Multiomic spatial analysis reveals a distinct mucosa-associated virome

ABSTRACT

The human gut virome has been increasingly explored in recent years. However, nearly all virome-sequencing efforts rely solely on fecal samples and few studies leverage multiomic approaches to investigate phage–host relationships. Here, we combine metagenomics, metaviromics, and metatranscriptomics to study virome-bacteriome interactions at the colonic mucosal-luminal interface in a cohort of three individuals with inflammatory bowel disease; non-IBD controls were not included in this study. We show that the mucosal viral population is distinct from the stool virome and houses abundant crAss-like phages that are undetectable by fecal sampling. Through viral protein prediction and metatranscriptomic analysis, we explore viral gene transcription, prophage activation, and the relationship between the presence of integrase and temperate phages in IBD subjects. We also show the impact of deep sequencing on virus recovery and offer guidelines for selecting optimal sequencing depths in future metaviromic studies. Systems biology approaches such as those presented in this report will enhance our understanding of the human virome and its interactions with our microbiome and our health.

KEYWORDS:

• Virome
• bacteriophages
• gut microbiome
• phageome
• gut mucosa

Abbreviations

DC, distal colon; MLI, mucosal-luminal interface; IC, integration-capable; NI, non-integrated; NRA, normalized relative abundance; ORF: open reading frame; PC, proximal colon; STL: stool; TA, transcriptionally active; VC: viral contig; VLP: virus-like particle

Acknowledgments

The authors would like to acknowledge the patients and their families for their participation in our study. We also thank Ruth Singleton for her help in enrolling patients and assistance in collecting intestinal aspirate samples and Dr. Kendra Hodgkinson for her proofreading and review of this manuscript. The multiomic analyses presented herein were enabled in part by Compute Ontario, and the Digital Research Alliance of Canada (https://alliancecan.ca/en).

AY is supported by the Frederick Banting and Charles Best Canada Graduate Scholarships Doctoral Award from the Canadian Institutes of Health Research. DRM is supported in part through a Distinguished Clinical Chair in Pediatric IBD through the Faculty of Medicine, University of Ottawa. This work was supported by the Government of Canada through Genome Canada and the Ontario Genomics Institute under Grant OGI-149; the Canadian Institutes of Health Research under Grant ECD-144627; and the Ontario Ministry of Economic Development and Innovation under Project 13440. The funders had no role in study design, data collection and analysis, or preparation of the manuscript.

Disclosure statement

AS and DM are co-founders of MedBiome, a clinical microbiomics company. The other authors have no competing interests to declare.

Data Availability Statement

Host-removed, high-quality sequencing reads are available under BioProject PRJNA81830 https://www.ncbi.nlm.nih.gov/bioproject/PRJNA818303.

Author contributions

AY and AS designed the experiments. AY performed all virome extractions, data analysis, and wrote the initial manuscript. Whole genome extractions were performed by AY, while LS performed the metatranscriptome extractions. DM was responsible for sample collection and clinical data generation. JB assisted in bioinformatic analysis and data interpretation. All authors reviewed and provided comments on the final manuscript.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2023.2177488

Additional information

Funding

This work was supported by the Canadian Institutes of Health Research [ECD-144627]; Genome Canada [OGI-149]; Ontario Ministry of Research and Innovation [Project 13440]; Frederick Banting and Charles Best [Scholarship]; Faculty of Medicine, University of Ottawa [Distinguished Clinical Chair].