Synthetic gut microbiotas infected with B. uniformis phage

Phages are under intense study as therapeutics and mediators of microbial community behavior; however, tractable models are needed to study phages in the context of the mammalian gut. To address this gap, we isolated phages against members of a synthetic gut microbial community (sFMT), identifying the Bacteroides uniformis JEB00023 (DSM 6597) strain-specific phage HKP09. While resistance to HKP09 was observable within hours of infection in monoculture, high titers of HKP09 were maintained in vitro and in gnotobiotic mouse models over extended periods. Sequencing of resistant B. uniformis lines revealed phase variation upstream of a capsular polysaccharide locus driving the spontaneous regeneration of resistant and sensitive subpopulations, demonstrating a mechanism allowing persistence of both virus and host. Communities infected in vitro and in vivo with HKP09 showed reduced loads of B. uniformis DSM 6597; however, its impact in the gut was distinct from communities constructed without its host B. uniformis strain (sFMTdJEB00023). Rather than a compensatory increase in closely related Bacteroides strains, the most significant impacts were observed on distantly related strains, demonstrating that phage perturbations more broadly impact community structure in ways not easily predicted by phylogeny or simple strain exclusion. Metabolomic analyses of the feces of HKP09-infected sFMT-colonized gnotobiotic animals demonstrated a unique metabolite pool compared to uninfected mice and those colonized with sFMTdJEB00023. Taken together, these data demonstrate a controlled model for studying phages in the context of the mammalian gut and insights into the mechanisms through which predator-prey relationships impact the function of microbial communities.