The Emerging Role of the Gut Virome in Health and Inflammatory Bowel Disease: Challenges, Covariates and a Viral Imbalance

• Published in: Viruses Vol. 15; no. 1; p. 173
• Main Authors: Jansen, Daan, Matthijnssens, Jelle
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 06.01.2023; MDPI
• Subjects: Bacteria; Bacteriophages; Bioinformatics; Cell division; Cholera; Diabetes; Environmental factors; eukaryotic viruses; Gastrointestinal Microbiome; Genetic engineering; Genomes; Humans; IBD; Inflammation; Inflammatory bowel disease; Inflammatory Bowel Diseases; Intestine; Metagenomics; Microbiomes; Microbiota; Microviridae; Pathogens; Pathophysiology; Phages; Relative abundance; Review; Virome; virota; Virulence; Viruses; virome; IBD; virota; eukaryotic viruses; metagenomics; bacteriophages
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v15010173

Virome research is a rapidly growing area in the microbiome field that is increasingly associated with human diseases, such as inflammatory bowel disease (IBD). Although substantial progress has been made, major methodological challenges limit our understanding of the virota. In this review, we describe challenges that must be considered to accurately report the virome composition and the current knowledge on the virome in health and IBD. First, the description of the virome shows strong methodological biases related to wetlab (e.g., VLP enrichment) and bioinformatics approaches (viral identification and classification). Second, IBD patients show consistent viral imbalances characterized by a high relative abundance of phages belonging to the and a low relative abundance of phages belonging to the . Simultaneously, a sporadic contraction of CrAss-like phages and a potential expansion of the lysogenic potential of the intestinal virome are observed. Finally, despite numerous studies that have conducted diversity analysis, it is difficult to draw firm conclusions due to methodological biases. Overall, we present the many methodological and environmental factors that influence the virome, its current consensus in health and IBD, and a contributing hypothesis called the "positive inflammatory feedback loop" that may play a role in the pathophysiology of IBD.