Reintroducing virulent viruses to synthetic microbiomes

An emerging area of interest is how virulent bacteriophages impact the assembly, structure, and function of commensal bacterial populations in the human gut. Synthetic microbiomes are a powerful tool to study these interactions in vitro, however, a major challenge is obtaining a representative bacteriophage population during the isolation process. In this study we demonstrate that standard colony isolation procedures reliably exclude virulent viruses from synthetic microbiomes. Furthermore, we construct a synthetic microbiome comprised of 73 bacterial strains isolated from a single fecal sample and systematically interrogate the effect of re-introducing purified virulent bacteriophages from the source community in a bioreactor model of the human colon. Overall, the findings indicate that current culture-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.