Gut microbiome in alcoholic hepatitis, case-control
159 fecal samples from controls and patients with alcoholic hepatitis, profiled by shotgun metagenomic sequencing to study gut microbiota in alcoholic liver disease, using a case-control design. machine-written summary
159 samples · 159 runs · Age unknown · 2021 · 3.19 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 318 sample values (health condition detail, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12162233, PMC8781791, PMC9685977 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 148 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 | 0 | 0% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 159 | 100% | 159 | |||
| health_condition_detail | 159 | 100% | 159 |
- Machine Learning Applied to Omics Datasets Predicts Mortality in Patients with Alcoholic Hepatitis. 2022 PMID 35050163 PMC8781791 own_data
- Targeted inhibition of pathobiont virulence factor mitigates alcohol-associated liver disease. 2025 PMID 40441146 PMC12162233 own_data
- Machine learning for data integration in human gut microbiome. 2022 PMID 36419034 PMC9685977 unsure
Archive description
Alcohol-associated bacterial dysbiosis is important for the pathogenesis of alcoholic liver disease. To investigate if the intestinal microbiota mediate alcoholic liver disease, we perform shotgun metagenomic sequencing on human fecal samples (both control and patients with alcoholic hepatitis) to profile the gut microbiota communities, as well as differentially abundant bacterial species and genes. Whole-genome shotgun metagenomic sequencing is performed on HiSeq 4000 150PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.80. Assay shotgun_dna.
- host study.description · “human fecal samples”
- body site study.description · “human fecal samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104665844 | health_condition_detail | Human Gut Microbiota | R1 | 0.90 | sample.attr.arrayexpress_phenotype | Human Gut Microbiota |
| SAMEA104665844 | subject_id | 5207STDY7327544 | R1 | 0.85 | sample.attr.subject_id | 5207STDY7327544 |
Sequencing
159 runs over 159 samples · mean 3.16 Gbp per run (median 3.19 Gbp, total 503.00 Gbp; 159 runs with a base count) · layout PAIRED 159 · platform ILLUMINA 159 · models Illumina HiSeq 4000 (159) · 93% of runs with a Sandpiper profile · first public 2021-12-03
Authors (41)
Gao B first · Wu TC · Lang S · Jiang L · Duan Y · Fouts DE · Zhang X · Tu XM · Schnabl B last · Li P first · Luo H · Ji B · Nielsen J last · Yang Y first · Fondevila MF · Schöler D · Harberts A · Cabré N · Chen S · Shao Y · Vervier K · Miyamoto Y · Chu H · Yang L · Tan C · Eckmann L · Bosques-Padilla F · Verna EC · Abraldes JG · Brown RS · Vargas V · Altamirano J · Caballería J · Shawcross DL · Louvet A · Lucey MR · Mathurin P · Garcia-Tsao G · Bataller R · Stärkel P · Lawley TD
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, country, health_condition. Share metadata
Downloads
PRJEB25008.csv.gz (4.7 KB) · parquet (75.5 KB) — all 159 samples, every field with route and confidence · PRJEB25008_determinations.csv.gz (2.5 KB) — 318 evidence rows