Box 1.

Getting access to the virome.

To study the virome, VLPs are separated from cellular components, usually using a combination of filtration, density centrifugation and enzymatic treatments to eliminate free nucleic acids.9 The nucleic acids are then sequenced and analysed. Compared to the bacterial component of the intestinal microbiome, the intestinal virome has been under-investigated and largely ignored, in large part due to the limited tools available for their identification and classification. Recent advances in high-throughput, next-generation sequencing has allowed detailed and in-depth analysis of microbial communities (metagenomics), leading to the identification of new microbial species, which has only recently been applied to the characterization of the virome.10 There are, however, too few reference viromes, and those that do exist are dominated by unknown sequences with 60–90% of the reads often lacking functional or taxonomic annotations (the ‘viral dark matter’).2,11 Currently, it is estimated that roughly 1% of the virome has been sequenced, leaving the bulk yet to be characterized.8