Stability of the Human Gut Virome and Effect of Gluten-Free Diet

The human gut microbiome is a complex ecosystem of bacteria, archaea, eukaryotes, and viruses. The composition and dynamics of the gut viruses, commonly termed the gut virome, are relatively underexplored. We performed a longitudinal analysis of the gut viral communities in 11 healthy adults in order to study individual variations, virome stability, and the effect of a gluten-free diet (GFD). Using viral enrichment and a de novo assembly-based approach, we demonstrate the quantitative dynamics of the gut virome, including dsDNA, ssDNA, dsRNA, and ssRNA viruses. We observe that individual’s viral communities are highly divergent, carrying on average 2,143 viral genomes, 13.1% of which were present at all time points. During the GFD, the virome was stable at the family level but showed substantial variation at the ranks of genera and species. Finally, we demonstrate that a lower initial viral diversity leads to a more pronounced effect of the dietary intervention.