Multi-omics analyses show disease, diet, and transcriptome interactions with the virome [journal]

Journal

Gastroenterology - October 1, 2021

Authors

Kathie A Mihindukulasuriya, Ruben AT Mars, Abigail J Johnson, Tonya Ward, Sambhawa Priya, Heather R Lekatz, Krishna R Kalari, Lindsay Droit, Tenghao Zheng, Ran Blekhman, Mauro D’Amato, Gianrico Farrugia, Dan Knights (professor), Scott A Handley, Purna C Kashyap

Abstract

Background & Aims

The gut virome includes eukaryotic viruses and bacteriophages that can shape the gut bacterial community and elicit host responses. The virome can be implicated in diseases, such as irritable bowel syndrome (IBS), where gut bacteria play an important role in pathogenesis. 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.

Methods

We selected 2 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.

Results

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 diarrhea-predominant IBS, and other Microviridae and Myoviridae species were elevated in constipation-predominant IBS compared to healthy controls. We identified correlations between subsets of the virome and bacterial composition (unclassifiable “dark matter” and phages) and diet (eukaryotic viruses).

Conclusions

We found that the gut virome is stable over time but varies among subsets of patients with IBS. It can be affected by diet and potentially influences host function via interactions with gut bacteria and/or altering host gene expression.

Link to full paper

Multi-omics analyses show disease, diet, and transcriptome interactions with the virome

Keywords

computational biology, bioinformatics

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