The gut virome includes eukaryotic viruses and bacteriophages that can shape the gut bacterial community and elicit host responses. The virome may be implicated in diseases such as irritable bowel syndrome (IBS), where gut bacteria play an important role in pathogenesis. Herein we provide a comprehensive and longitudinal characterization of the virome including DNA and RNA viruses and paired multi-omics data in a cohort of healthy subjects and patients with IBS.
We selected two consecutive stool samples per subject from a longitudinal study cohort and performed metagenomic sequencing on DNA and RNA viruses after enriching for viral-like particles. Viral sequence abundance was evaluated over time as well as in the context of diet, bacterial composition and function, metabolite levels, colonic gene expression, host genetics, and IBS subsets.
We found that the gut virome was temporally stable and correlated with the colonic transcriptome. We identified IBS-subset specific changes in phage populations- Microviridae, Myoviridae, and Podoviridae species were elevated in IBS-D, and other Microviridae and Myoviridae species were elevated in IBS-C compared to healthy controls. We identified correlations between subsets of the virome and bacterial composition (unclassifiable “dark matter” and phages) and diet (eukaryotic viruses).
We found that the gut virome is stable over time but varies among subsets of IBS patients. It can be affected by diet and potentially influences host function via interactions with gut bacteria and/or altering host gene expression.

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