Human gut virome in liver disease across multiple countries
Shotgun sequencing of DNA and RNA viruses from the fecal viral fraction of 139 samples from adults and elderly individuals in Belgium, the USA, France, the UK, Spain, and Mexico, mostly with liver disease or other disease. machine-written summary
139 samples · 139 runs · US, BE, FR · Adult · 2020 · 0.29 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,070 sample values (age, bmi, collection date, country, health condition, health condition detail, location locality, location region) |
| – Abstract / description | no abstract or project description |
| ○ Full text | read; no usable statement or table · PMC8159727 |
| – 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 97 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 | 139 | 100% | ||||
| country | 134 | 96% | 134 | |||
| health_condition | 124 | 89% | 124 | |||
| subject_id | 139 | 100% | 139 | |||
| health_condition_detail | 139 | 100% | 139 | |||
| age_at_collection_days | 138 | 99% | 138 | |||
| sex | 138 | 99% | 138 | |||
| bmi | 126 | 91% | 126 | |||
| collection_date | 82 | 59% | 82 | |||
| detailed_location | 50 | 36% | ||||
| location_region | 28 | 20% | 28 | |||
| location_locality | 22 | 16% | 22 |
- Intestinal Virome in Patients With Alcoholic Hepatitis. 2020 PMID 32654263 PMC8159727 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 by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “viral fraction from human feces”
- life stage sample.attr.host_age · “53 (n=123/139)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN14968302 | age_at_collection_days | 17897.2 | R1 | 0.70 | sample.attr.host_age | 49 |
| SAMN14968302 | bmi | 29.5 | R1 | 0.90 | sample.attr.host_body_mass_index | 29.5 |
| SAMN14968302 | collection_date | 2014-06 | R1 | 0.90 | biosample.attribute:collection_date | 2014-06 |
| SAMN14968302 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Wisconsin |
| SAMN14968302 | health_condition | liver_disease | R1 | 0.90 | biosample_attr | alcoholic hepatitis |
| SAMN14968302 | health_condition_detail | AH | R1 | 0.90 | sample.attr.liver_disord | AH |
| SAMN14968307 | location_locality | San Diego | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: San Diego |
| SAMN14968302 | location_region | Wisconsin | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Wisconsin |
| SAMN14968302 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN14968302 | subject_id | 56 | R1 | 0.85 | sample.attr.host_subject_id | 56 |
Sequencing
139 runs over 139 samples · mean 0.29 Gbp per run (median 0.29 Gbp, total 40.11 Gbp; 139 runs with a base count) · layout PAIRED 139 · platform ILLUMINA 139 · models Illumina HiSeq 2500 (130), Illumina MiniSeq (9) · 78% of runs with a Sandpiper profile · first public 2020-05-27
Authors (0)
No author record.
Downloads
PRJNA608022.csv.gz (5.8 KB) · parquet (77.9 KB) — all 139 samples, every field with route and confidence · PRJNA608022_determinations.csv.gz (8.9 KB) — 1,070 evidence rows