Prophage 919TP is widely distributed among Vibrio cholera and is induced to produce free ϕ919TP phage particles. However, the interactions between prophage ϕ919TP, the induced phage particle, and its host remain unknown. In particular, phage resistance mechanisms and potential fitness trade-offs, resulting from phage resistance, are unresolved. In this study, we examined a prophage 919TP-deleted variant of V. cholerae and its interaction with a modified lytic variant of the induced prophage (ϕ919TP cI^- ). Specifically, the phage-resistant mutant was isolated by challenging a prophage-deleted variant with lytic phage ϕ919TP cI^- . Further, the comparative genomic analysis of wild-type and ϕ919TP cI^--resistant mutant predicted that phage ϕ919TP cI^- selects for phage-resistant mutants harboring a mutation in key steps of lipopolysaccharide (LPS) O-antigen biosynthesis, causing a single-base-pair deletion in gene gmd. Our study showed that the gmd-mediated O-antigen defect can cause pleiotropic phenotypes, e.g., cell autoaggregation and reduced swarming motility, emphasizing the role of phage-driven diversification in V. cholerae. The developed approach assists in the identification of genetic determinants of host specificity and is used to explore the molecular mechanism underlying phage-host interactions. Our findings contribute to the understanding of prophage-facilitated horizontal gene transfer and emphasize the potential for developing new strategies to optimize the use of phages in bacterial pathogen control.