 1.56 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 255 sample values (collection date, country, latitude, location locality, longitude) |
| – Abstract / description | no abstract or project description |
| ✓ Full text | 102 sample values (location site, subject id) · PMC11785905 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 204 sample values (age, health condition, health condition detail, sex) · 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 47 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 | 51 | 100% | ||||
| country | 51 | 100% | 51 | |||
| health_condition | 51 | 100% | 51 | |||
| subject_id | 51 | 100% | 51 | |||
| age_at_collection_days | 51 | 100% | 51 | |||
| collection_date | 51 | 100% | 51 | |||
| detailed_location | 51 | 100% | ||||
| health_condition_detail | 51 | 100% | 51 | |||
| latitude | 51 | 100% | 51 | |||
| location_locality | 51 | 100% | 51 | |||
| location_site | 51 | 100% | 51 | |||
| longitude | 51 | 100% | 51 | |||
| sex | 51 | 100% | 51 |
- Shotgun Metagenomics Reveals Bacteroides stercoris as a Fecal Biomarker Depleted in Late-Stage Hepatocellular Carcinoma. 2025 PMID 39895875 PMC11785905 own_data
Archive description
Simultaneous study of the gut and the liver is promising for a better understanding of hepatic malignancies, since both organs communicate through the gut-liver axis. Gut Microbiota (GM), which under normal circumstances contributes to the host homeostasis, may become dysbiotic, which can in turn contribute to liver inflammation. Prolonged liver inflammation in cirrhotic patients, for example due to gut-liver translocation and/or alcohol exposure, can lead to the development of Hepatocellular Carcinoma (HCC), the most frequent form of primary liver cancer, which is associated with a poor prognosis especially since it is often diagnosed at a stage too advanced to be curable. In this study, we characterized using shotgun metagenomics the GM of 51 HCC patients included in the prospective French CHIEF cohort in order to elucidate how the GM changes alongside HCC progression. Patients were retrospectively selected from the cohort of the Amiens University Hospital based on the availability of the stool samples and the Barcelona Classification of Liver Cancer (BCLC) of the liver biopsy at the inclusion.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “availability of the stool samples”
- life stage study.description · “HCC patients included in the prospective French CHIEF cohort”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN41388043 | age_at_collection_days | 25202.25 | R2 | 0.75 | external.gmrepo source | host_age: 69.0 |
| SAMN41388043 | collection_date | 2020-04-08 | R1 | 0.90 | biosample.attribute:collection_date | 2020-04-08 |
| SAMN41388043 | country | FR | R1 | 0.90 | sample.attr.geo_loc_name | France: Amiens |
| SAMN41388043 | health_condition | liver_disease | R2 | 0.75 | external.gmrepo source | phenotype: Carcinoma, Hepatocellular |
| SAMN41388043 | health_condition_detail | Carcinoma, Hepatocellular | R2 | 0.75 | external.gmrepo source | phenotype: Carcinoma, Hepatocellular |
| SAMN41388043 | latitude | 49.5200 | R1 | 0.90 | biosample.attribute:lat_lon | 49.52 N 2.15 E |
| SAMN41388043 | location_locality | Amiens | R1 | 0.85 | biosample.attribute:geo_loc_name | France: Amiens |
| SAMN41388043 | location_site | Amiens University Hospital | R3 | 0.60 | paper.fulltext.methods | cohort of the Amiens University Hospital based on the availability |
| SAMN41388043 | longitude | 2.1500 | R1 | 0.90 | biosample.attribute:lat_lon | 49.52 N 2.15 E |
| SAMN41388043 | sex | male | R2 | 0.75 | external.gmrepo source | sex: male |
| SAMN41388043 | subject_id | SAMN41388043 | R3 | 0.70 | design.one_sample_per_subject:fulltext | we characterized the GM of 51 HCC patients included in the prospective French CHIEF |
Sequencing
51 runs over 51 samples · mean 1.93 Gbp per run (median 1.56 Gbp, total 98.31 Gbp; 51 runs with a base count) · layout PAIRED 51 · platform ILLUMINA 51 · models NextSeq 550 (51) · 92% of runs with a Sandpiper profile · first public 2024-07-23
Authors (6)
Esparteiro D first · Fouquet G · Courtois A · Naassila M · Nguyen-Khac E · Marcq I last
Downloads
PRJNA1111312.csv.gz (2.8 KB) · parquet (73.4 KB) — all 51 samples, every field with route and confidence · PRJNA1111312_determinations.csv.gz (5.8 KB) — 561 evidence rows