Gut virome in IBD vs healthy controls, China
139 fecal samples from a Chinese case-control study comparing IBD patients (Crohn's disease and ulcerative colitis) with healthy controls, using viral-like particle and bulk virome sequencing to characterize gut virome alterations. machine-written summary
139 samples · 139 runs · CN · Age unknown · 2023 · 7.42 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 556 sample values (collection date, country, health condition, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 278 sample values (antibiotic exposure, location locality) · PMC11256409, PMC12615640, PMC12988232, PMC13057028 |
| ○ 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 118 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 | 139 | 100% | 139 | |||
| health_condition | 139 | 100% | 139 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 139 | 100% | 139 | |||
| collection_date | 139 | 100% | 139 | |||
| detailed_location | 139 | 100% | ||||
| health_condition_detail | 139 | 100% | 139 | |||
| location_locality | 139 | 100% | 139 |
- Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease. 2024 PMID 39026313 PMC11256409 own_data
- Human intestinal fungus Clavispora lusitaniae attenuates colitis through Pyruvate decarboxylase-derived Indole-3-ethanol. 2025 PMID 41233306 PMC12615640 unsure
- Microbiota-derived IPA protects against colitis by regulating intestinal HMGCS2-mediated ketogenesis to facilitate mucosal healing. 2026 PMID 41651833 PMC12988232 unsure
- A microbiota-IPA axis facilitates intestinal stem cell-mediated regeneration in colitis through a Hopx-associated program. 2026 PMID 41741429 PMC13057028 unsure
Archive description
The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of it in IBD patients, especially across diverse geographic populations, remains limited. In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 Crohn's disease and 56 ulcerative colitis) and 166 healthy counterparts, via viral-like particle (VLP) and bulk virome sequencing of their feces. Building upon these insights into the IBD gut virome, we have illuminated potential biomarkers for prognosis and therapy in IBD patients, setting the stage for further exploration of viromes in related conditions.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host study.description · “71 IBD patients”
- body site study.description · “gut virome-wide association study”
- body site study.description · “sequencing of their feces”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114624372 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | none of the participants had taken antibiotics within 1 month |
| SAMEA114624372 | collection_date | 2021 | R1 | 0.90 | biosample.attribute:collection_date | 2021 |
| SAMEA114624372 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA114624372 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:description | description: gut metagenome of healthy controls |
| SAMEA114624372 | health_condition_detail | gut metagenome of healthy controls | R1 | 0.85 | biosample.attribute:description | description: gut metagenome of healthy controls |
| SAMEA114624372 | location_locality | Dalian | R3 | 0.70 | paper.fulltext.methods | recruited from Dalian, Liaoning province, China |
Sequencing
139 runs over 139 samples · mean 7.91 Gbp per run (median 7.42 Gbp, total 1,098.98 Gbp; 139 runs with a base count) · layout PAIRED 139 · platform ILLUMINA 139 · models Illumina NovaSeq 6000 (139) · 85% of runs with a Sandpiper profile · first public 2023-11-16 – 2023-11-20
Authors (40)
Tian X first · Li S · Wang C · Zhang Y · Feng X · Yan Q · Guo R · Wu F · Wu C · Wang Y · Huo X · Ma X last · Mai Z · Xu Z · Li Y · Yin R · Li J · Yu Z · Wu Y · Tu S · Shao X · Meng J · Zhang Z · Wei W · Jing X · Qin Z · Wu J · Xu W · Dong B · Gao J · Qu A · Chen S · Zhang L · Gong P · Shan B · Shi H · Zhu SJ last · Ma L · Zhao X · Cheng H
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJEB67456.csv.gz (4.2 KB) · parquet (74.8 KB) — all 139 samples, every field with route and confidence · PRJEB67456_determinations.csv.gz (4.5 KB) — 834 evidence rows