Metatranslatomics enables functional profiling of microbial competition in the Salmonella-perturbed gut

PROJECT SUMMARY: Salmonella Typhimurium (STm) and other non-typhoidal Salmonella serovars cause 100 million infections per year worldwide, and treatment options are limited due to the general contraindication of broad-spectrum antimicrobials which can exacerbate the inflammation in which Salmonella thrives. Therefore, there is a need for alternative, targeted therapeutic strategies to mitigate Salmonella infection and subsequent disease. Natural resistance to STm infection is mediated in part by the commensal gut microbiota, the consortium of trillions of microbes encompassing hundreds of individual species that exist in symbiosis with the host. The gut microbiota contributes to colonization resistance against enteric pathogens like STm by forcing the pathogen to compete for resources in order to establish infection; and, to overcome this barrier, STm exploits aspects of host immunity in order to antagonize gut commensals and establish a niche within the inflamed gut. While it is known that the outcome of this competition between STm and the gut microbiota is a critical determinant of whether or not infection is established, the specific mechanisms employed by STm and the gut microbiota respectively during this competition are only partially understood. To address this knowledge gap, herein I employ a combined approach that integrates quantitative metagenomics (metaG), metatranscriptomics (metaT), and a novel sequencing modality, metatranslatomics, (metaRS) to gain unprecedented mechanistic insights into microbial and host metabolism in the STm-perturbed gut. In my preliminary work, application of functional community-level ribosome profiling (metaRS) to STm infection in a resistant mouse model of salmonellosis (Nramp1+) revealed that STm shares a metabolic profile with discrete members of the gut microbiota (e.g. Faecalibaculum rodentium) in vivo. Combined with the observed loss of F. rodentium and other microbes sharing metabolic overlap with STm post-infection, these data suggest their potential role as STm competitors. Furthermore, depletion of F. rodentium also occurred concurrently with increased expression of the host antimicrobial lectin Reg3γ. Based on these findings, my central hypothesis is that elucidating microbial metabolism in the gut, in conjunction with analysis of host responses will unveil new competitors and mechanisms of competition between STm and the microbiota. In the first aim of this proposal, I will analyze bacterial metabolism to identify potential STm competitors, and apply metaRS to predict competition and identify prebiotic substrates to guide this competition in favor of the commensal microbiota. The proposal's second aim will investigate the role of host Reg3γ in facilitating clearance of STm competitors. Collectively, the expected outcomes of these studies will provide insights concerning mechanisms governing microbial competition in the context of host responses and inform the ultimate implementation of microbiota-directed therapies aimed at reducing STm colonization and maintaining homeostasis.