Divergent roles of hcp genes in Salmonella typhimurium T6SS shape gut microbiota dysbiosis during infection

ABSTRACT Salmonella enterica subsp. enterica serovar typhimurium ( S. typhimurium ) is a facultative intracellular pathogen causing significant gastrointestinal infections in both humans and animals. The type VI secretion system (T6SS) plays a crucial role in its virulence, facilitating competition with host gut microbiota and promoting infection. While S. typhimurium possesses a single T6SS, it encodes three hcp genes, which are essential for its functionality. To investigate the non-redundant roles of each hcp gene, in this study, we used 16S rRNA sequencing to analyze gut microbiota in BALB/c mice after infection with wild-type (WT) S. typhimurium or three mutant strains (Δ hcp1 , Δ hcp2 , and Δ hcp3 ). Our findings revealed that S. typhimurium infection induced severe gut dysbiosis especially on the second day post-infection, which was characterized by a notable increase in Firmicutes and activation of the energy pathways. The deletion of each hcp gene led to distinct changes in bacterial taxa, underscoring the non-redundant function of each hcp. Lactobacillus showed significant effects in both strain main effects and strain-time interaction effects. Despite having only one T6SS, S. typhimurium achieves precise modulation of its functions through the divergent roles of its Hcp proteins, enabling efficient colonization and persistence in the host gut. These findings provide insights into the intricate mechanisms of bacterial adaptation and host-pathogen interactions, offering potential avenues for therapeutic interventions targeting T6SS-mediated dysbiosis. IMPORTANCE Salmonella enterica subsp. enterica serovar typhimurium ( S. typhimurium ) is a facultative intracellular pathogen causing significant gastrointestinal infections in humans and animals. The type VI secretion system (T6SS) plays a crucial role in its virulence, facilitating competition with host gut microbiota and promoting infection. While S. typhimurium possesses a single T6SS, it encodes three hcp genes, which are crucial for its functionality and may exhibit non-redundant roles. In this study, we used 16S rRNA sequencing to analyze gut microbiota in BALB/c mice after infection with wild-type (WT) S. typhimurium or mutant strains (Δ hcp1 , Δ hcp2 , Δ hcp3 ). Our findings revealed that the deletion of individual hcp genes led to distinct bacterial taxa changes, underscoring the non-redundant functions of each hcp . Despite having only one T6SS, S. typhimurium achieves precise modulation of its functions through the divergent roles of its Hcp proteins, enabling efficient colonization and persistence in the host gut.