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The colonic virome in inflammatory bowel disease

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Dataset overview

Participants 51
Samples 97
Reuse readiness 7.3/10 evidence-backed score

The colonic mucosal virome in inflammatory bowel disease reveals Crassvirales depletion and disease-specific virome features.

Yan A, Butcher J, Mack DR, Stintzi A. · Gut microbes · 2025

Abstract

The mucosal virome is increasingly recognized for its potential role in shaping intestinal health and disease. Building on previous findings, we analyzed the mucosal virome from 51 individuals, including newly diagnosed treatment naïve participants with ulcerative colitis (UC), Crohn's disease (CD), and non-inflammatory bowel disease (non-IBD) controls, incorporating longitudinal sampling for a subset of the participants. Viromes were highly individualized, with no shared or core components across participants. Unlike fecal virome studies, we observed no significant associations between mucosal virome diversity and mucosal inflammation, disease subtype, or sampling site. However, there was positive correlation between virome and bacteriome diversity, particularly in CD, suggesting the presence of dynamic interactions that influence microbial community structure. <i>Crassvirales</i> was abundant in the mucosa layer and, consistent with prior studies, <i>Crassvirales</i> abundance was reduced in IBD, irrespective of inflammation status or IBD subtype. These findings highlight their potential as biomarkers of virome health. Our data also revealed the potential presence of altered bacteriome-virome interactions and longitudinal sampling revealed a persistent subset of viruses, potentially shaping disease progression and remission dynamics. Our study underscores the importance of distinguishing microbial community dynamics across IBD subtypes and highlights <i>Crassvirales</i> as key players in mucosal immunity.

doi:10.1080/19490976.2025.2539450 ↗ PMID 40754936 ↗ PMC12323425 ↗

Study facts

Organism
human gut metagenome
Platform
Illumina NovaSeq 6000
Age group
paediatric
Disease groups
Crohn's disease, Non-IBD controls, Ulcerative colitis
Anatomical sites
—

Data availability

Specific data assets have not been resolved from the source yet — see the source repository below for the full file listing.

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Participant counts are documented
  • Sample counts are documented

Limitations

  • Not documented: feature/otu tables are advertised
  • Not documented: taxonomic tables are advertised
Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

FieldValueEvidence
assay.platform Illumina NovaSeq 6000 from source
ENA instrument_model=Illumina NovaSeq 6000

Section ENA study report, offset —
assay.sequencing_type shotgun_metagenomics
Shotgun DNA sequencing was performed at the Génome Québec CES using the NEB Ultra II library preparation kit

Section Materials and methods—Virome sequencing and host-read removal, offset 11200

Cohort

FieldValueEvidence
cohort.age_group paediatric
A cross-sectional cohort of 51 pediatric participants were recruited

Section Materials and methods—Participants, offset 5040
cohort.crohns_disease_participants 21
35 children newly diagnosed with IBD [CD: n = 21 (60%); UC: n = 14 (40%)].

Section Materials and methods—Participants, offset 5150
cohort.disease_activity_metadata_available True
clinical severity at initial colonoscopy was reported using the Pediatric Crohn’s Disease Activity Index

Section Materials and methods—Participants, offset 5600
cohort.non_ibd_controls 16
Additionally, 16 participants who underwent diagnostic colonoscopy for suspected IBD... were included as a non-IBD control group.

Section Materials and methods—Participants, offset 5300
cohort.study_design cross_sectional
A cross-sectional cohort of 51 pediatric participants

Section Materials and methods—Participants, offset 5000
cohort.total_participants 51
A cross-sectional cohort of 51 pediatric participants were recruited between April 2018 and December 2019.

Section Materials and methods—Participants, offset 5000
cohort.treatment_exposure_documented True
subsequent samples were influenced by varying illness severities and the introduction of different IBD treatments

Section Results—Exploratory analysis assessing the temporal stability of the MLI virome, offset 28000
cohort.ulcerative_colitis_participants 14
35 children newly diagnosed with IBD [CD: n = 21 (60%); UC: n = 14 (40%)].

Section Materials and methods—Participants, offset 5150

Data_Assets

FieldValueEvidence
data_assets.open_access True from source
"inPMC": "Y", "isOpenAccess": "Y"

Section Publication metadata, offset —
data_assets.pipeline_or_tool_versions True
raw sequencing reads were trimmed and filtered using Cutadapt 2.10 ... and Trimmomatic 0.36

Section Materials and methods—Virome sequencing and host-read removal, offset 11400
data_assets.raw_reads True
Host-removed, high-quality sequencing reads are available under BioProject PRJNA1004560.

Section Data availability statement, offset 41000

Specimens

FieldValueEvidence
specimens.body_site colonic mucosal-luminal interface, proximal and distal colon
These regional MLI samples were collected from both the PC and DC of each participant

Section Materials and methods—Sample processing and VLP extraction, offset 9550
specimens.inflamed_status_available True
Active colonic IBD (i.e., inflamed mucosa) was described by the visual appearance of colonic mucosa during colonoscopy

Section Materials and methods—Participants, offset 6200
specimens.longitudinal_sampling True
Longitudinal regional colonic MLI samples were available for some participants (n = 8)

Section Results—Study population, offset 14200
specimens.number_of_samples 97 from source
ENA sample_count=97

Section ENA study report, offset —
specimens.sample_type luminal_aspirate
Mucosal-luminal interface (MLI) aspirates were obtained during colonoscopy

Section Materials and methods—Sample processing and VLP extraction, offset 9000