Time-resolved multi-omics reveals diverse metabolic strategies of <i>Salmonella</i> during diet-induced inflammation

With a rise in antibiotic resistance and chronic infection, the metabolic response of <i>Salmonella enterica</i> serovar Typhimurium to various dietary conditions over time remains an understudied avenue for novel, targeted therapeutics. Elucidating how enteric pathogens respond to dietary variation not only helps us decipher the metabolic strategies leveraged for expansion but also assists in proposing targets for therapeutic interventions. In this study, we use a multi-omics approach to identify the metabolic response of <i>Salmonella enterica</i> serovar Typhimurium in mice on both a fibrous diet and high-fat diet over time. When comparing <i>Salmonella</i> gene expression between diets, we found a preferential use of respiratory electron acceptors consistent with increased inflammation in high-fat diet mice. Looking at the high-fat diet over the course of infection, we noticed heterogeneity in samples based on <i>Salmonella</i> ribosomal activity, which is separated into three infection phases: early, peak, and late. We identified key respiratory, carbon, and pathogenesis gene expressions descriptive of each phase. Surprisingly, we identified genes associated with host cell entry expressed throughout infection, suggesting subpopulations of <i>Salmonella</i> or stress-induced dysregulation. Collectively, these results highlight not only the sensitivity of <i>Salmonella</i> to its environment but also identify phase-specific genes that may be used as therapeutic targets to reduce infection.IMPORTANCEIdentifying novel therapeutic strategies for <i>Salmonella</i> infection that occur in relevant diets and over time is needed with the rise of antibiotic resistance and global shifts toward Western diets that are high in fat and low in fiber. Mice on a high-fat diet are more inflamed compared to those on a fibrous diet, creating an environment that results in more favorable energy generation for <i>Salmonella</i>. We observed differential gene expression across infection phases in mice over time on a high-fat diet. Together, these findings reveal the metabolic tuning of <i>Salmonella</i> to dietary and temporal perturbations. Research like this, which explores the dimensions of pathogen metabolic plasticity, can pave the way for rationally designed strategies to control disease.