Citrobacter rodentium is a murine host adapted member of the attaching and effacing (A/E) family of pathogens, and is an important model in the study of the closely related diarrheal pathogens, Enteropathogenic Escherichia coli (EPEC) and Enterohaemorrhagic E. coli (EHEC). Much complexity of this model remains unknown, including the interaction between phages and the virulence of C. rodentium. Previous research has shown that C. rodentium DBS100 contains 10 prophages, while only two have been shown to be active temperate phages. This study examines 1) the in vivo role of phage phiNP and Shae_phiSM in the bacterium’s colonization of the gut environment including 2) the in vitro role of these phage during bacterial competition and 3) the impact of polylysogeny on host colonization in vitro. We are studying the contribution of these phage to the competitiveness of their host, DBS100. Measuring maintenance of lysogeny and release of the phage during in vivo colonization and competition with commensal E.coli in the gastrointestinal (GI) tract will help us understand the role of these phage in this context. We hypothesize a competitive advantage of the lysogens compared to the nonlysogen counterpart in vitro, given the presence of virulence genes and the polylysogenic nature of the host. Polylysogeny, has been shown to mediate bacteria–bacteria competition, with this in mind we aim to understand how phages phiNP and Shae_phiSM contribute to the polylysogenic nature of DBS100. In vivo, we show that these phages enter the lytic/lysogenic cycles opposite of each other and therefore do not compete in the gut environment. We further show that Shae_phiSM is a P2-like temperate phage integrated along with a putative P4-like satellite, CRPr20. This P2-P4 interaction may be used as a model to understand one role of polylysogeny and the importance of phage interactions for the colonization of C.rodentium DBS100.