Abstract
While the human gut virome has been increasingly explored in recent years, nearly all studies have been limited to fecal sampling. The mucosal–luminal interface has been established as a viable sample type for profiling the microbial biogeography of the gastrointestinal tract. We have developed a protocol to extract nucleic acids from viruses at the mucosal–luminal interface of the proximal and distal colon. Colonic viromes from pediatric patients with Crohn's disease demonstrated high interpatient diversity and low but significant intrapatient variation between sites. Whole metagenomics was also performed to explore virome–bacteriome interactions and to compare the viral communities observed in virome and whole metagenomic sequencing. A site-specific study of the human gut virome is a necessary step to advance our understanding of virome–bacteriome–host interactions in human diseases.
Highlights
The human microbiome represents a complex ecosystem of microbes, including bacteria, viruses, fungi, protozoa, and archaea
Twelve samples were processed for virome extraction: mucosal–luminal interface (MLI) aspirates from the proximal colon (PC) and distal colon (DC) were collected from all patients; MLI aspirates from the terminal ileum (TI) of subjects A and B were available for analyses
A negative control of sterile water subjected to the virome protocol yielded no detectable quantities of nucleic acids
Summary
The human microbiome represents a complex ecosystem of microbes, including bacteria, viruses, fungi, protozoa, and archaea. These microbes mostly reside in the gastrointestinal tract and are implicated in human health and disease, ranging from immune system development (Belkaid and Timothy, 2014) to nutrient and drug metabolism (Carmody and Turnbaugh, 2014) to involvement in conditions including obesity, inflammatory bowel disease, and cancer (Boulangé et al, 2016; Sartor and Wu, 2017; Franzosa et al, 2019). Despite major developments in microbiome research, most existing knowledge is focused on the bacteriome. Bacteriophages can modulate the bacteriome (Lopes et al, 2017; Hannigan et al, 2018; Clooney et al, 2019) and have a potential role in microbiome transplantation or manipulation therapies (Zuo et al, 2017; Draper et al, 2018; Lin et al, 2019; Rasmussen et al, 2020); examining the virome is essential for any comprehensive model of the host–microbiome relationship
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