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.
Highlights
In recent years it has become apparent that the microbes resident in and on us play a significant role in our health and well-being
The genetic symbiosis established by temperate phage, persisting as prophage within host cells, is important for genetic exchange between bacterial hosts, alteration of host phenotypes via lysogenic conversion (Brüssow et al, 2004; Reyes et al, 2010), which in turn impacts on bacterial host fitness as well as human gut microbial dynamics (Thingstad et al, 2008; Duerkop et al, 2012)
These most recent publications demonstrating alternative approaches to the re-analysis of human gut microbiomes and viromes (Stern et al, 2012; Ogilvie et al, 2013; Dutilh et al, 2014), challenge the notion that our gut viromes are highly individualized due to the perceived fast-paced evolutionary race with their bacterial hosts, and are perhaps surprising in light of the vast genetic diversity reported in many ecosystems
Summary
In recent years it has become apparent that the microbes resident in and on us play a significant role in our health and well-being. Recent work has revealed a surprisingly rich functional repertoire is encoded by the gut virome, with phages conferring a range of beneficial traits to their bacterial hosts that help maintain community stability, and afford resilience to invasion or disruption (Breitbart et al, 2003, 2008; Zhang et al, 2006; Reyes et al, 2010; Colomer-Lluch et al, 2011; Kim et al, 2011; Minot et al, 2011, 2012a,b; Modi et al, 2013; Ogilvie et al, 2013) Given this renewed interest and realization that human gut phages may play a significant role in shaping the development and functional outputs of host microbiomes, their potential for application in novel diagnostic, therapeutic, and biotechnological applications is of considerable interest. We highlight the challenges to viral discovery and future routes of investigation
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