Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease

Adam G. Clooney, Thomas D.S. Sutton, Andrey N. Shkoporov, Ross K. Holohan, Karen M. Daly, Orla O'Regan, Feargal Ryan, Lorraine A. Draper, Scott E. Plevy, R. Paul Ross, Colin Hill

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

The human gut virome is thought to significantly impact the microbiome and human health. However, most virome analyses have been performed on a limited fraction of known viruses. Using whole-virome analysis on a published keystone inflammatory bowel disease (IBD) cohort and an in-house ulcerative colitis dataset, we shed light on the composition of the human gut virome in IBD beyond this identifiable minority. We observe IBD-specific changes to the virome and increased numbers of temperate phage sequences in individuals with Crohn's disease. Unlike prior database-dependent methods, no changes in viral richness were observed. Among IBD subjects, the changes in virome composition reflected alterations in bacterial composition. Furthermore, incorporating both bacteriome and virome composition offered greater classification power between health and disease. This approach to analyzing whole virome across cohorts highlights significant IBD signals, which may be crucial for developing future biomarkers and therapeutics.

LanguageEnglish
Pages764-778.e5
JournalCell Host and Microbe
Volume26
Issue number6
DOIs
Publication statusPublished - 11 Dec 2019

Keywords

  • 16S
  • CD
  • Crohn's disease
  • IBD
  • inflammatory bowel disease
  • phage
  • phageome
  • UC
  • ulcerative colitis
  • virome
  • virus

ASJC Scopus subject areas

  • Parasitology
  • Microbiology
  • Virology

Cite this

Clooney, A. G., Sutton, T. D. S., Shkoporov, A. N., Holohan, R. K., Daly, K. M., O'Regan, O., ... Hill, C. (2019). Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease. Cell Host and Microbe, 26(6), 764-778.e5. https://doi.org/10.1016/j.chom.2019.10.009