Enrichment-based discovery and cataloguing of gut bacteriophages

An overwhelming majority of the human gut bacteriophages, often referred to as 'the viral dark matter', remain uncharacterised with their hosts unknown. Here we describe a method that enables rapid discovery and host-linking of novel phages in the gut via a combination of serial enrichment culturing and shotgun metagenomic sequencing of the viral supernatant. Using this approach dozens of novel and known bacteriophages were detected, including some infecting difficult-to-culture anaerobic gut bacteria.