Applied Metatranscriptomics and Metatranslatomics to identify new mechanisms of Salmonella-microbiota competition - SUMMARY The pathogen Salmonella enterica serovar Typhimurium (STm) exploits aspects of host immunity to establish a niche in the gut and outcompete the resident microbiota. Despite significant progress in understanding the competitive dynamics between STm and the gut microbiota, there remain gaps in our knowledge regarding the specific mechanisms involved in their interactions. Herein, we propose a combined approach that integrates metagenomic (metaG), metatranscriptomic (metaT), and metatranslatomic (metaRS) profiles to elucidate new mechanistic interactions between STm and the gut microbiota. Specifically, we will use quantitative metaG, metaT, and integrate innovative community-level ribosome footprinting (metaRS) to construct a comprehensive profile of resource allocation and substrate preferences within the gut microbiota. It is our expectation that these combined approaches will lend insight into how metabolic niches are perturbed by STm colonization and associated host immune responses. Through the integration of these multiomics, we have generated testable hypotheses regarding potential mechanisms of competition between STm and the gut microbiota. We intend to test these hypotheses in this research application. Our central hypothesis is that elucidating microbial metabolism in the gut, in conjunction with the analysis of host responses, will unveil new competitors and mechanisms of competition between STm and the gut microbiota. We will test our hypothesis by pursuing two Specific Aims: In Aim 1, we will analyze bacterial metabolism to identify potential Salmonella competitors in mice and test the predictions in vitro and in vivo. We will validate the preliminary finding that STm infection depletes specific members of the microbiota with similar metabolic profiles. We will also test the prediction that metabolic overlap between STm and specific members of the microbiota reflects competition for resources in the gut. In Aim 2, we will investigate whether host antimicrobial responses promote Salmonella competition with selected members of the gut microbiota. Collectively, this study will provide a comprehensive analysis of bacterial metabolism in the gut and how this is perturbed in the context of STm infection. Moreover, the study will test hypotheses stemming from our preliminary data as well as generate and test new hypotheses concerning mechanisms governing microbial competition, also in the context of host responses. Moving forward, the insights garnered from this research hold promise for therapeutic interventions aimed at reducing STm colonization and reinstating intestinal homeostasis.
