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GI highlights from the literature

► Clooney AG, Sutton TDS, Shkoporov AN, et al. Wholevirome analysis sheds light on viral dark matter in IBD. Cell Host Microbe 2019;26:1–15. Analysing whole virome signatures within the human gut is the next major step in the field of the gut microbiome. To date, most virome analyses have detailed only a limited fraction of known viruses. However, it is estimated that the identifiable fraction of the virome can be as little as 15%, leaving approximately 85% of ‘dark matter’. In the context of IBD, increased overall virome diversity with a specific increase in Caudovirales abundance has been demonstrated in several studies. Clooney and colleagues aimed to make sense of the dark matter by revisiting a previously published keystone dataset (Norman, 2014) using a databaseindependent approach. This assembles the short metagenomic reads to resolve viral genomes and to determine their relative abundance. This allowed the authors to describe compositional change across the whole virome. By using this approach, they were able to show that a predominantly virulent core virome is linked to a healthy gut, with a shift from lysogenic to lytic replication in the temperate phage population in IBD. They did not confirm previous reports of a loss in overall viral diversity, with virome changes appearing to reflect bacterial compositional changes. Furthermore, incorporating both datasets into a disease classifier model offered improved patient group stratification, which they validated using a longitudinal cohort of patients with UC. The findings demonstrate a significant step forward in understanding the virome and its contribution to health and disease. This knowledge and capability will be vital in our continued search for future therapeutic strategies for IBD.