Gut microbiome in alcohol use disorder abstinence, USA
76 gut metagenome samples from adults in the USA (67 patient samples, 9 healthy controls) in a case-control study of alcohol use disorder patients undergoing two-week alcohol abstinence. machine-written summary
76 samples · 76 runs · US · Adult · 2020 · 3.20 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 532 sample values (country, health condition, health condition detail, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 76 sample values (antibiotic exposure) · PMC7193112, PMC8621614 |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
Schedule stated by the source: “Fecal samples compared at WEEK 1 and WEEK 3 (before and after 2-week alcohol abstinence)”; stated follow-up 14 d.
Genera, mean relative abundance over 70 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 | 76 | 100% | ||||
| country | 76 | 100% | 76 | |||
| health_condition | 76 | 100% | 76 | |||
| subject_id | 76 | 100% | 76 | |||
| antibiotic_exposure | 76 | 100% | 76 | |||
| detailed_location | 76 | 100% | ||||
| health_condition_detail | 76 | 100% | 76 | |||
| latitude | 76 | 100% | 76 | |||
| location_region | 76 | 100% | 76 | |||
| longitude | 76 | 100% | 76 |
- Functional Microbial Responses to Alcohol Abstinence in Patients With Alcohol Use Disorder. 2020 PMID 32390870 PMC7193112 own_data
- Integrative Analysis of Metabolome and Microbiome in Patients with Progressive Alcohol-Associated Liver Disease. 2021 PMID 34822424 PMC8621614 own_data
Archive description
Excessive alcohol consumption is associated with hepatic steatosis and dysregulation of the gut microbiota in patients with alcohol use disorder. However, how gut microbiota responds when patients stop drinking has not been well studied. In this study, we use shotgun metagenomic sequencing to elucidate the alterations in the functional capacity of gut microbiota in patients with alcohol use disorder when they stop drinking for two-weeks.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.71. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “alterations in the functional capacity of gut microbiota”
- life stage study.title · “Patients with Alcohol Use Disorder”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN14420296 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | did not take antibiotics or immunosuppressive medication during the 2 months |
| SAMN14420296 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN14420296 | health_condition | healthy_control | R1 | 0.80 | biosample_attr | Group1_Ctrl |
| SAMN14420296 | health_condition_detail | Group1_Ctrl | R1 | 0.90 | sample.attr.host_disease | Group1_Ctrl |
| SAMN14420296 | latitude | 32.7157 | R1 | 0.90 | biosample.attribute:lat_lon | 32.7157 N 117.1611 W |
| SAMN14420296 | location_region | California | R1 | 0.60 | biosample.attribute:lat_lon | 32.7157 N 117.1611 W |
| SAMN14420296 | longitude | -117.1611 | R1 | 0.90 | biosample.attribute:lat_lon | 32.7157 N 117.1611 W |
| SAMN14420296 | subject_id | 25544_5#1 | R1 | 0.85 | sample.attr.host_subject_id | 25544_5#1 |
Sequencing
76 runs over 76 samples · mean 3.23 Gbp per run (median 3.20 Gbp, total 245.28 Gbp; 76 runs with a base count) · layout PAIRED 76 · platform ILLUMINA 76 · models Illumina HiSeq 4000 (76) · 92% of runs with a Sandpiper profile · first public 2020-03-23
Authors (31)
Gao B first · Emami A · Zhou R · Lang S · Duan Y · Wang Y · Jiang L · Loomba R · Brenner DA · Stärkel P · Schnabl B last · Zhu Y · Gao N · Shen W · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last
Downloads
PRJNA613834.csv.gz (2.7 KB) · parquet (73.5 KB) — all 76 samples, every field with route and confidence · PRJNA613834_determinations.csv.gz (4.3 KB) — 608 evidence rows