Going viral: next-generation sequencing applied to phage populations in the human gut

Viruses are the most diverse and uncharacterized components of all the major ecosystems on Earth, including that within the mammalian gut. Here, Gordon and colleagues review our current understanding of the diversity and ecology of the bacteriophages present in the human gut and discuss how an improved understanding of phage dynamics could revitalize phage therapy. Over the past decade, researchers have begun to characterize viral diversity using metagenomic methods. These studies have shown that viruses, the majority of which infect bacteria, are probably the most genetically diverse components of the biosphere. Here, we briefly review the incipient rise of a phage biology renaissance, which has been catalysed by advances in next-generation sequencing. We explore how work characterizing phage diversity and lifestyles in the human gut is changing our view of ourselves as supra-organisms. Finally, we discuss how a renewed appreciation of phage dynamics may yield new applications for phage therapies designed to manipulate the structure and functions of our gut microbiomes.