Gut virome/bacteria in IBD vs healthy controls, UK
171 stool samples from UK Crohn's disease, ulcerative colitis, and healthy control subjects, analyzed for viral and bacterial composition in a case-control design. machine-written summary
171 samples · 171 runs · GB · Age unknown · 2015 · 0.60 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,026 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ✓ Abstract / description | 171 sample values (health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10072058, PMC10563150, PMC10919464, PMC4312520, PMC5796561, PMC7729129, PMC9927247 |
| ○ 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 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 | 0 | 0% | ||||
| country | 171 | 100% | 171 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 171 | 100% | 171 | |||
| collection_date | 171 | 100% | 171 | |||
| detailed_location | 171 | 100% | ||||
| health_condition_detail | 171 | 100% | 171 | |||
| latitude | 171 | 100% | 171 | |||
| location_region | 171 | 100% | 171 | |||
| longitude | 171 | 100% | 171 |
- Disease-specific alterations in the enteric virome in inflammatory bowel disease. 2015 PMID 25619688 PMC4312520 own_data
- Temperate bacteriophages infecting the mucin-degrading bacterium Ruminococcus gnavus from the human gut. 2023 PMID 36994608 PMC10072058 own_data
- Phables: from fragmented assemblies to high-quality bacteriophage genomes. 2023 PMID 37738590 PMC10563150 own_data
- Gut microbiota-based discriminative model for patients with ulcerative colitis: A meta-analysis and real-world study. 2024 PMID 38457570 PMC10919464 own_data
- A human gut phage catalog correlates the gut phageome with type 2 diabetes. 2018 PMID 29391057 PMC5796561 unsure
3 more
- Gut Microbiota and Metabolic Specificity in Ulcerative Colitis and Crohn's Disease. 2020 PMID 33330572 PMC7729129
- A Matching Strategy To Guide Donor Selection for Ulcerative Colitis in Fecal Microbiota Transplantation: Meta-Analysis and Analytic Hierarchy Process. 2023 PMID 36472435 PMC9927247
- Characterization of the phyllosphere virome of fresh vegetables and potential transfer to the human gut. 2025 PMID 40210629 PMC11986028
Archive description
Decreases in the diversity of enteric bacterial populations are observed in patients with Crohn’s disease (CD) and ulcerative colitis (UC). Less is known about the virome in these diseases. We show that the enteric virome is abnormal in CD and UC patients. In-depth analysis of preparations enriched for free virions in the intestine revealed that CD and UC were associated with a significant expansion of Caudovirales bacteriophages. The viromes of CD and UC patients were disease- and cohort-specific. Importantly, it did not appear that expansion and diversification of the enteric virome was secondary to changes in bacterial populations. These data support a model in which changes in the virome may contribute to intestinal inflammation and bacterial dysbiosis. We conclude that the virome is a candidate for contributing to, or being a biomarker for, human inflammatory bowel disease and speculate that the enteric virome may play a role in other diseases.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.85. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.title · “stool samples from IBD patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA3323619 | collection_date | 2011 | R1 | 0.90 | biosample.attribute:collection_date | 2011 |
| SAMEA3323619 | country | GB | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | United Kingdom |
| SAMEA3323619 | health_condition_detail | mixed_case_control: Cohort includes both Crohn's disease, ulcerative colitis patients and healthy controls | R4 | 0.50 | study.title | IBD patients and healthy controls |
| SAMEA3323619 | latitude | 52.0868 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.08675 0.171567 |
| SAMEA3323619 | location_region | England | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.08675 0.171567 |
| SAMEA3323619 | longitude | 0.1716 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.08675 0.171567 |
| SAMEA3323619 | subject_id | 10568 | R1 | 0.50 | sample.attr.anonymized_name | 10568 |
Sequencing
171 runs over 171 samples · mean 0.59 Gbp per run (median 0.60 Gbp, total 101.65 Gbp; 171 runs with a base count) · layout PAIRED 171 · platform ILLUMINA 171 · models Illumina MiSeq (171) · 3% of runs with a Sandpiper profile · first public 2015-04-03
Authors (64)
Norman JM first · Handley SA · Baldridge MT · Droit L · Liu CY · Keller BC · Kambal A · Monaco CL · Zhao G · Fleshner P · Stappenbeck TS · McGovern DP · Keshavarzian A · Mutlu EA · Sauk J · Gevers D · Xavier RJ · Wang D · Parkes M · Virgin HW last · Zhang B first · Yang L · Ning H · Cao M · Chen Z · Chen Q · Lian G · Tang H · Wang Q · Wang J · Lin Z · Wen J · Liu Y · Xuan J · Li X · Lin A · He J · Zhang L · Hou X · Zeng Q · Xiao C last · Mallawaarachchi V first · Roach MJ · Decewicz P · Papudeshi B · Giles SK · Grigson SR · Bouras G · Hesse RD · Inglis LK · Hutton ALK · Dinsdale EA · Edwards RA last · Zhang R first · Chen J · Liu L · Qiu C last · Park JW first · Yun YE · Cho JA · Yoon SI · In SA · Park EJ · Kim MS last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJEB7772.csv.gz (4.9 KB) · parquet (77.3 KB) — all 171 samples, every field with route and confidence · PRJEB7772_determinations.csv.gz (8.3 KB) — 1,197 evidence rows