Understanding competition dynamics between Citrobacter rodentium and Escherichia coli in the gut microbiota

The gastrointestinal microbiota is a dynamic ecosystem in which bacteriophages play a role in killing bacteria from the “inside”, via prophage induction, and from the “outside”, by virulent bacteriophages. While prophage induction has been extensively studied in the laboratory through the lens of prophages encoding toxins, much less is known about the conditions and consequences of prophage induction in the intestinal microbiota. This study was initiated to investigate prophage induction during intestinal inflammation using gnotobiotic OMM12 mice infected by Citrobacter rodentium. Surprisingly, C. rodentium infection follows an original “peak and persistence” colonization pattern. Since the host immune response was insufficient for pathogen clearance, we introduced independently two murine commensal Escherichia coli strains (DN15 and Mt1B1) as well as the laboratory strain MG1655, all ahead of C. rodentium infection. Remarkably, DN15, but not Mt1B1 nor MG1655, substantially suppressed C. rodentium colonization. Comparative genomics and in vitro assays identified colicin Y, a plasmid-encoded antimicrobial peptide produced by DN15, as the key effector molecule responsible for inhibiting C. rodentium growth. Moreover, while DN15 and Mt1B1 loads remain constant, MG1655 loads decreased progressively, likely because of its susceptibility to two Citrobacter prophages (φNP and φSM). We leveraged this system by performing in vitro co-culture experiments with either wild-type or prophage-free mutants of C. rodentium and demonstrated that only φNP lysogenizes MG1655. Future plans include recording over time the in vivo induction of C. rodentium prophage and the detection of MG1655 lysogens. This study provides insights into the role of temperate phages as ecological modifiers of microbial communities in the gut.