Dataset S1

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 <i>in vitro</i>, 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.