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Review
. 2022 Nov 2;46(6):fuac027.
doi: 10.1093/femsre/fuac027.

The role of virome in the gastrointestinal tract and beyond

Kawtar Tiamani  1   2 , Shiqi Luo  1   2 , Sarah Schulz  1   2 , Jinling Xue  1   2 , Rita Costa  1   2 , Mohammadali Khan Mirzaei  1   2 , Li Deng  1   2
Affiliations
Review

The role of virome in the gastrointestinal tract and beyond

Kawtar Tiamani et al. FEMS Microbiol Rev. .

Abstract

The human gut virome is comprised of diverse commensal and pathogenic viruses. The colonization by these viruses begins right after birth through vaginal delivery, then continues through breastfeeding, and broader environmental exposure. Their constant interaction with their bacterial hosts in the body shapes not only our microbiomes but us. In addition, these viruses interact with the immune cells, trigger a broad range of immune responses, and influence different metabolic pathways. Besides its key role in regulating the human gut homeostasis, the intestinal virome contributes to disease development in distant organs, both directly and indirectly. In this review, we will describe the changes in the gut virome through life, health, and disease, followed by discussing the interactions between the virome, the microbiome, and the human host as well as providing an overview of their contribution to gut disease and disease of distant organs.

Keywords: Auxiliary metabolic genes; gastrointestinal tract; immune response; microbiome; phageome; virome.

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Figures

Figure 1.
Figure 1.
Changes in bacterial and viral populations inside the human gut across the lifespan of healthy individuals. Impact of different factors is illustrated: Health status, diet, and age are the most influential factors. Figure is adapted from (Gregory et al. 2020).
Figure 2.
Figure 2.
Direct interactions between phages and the immune system in homeostasis compared to dysbiosis. Phages cross the intestinal epithelium via specific transcytosis and receptor-mediated uptake in homeostatic conditions; or non-specific and non-controlled uptake in the case of a damaged epithelium. Once they have crossed the intestinal epithelium, phages interact with circulating immune cells and can elicit different responses and modulate inflammation. Phages can then drain into lymph nodes and disseminate to different organs throughout the body.
Figure 3.
Figure 3.
Overview of Hydrogen Sulphate (H2S) production pathways: Cysteine catabolism inside human colonocytes and potential phage AMG-mediated Sulphate reduction within Sulphate-reducing bacteria (SRB) and its effect on human health. H2S regulates DNA replication, metabolism, oxidative stress and inflammation in various organs of the body (e.g. brain, liver, heart, kidneys…). Other examples of AMGs in humans include genes that are involved in metabolisms of Fructo-oligosaccharides, Outer membrane glycans, etc., and bacterial exotoxins such as Zonula occludens toxin (Zot), Shiga toxin (Stx), and Botulinum neurotoxin (BoNT).
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