Time-Resolved Multiomics Illustrates Host and Gut Microbe Interactions during <i>Salmonella</i> Infection

<i>Salmonella</i> infection, also known as <i>Salmonellosis</i>, is one of the most common food-borne illnesses. <i>Salmonella</i> infection can trigger host defensive functions, including an inflammatory response. The provoked-host inflammatory response has a significant impact on the bacterial population in the gut. In addition, <i>Salmonella</i> competes with other gut microorganisms for survival and growth within the host. Compositional and functional alterations in gut bacteria occur because of the host immunological response and competition between <i>Salmonella</i> and the gut microbiome. Host variation and the inherent complexity of the gut microbial community make understanding commensal and pathogen interactions particularly difficult during a <i>Salmonella</i> infection. Here, we present metabolomics and lipidomics analyses along with the 16S rRNA sequence analysis, revealing a comprehensive view of the metabolic interactions between the host and gut microbiota during <i>Salmonella</i> infection in a CBA/J mouse model. We found that different metabolic pathways were altered over the four investigated time points of <i>Salmonella</i> infection (days -2, +2, +6, and +13). Furthermore, metatranscriptomics analysis integrated with metabolomics and lipidomics analysis facilitated an understanding of the heterogeneous response of mice, depending on the degree of dysbiosis.