Fecal virome in alcohol use disorder, Belgium, case-control
90 fecal samples from adults and elderly individuals in Belgium, studying the intestinal virome in alcohol use disorder during active use and after abstinence, with comparison to liver disease progression, using a case-control design. machine-written summary
90 samples · 99 runs · BE · Adult · 2022 · 0.40 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 990 sample values (age, bmi, country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 270 sample values (collection date, location locality, location site) · PMC10192041, PMC9315129 |
| ○ 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 |
intervention — arms not resolved
design observational_with_procedure
longitudinal — not resolved
33 of 57 people sampled more than once (66 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 66 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 | 90 | 100% | ||||
| country | 90 | 100% | 90 | |||
| health_condition | 90 | 100% | 90 | |||
| subject_id | 90 | 100% | 90 | |||
| age_at_collection_days | 90 | 100% | 90 | |||
| bmi | 90 | 100% | 90 | |||
| collection_date | 90 | 100% | 90 | |||
| detailed_location | 90 | 100% | ||||
| health_condition_detail | 90 | 100% | 90 | |||
| latitude | 90 | 100% | 90 | |||
| location_locality | 90 | 100% | 90 | |||
| location_region | 90 | 100% | 90 | |||
| location_site | 90 | 100% | 90 | |||
| longitude | 90 | 100% | 90 | |||
| sex | 90 | 100% | 90 | |||
| timepoint_label | 90 | 100% | 90 |
- Intestinal virome in patients with alcohol use disorder and after abstinence. 2022 PMID 35368152 PMC9315129 own_data
- Any alcohol use in NAFLD patients is associated with significant changes to the intestinal virome. 2023 PMID 36631002 PMC10192041 own_data
Archive description
Shotgun sequencing of 0.8 micron filtered and nuclease-digested viral fraction from human feces. Both viral DNA and RNA (via cDNA) was sequenced on Illumina platforms. Human reads were removed using Kneaddata and Pathseqs.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host study.description · “viral fraction from human feces”
- body site study.title · “Intestinal virome in alcohol use disorder”
- life stage sample.attr.host_age · “42 (n=76/90)”
- life stage sample.attr.host_age · “73 (n=10/90)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN23797318 | age_at_collection_days | 14610.0 | R1 | 0.70 | sample.attr.host_age | 40 |
| SAMN23797318 | bmi | 18.3 | R1 | 0.90 | sample.attr.host_body_mass_index | 18.3 |
| SAMN23797318 | collection_date | 2017-04/2019-01 | R3 | 0.70 | paper.fulltext.methods | Brussels, Belgium, from April 2017 to January 2019 |
| SAMN23797318 | country | BE | R1 | 0.90 | sample.attr.geo_loc_name | Belgium |
| SAMN23797318 | health_condition | other_disease | R1 | 0.90 | biosample_attr | alcohol use disorder |
| SAMN23797347 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:host_disease | host_disease: non-alcoholic control |
| SAMN23797318 | health_condition_detail | AUD | R1 | 0.90 | sample.attr.liver_disord | AUD |
| SAMN23797318 | latitude | 50.8503 | R1 | 0.90 | biosample.attribute:lat_lon | 50.8503 N 4.3517 E |
| SAMN23797318 | location_locality | Brussels | R3 | 0.70 | paper.fulltext.methods | St. Luc University Hospital in Brussels, Belgium |
| SAMN23797318 | location_region | Brussels Capital | R1 | 0.60 | biosample.attribute:lat_lon | 50.8503 N 4.3517 E |
| SAMN23797318 | location_site | St. Luc University Hospital, Brussels | R3 | 0.70 | paper.fulltext.methods | elective alcohol rehabilitation at St. Luc University Hospital in Brussels |
| SAMN23797318 | longitude | 4.3517 | R1 | 0.90 | biosample.attribute:lat_lon | 50.8503 N 4.3517 E |
| SAMN23797318 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN23797318 | subject_id | B47 | R1 | 0.85 | sample.attr.host_subject_id | B47 |
| SAMN23797318 | timepoint_label | B47_2 | R1 | 0.85 | biosample.attribute:label | label: B47_2 |
Sequencing
99 runs over 90 samples · mean 0.39 Gbp per run (median 0.37 Gbp, total 38.88 Gbp; 99 runs with a base count) · layout PAIRED 99 · platform ILLUMINA 99 · models Illumina HiSeq 2500 (99) · 89% of runs with a Sandpiper profile · first public 2022-01-07 – 2022-01-08
Authors (10)
Hsu CL first · Zhang X · Jiang L · Lang S · Hartmann P · Pride D · Fouts DE · Stärkel P · Schnabl B last · Demir M
Downloads
PRJNA786875.csv.gz (4.0 KB) · parquet (76.4 KB) — all 90 samples, every field with route and confidence · PRJNA786875_determinations.csv.gz (10.3 KB) — 1,260 evidence rows