Colon tissue virome in IBD and non-IBD patients, USA
26 colon tissue samples from USA patients, including ulcerative colitis, Crohn's disease, colorectal cancer/adenoma, and other conditions, examining the enteric virome in a case-control design. machine-written summary
26 samples · 26 runs · US · Infant / toddler · 2021 · 3.76 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 205 sample values (age, collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 26 sample values (location site) · PMC9416881 |
| ○ 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 |
age: two sequence archives disagree for 4 samples (e.g. 23.0 vs 230.1) — withheld.
The sources disagree on 4 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (4)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA8584004 | age | 23.0 (sequence archive) | 230.1 (sequence archive) | withheld: neither value published |
| SAMEA8584008 | age | 23.0 (sequence archive) | 230.1 (sequence archive) | withheld: neither value published |
| SAMEA8584015 | age | 23.0 (sequence archive) | 230.1 (sequence archive) | withheld: neither value published |
| SAMEA8584026 | age | 16.0 (sequence archive) | 164.4 (sequence archive) | withheld: neither value published |
Genera, mean relative abundance over 1 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 | 26 | 100% | ||||
| country | 26 | 100% | 26 | |||
| health_condition | 26 | 100% | 26 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 26 | 100% | 26 | |||
| detailed_location | 26 | 100% | ||||
| health_condition_detail | 26 | 100% | 26 | |||
| latitude | 26 | 100% | 26 | |||
| location_region | 26 | 100% | 26 | |||
| location_site | 26 | 100% | 26 | |||
| longitude | 26 | 100% | 26 | |||
| age_at_collection_days | 22 | 85% | 22 | |||
| sex | 1 | 4% | 1 |
- Human enteric viruses autonomously shape inflammatory bowel disease phenotype through divergent innate immunomodulation. 2022 PMID 35394816 PMC9416881 own_data
Archive description
Altered enteric microorganisms in the context of genetics shape inflammatory bowel disease (IBD)phenotypes,but insight is limited to bacteria and fungi. We found that healthy human intestine resident eukaryotic viruses and bacteriophages(collectively, the virome) directly immunomodulate by eliciting atypical anti-inflammatory innate immune programs. Conversely, IBD patient viromes provoked an inflammatory response, which could be dampened by healthy virome responses. The colon tissue virome was perturbed in IBD patients, including enriched Enterovirus B that helps explain detrimental consequences of MDA5loss-of-function in IBD. 10Mice with a “humanized” healthy virome had attenuated intestinal inflammation while those with an IBD-derived virome exhibited exacerbated inflammation. Our results demonstrate that enteric virome fluctuations do not just correlate with disease but active innate recognition of healthy or IBD human enteric viromes autonomously drives disease phenotypes. Harnessing the virome may be beneficial in IBD and other diseases.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host study.title · “Human enteric viruses shape disease phenotype”
- body site study.description · “healthy human intestine resident eukaryotic viruses”
- life stage sample.attr.host_age · “0.51 (n=24/26)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA8584005 | age_at_collection_days | 186.0 | R1 | 0.85 | sample.attr.host_age | 0.51 |
| SAMEA8584004 | collection_date | 2019-02-14 | R1 | 0.90 | biosample.attribute:collection_date | 2019-02-14 |
| SAMEA8584004 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA8584004 | health_condition | colorectal_cancer | R1 | 0.90 | biosample_attr | Colon cancer |
| SAMEA8584004 | health_condition_detail | Colon cancer | R1 | 0.90 | sample.attr.gastrointestinal_tract_disorder | Colon cancer |
| SAMEA8584004 | latitude | 42.3626 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 42.3626 n 71.0676 w |
| SAMEA8584004 | location_region | Massachusetts | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 42.3626 n 71.0676 w |
| SAMEA8584004 | location_site | Massachusetts General Hospital | R3 | 0.70 | paper.fulltext.methods | Prospective Registry in IBD Study at Massachusetts General Hospital |
| SAMEA8584004 | longitude | -71.0676 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 42.3626 n 71.0676 w |
| SAMEA8584004 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
Sequencing
26 runs over 26 samples · mean 3.92 Gbp per run (median 3.76 Gbp, total 102.05 Gbp; 26 runs with a base count) · layout PAIRED 26 · platform ILLUMINA 26 · models NextSeq 500 (26) · 54% of runs with a Sandpiper profile · first public 2021-06-01
Authors (15)
Adiliaghdam F first · Amatullah H · Digumarthi S · Saunders TL · Rahman RU · Wong LP · Sadreyev R · Droit L · Paquette J · Goyette P · Rioux JD · Hodin R · Mihindukulasuriya KA · Handley SA · Jeffrey KL last
Downloads
PRJEB44121.csv.gz (2.0 KB) · parquet (72.2 KB) — all 26 samples, every field with route and confidence · PRJEB44121_determinations.csv.gz (3.0 KB) — 231 evidence rows