The human gut virome: a multifaceted majority

Abstract

Here, we outline our current understanding of the human gut virome, in particular the phage component of this ecosystem, highlighting progress, and challenges in viral discovery in this arena. We reveal how developments in high-throughput sequencing technologies and associated data analysis methodologies are helping to illuminate this abundant ‘biological dark matter.’ Current evidence suggests that the human gut virome is a highly individual but temporally stable collective, dominated by phages exhibiting a temperate lifestyle. This viral community also appears to encode a surprisingly rich functional repertoire that confers a range of attributes to their bacterial hosts, ranging from bacterial virulence and pathogenesis to maintaining host–microbiome stability and community resilience. Despite the significant advances in our understanding of the gut virome in recent years, it is clear that we remain in a period of discovery and revelation, as new methods and technologies begin to provide deeper understanding of the inherent ecological characteristics of this viral ecosystem. As our understanding increases, the nature of the multi-partite interactions occurring between host and microbiome will become clearer, helping us to more rationally define the concepts and principles that will underpin approaches to using human gut virome components for medical or biotechnological applications.

Modification ofEscherichia coli–bacteriophage interactions by surfactants and antibioticsin vitro

“…The impact of antibiotics may be modified by phages that are naturally present in humans and animals (Breitbart et al. 2003; Ogilvie and Jones 2015), and combination therapy using phages and antibiotics may be more or less effective depending on these interactions (Viertel, Ritter and Horz 2014). In support, analogous interactions between pairs of antibiotics have been shown to strongly affect clearance, resistance and optimal dosing in vitro (Hegreness et al.…”

Experimental metagenomics and ribosomal profiling of the human skin microbiome

“…[27][28][29] Although several microbiome studies are unravelling the complementary aspects of the skin microbiome, [28,30] further research is required to truly understand the complex interplay between the host and the resident microbiome.…”

Emerging Concepts on the Gut Microbiome and Multiple Sclerosis

“…Bacteriophages have not been evaluated for association with MS/EAE, though there has been postulation about the association of bacteriophages and autoimmunity (Riley 2004;Dalmasso and others 2014;Ogilvie and Jones 2015). As dysbiosis has been hypothesized as a risk factor for many autoimmune diseases, one method of causing underlying dysbiosis could be bacteriophage infection in which destabilization of bacterial populations occurs.…”