The Human Intestinal Virome at the Mucosal-luminal Interface

Abstract

The virome is a core but understudied part of the human gut microbiome. New laboratory and bioinformatic technologies have greatly advanced our understanding of our gut viruses, however most studies are based on fecal sampling. The objective of this research was to study the human virome at the intestinal mucosal surface, which enables multisite sampling and the characterization of mucosal viruses at the site of intestinal inflammation. First, I developed a protocol to extract viral nucleic acids from human mucosal-luminal interface (MLI) samples, which are obtained during endoscopy. I showed that we could reproducibly profile the mucosal virome community. Second, I performed deep multiomic sequencing on MLI samples from three pediatric participants with ulcerative colitis, demonstrating a distinct mucosa-associated viral community in comparison to stool. The combination of metavirome, metagenome, and metatranscriptome sequencing enabled studies of microbial interactions, including bacteriome-virome relationships and prophage analysis. Lastly, we applied our virome methodology in a cohort of over fifty pediatric subjects undergoing investigation for inflammatory bowel disease. We demonstrated that viromes are highly individualized and found that Crassvirales were enriched in the proximal colon in participants without IBD. We also performed longitudinal sampling to identify a persistent and highly abundant viral subpopulation. Altogether, we have contributed methodology and commentary for virome sequencing of an important human sample type, extended the repertoire of virome sequences, and characterized the mucosa-associated virome in the setting of inflammatory bowel disease. These efforts provide practical guidance for future studies on the intestinal virome in human health and disease.