UC Davis

Microbial invaders of the gastrointestinal ecosystem must overcome a myriad of oppositional forces in order to engraft themselves into the gut environment. While commensal gut microbes have evolved dispersal strategies that lack negative consequences for the host, these strategies only rarely allow for successful invasion into a microbiota that has matured past the initial stages of community assembly. In contrast, gastrointestinal pathogens have evolved virulence strategies that facilitate their dispersal into mature gut microbiotas. The mechanisms governing this antagonism and attempted exclusion of microbial newcomers, which we term colonization resistance, are not fully understood. Here, we utilize a model invader of the large intestinal ecosystem, the pathogen Salmonella enterica subsp. enterica serovar (S.) Typhimurium, to gain mechanistic insight into the determinants of gastrointestinal colonization resistance.In Chapter 1, we review the current understanding of colonization resistance to S. Typhimurium in the large intestine. Beginning with the principles microbiota assembly and the properties of the gut ecosystem during both homeostasis and dysbiosis, we provide a framework for understanding gut microbiome as a product of host-derived habitat filters. Evidence of colonization resistance being a phenomenon derived of both host and microbial activities is discussed, as is the fact that newcomer engraftment can occur if either part of this chimera is disturbed. Finally, we highlight the genus Salmonella’s contribution to our understanding of the large intestinal microbiota’s role in health and disease. Chapter 2 presents our use of an oral S. Typhimurium infection in an antibiotic-naïve mouse model of to study ecosystem invasion by the pathogen in the presence of an intact microbiota. We find that S. Typhimurium overcomes colonization resistance on day 3 after infection, as evidenced by its increased population size in both the feces and the cecum. Metabolomics, microbial community profiling by 16S rRNA amplicon sequencing, and literature-informed reverse genetics approaches allowed us to elucidate mechanisms by which S. Typhimurium overcomes microbiota-mediated colonization resistance. We establish that S. Typhimurium targets the host to abolish epithelial hypoxia, inhibit short-chain fatty acid production by the microbiota, and gain access to simple carbohydrates. The resulting bloom of S. Typhimurium occurs in the presence of a compositionally intact microbiota and is driven by mixed acid fermentation and aerobic respiration via the nitric oxide-resistant cytochrome bd oxidase CydAB. An extended discussion and contextualization of the findings presented in Chapter 2 is provided in Chapter 3. We discuss infection kinetics as a simple yet effective tool for gaining insight into colonization resistance, microbiota composition vs. microbiota function, the roles of Clostridia in colonization resistance, and the importance of host epithelial metabolism as the foundation of the gut ecosystem. Finally, potential future directions for the study of the gut environment using S. Typhimurium are discussed. In conclusion, we provide new insights into the strategies that S. Typhimurium uses to successfully overcome microbiota-mediated colonization resistance in the gastrointestinal tract.