Reintroducing virulent viruses to synthetic microbiomes

An emerging area of interest is how virulent viruses impact the assembly, structure, and function of commensal bacterial populations in the human gut. Synthetic microbiomes offer a powerful way to study these interactions in vitro, however, a major challenge is obtaining a representative bacteriophage population during the isolation process. Here, we demonstrate that standard colony isolation procedures reliably exclude virulent viruses from synthetic microbiomes. When the virulent virome was reintroduced to a 73-strain synthetic microbiome and cocultured in a bioreactor model of the human colon, we found that phage predation had a targeted effect on susceptible strains, but little overall impact on community structure and metabolism. Overall, the findings indicate that dilution-based isolation methods are prone to generating synthetic microbiomes heavily depleted, if not devoid, of virulent viruses, and that those viruses, if reintroduced, impact community assembly, metabolism, and prophage induction.