Gut virome in inflammatory bowel disease and beyond

Abstract

ObjectiveThe gut virome is a dense community of viruses inhabiting the gastrointestinal tract and an integral part of the microbiota. The virome coexists with the other components of the microbiota and with the host in a dynamic equilibrium, serving as a key contributor to the maintenance of intestinal homeostasis and functions. However, this equilibrium can be interrupted in certain pathological states, including inflammatory bowel disease, causing dysbiosis that may participate in disease pathogenesis. Nevertheless, whether virome dysbiosis is a causal or bystander event requires further clarification.DesignThis review seeks to summarise the latest advancements in the study of the gut virome, highlighting its cross-talk with the mucosal microenvironment. It explores how cutting-edge technologies may build upon current knowledge to advance research in this field. An overview of virome transplantation in diseased gastrointestinal tracts is provided along with insights into the development of innovative virome-based therapeutics to improve clinical management.ResultsGut virome dysbiosis, primarily driven by the expansion ofCaudovirales, has been shown to impact intestinal immunity and barrier functions, influencing overall intestinal homeostasis. Although emerging innovative technologies still need further implementation, they display the unprecedented potential to better characterise virome composition and delineate its role in intestinal diseases.ConclusionsThe field of gut virome is progressively expanding, thanks to the advancements of sequencing technologies and bioinformatic pipelines. These have contributed to a better understanding of how virome dysbiosis is linked to intestinal disease pathogenesis and how the modulation of virome composition may help the clinical intervention to ameliorate gut disease management.

Metagenomic analysis of the gut virome in patients with irritable bowel syndrome

“…42 At the vOTU level, IBS-enriched vOTUs belonged to crAsslike, Siphoviridae, Myoviridae, Quimbyviridae, as well as several less prevalent viral families like Flandersviridae and Gratiaviridae, while control-enriched vOTUs primarily consisted of crAss-like and some other viral families. CrAss-like viruses, known to be abundant in the human gut, 43 have been associated with various diseases, including IBD, 44,45 RA, SLE, 40 Parkinson's disease, atherosclerosis, 46 liver cirrhosis, and ankylosing spondylitis. 47 Siphoviridae, Myoviridae, and Podoviridae were also reported to be enriched in IBS patients in other gut virome studies, 23 as well as in CRC patients, 48 further supporting our findings.…”

Microbiota Therapy in Inflammatory Bowel Disease

“…Fungal commensalism in the gut is influenced by the formation of antifungal antibodies in IBD [7]. Changes in the gut virome have been shown to impact intestinal barrier function and consecutive immune reactions leading to inflammatory responses [8][9][10]. There is evidence that also the phage community structure in IBD is altered having a direct influence on the gut bacterial ecosystem [11].…”

Shared Immune Associations Between COVID-19 and Inflammatory Bowel Disease: A Cross-Sectional Observational Study in Shanghai, China

“…For example, phages and specific factors derived from the virome can damage intestinal barrier; Enterovirus B and Picornaviridae are implicated in intestinal inflammation; and Pseudomonas aeruginosa affects innate immunity. 9 Nonetheless, limited research has explored the connection between COVID-19 and IBD. Given that IBD-like ulcers have been observed in the colon of patients with COVID-19, it’s imperative to investigate the association between these two diseases.…”