Review article: the human intestinal virome in health and disease

Abstract

SummaryBackgroundThe human virome consists of animal‐cell viruses causing transient infections, bacteriophage (phage) predators of bacteria and archaea, endogenous retroviruses and viruses causing persistent and latent infections. High‐throughput, inexpensive, sensitive sequencing methods and metagenomics now make it possible to study the contribution dsDNA, ssDNA and RNA virus‐like particles make to the human virome, and in particular the intestinal virome.AimTo review and evaluate the pioneering studies that have attempted to characterise the human virome and generated an increased interest in understanding how the intestinal virome might contribute to maintaining health, and the pathogenesis of chronic diseases.MethodsRelevant virome‐related articles were selected for review following extensive language‐ and date‐unrestricted, electronic searches of the literature.ResultsThe human intestinal virome is personalised and stable, and dominated by phages. It develops soon after birth in parallel with prokaryotic communities of the microbiota, becoming established during the first few years of life. By infecting specific populations of bacteria, phages can alter microbiota structure by killing host cells or altering their phenotype, enabling phages to contribute to maintaining intestinal homeostasis or microbial imbalance (dysbiosis), and the development of chronic infectious and autoimmune diseases including HIV infection and Crohn's disease, respectively.ConclusionsOur understanding of the intestinal virome is fragmented and requires standardised methods for virus isolation and sequencing to provide a more complete picture of the virome, which is key to explaining the basis of virome‐disease associations, and how enteric viruses can contribute to disease aetiologies and be rationalised as targets for interventions.

Gut Microbial Metabolism and Nonalcoholic Fatty Liver Disease

“…(Table ) The healthy gut microbiome comprises a large diversity of phylogenetically distinct microbial species, with even greater interindividual diversity observed at the subspecies or strain level . Although culture‐independent studies of the gut microbiome have more traditionally focused on bacteria, investigation of fungal and viral species has increased, leading to their recognition as integral members of the gut microbiome and implicating trans‐kingdom interactions in microbiome composition and function …”

Regulation of mononuclear phagocyte function by the microbiota at mucosal sites

“…Intestinal MNPs, including DCs and macrophages, are essential for both immune tolerance and protective immunity in the intestine but these cells perform distinct functions and are differentially modulated by the microbiota to perform these roles. Although the intestinal microbiota predominantly comprises bacteria, interactions between intestinal fungi, viruses and MNPs directly modulate MNP function (reviewed in refs 3,4). However, given the vast amount of bacteria in the intestine combined with the large amount of information regarding bacterial modulation of intestinal MNP function, this section will focus on bacteria and their associated metabolites in tailoring intestinal immunity.…”

Gut microbes as future therapeutics in treating inflammatory and infectious diseases: Lessons from recent findings

“…Lim et al [225] have studied that Siphoviridae and Anelloviridae are prevalent in the early life but gradually decrease with age while Microviridae gradually increases with the age. In addition to metabolic disorders and cardiovascular disease, changes in the virome community are often associated with several infectious and autoimmune diseases [226,227]. Human stool derived phagebased therapies are emerging as new hopes for preventing the pathogenesis of multi-drug resistant Enterobacteria [228], and, burn wound-causing Escherichia coli and Pseudomonas aeruginosa [229].…”

“…The characterization of the gut virome showed a dearth of 16S or 18S rRNA genes, thus the empirical metataxonomic approaches to characterize virus-like particles (VLPs) is dependent on the isolation and sequencing of DNA from VLPs along with the classical techniques like microscopy and cultivation [235]. The gut-associated phages are isolated directly from the human microbiota rather being isolated from the sewage or water sources [226] for proper characterization, which will surely play a promising role in improving the knowledge on the gut virome and will serve as a key for the metagenomic studies that will further furnish the idea about the influence of the phages on the human gut. Lately, the Virome Capture Sequencing platform for Vertebrate viruses (VirCapSeq-VERT) system has been introduced to study the viruses in the clinical settings [236].…”