SRA

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.