Microbial dynamics in health and disease : from strain-level adaptations to microbe-microbe interactions in the gut microbiome

This thesis deals with the evolution of bacteria in the gut microbiome, and the potential of therapeutic exploitation. The gut microbiome changes in a predictable manner during disease. However, strain-level changes in the gut microbiome during disease development remain unclear. Here, I explore the evolution of Escherichia coli, a commensal of the human gut microbiome, in a mouse model of inflammatory bowel disease through a multi-omics approach to understand the bacterial adaptation to host inflammation. In other chapters of the thesis, I explore how commensal bacteria in the gut microbiome may interact with each. Bacterial interactions between naturally co-existing Bacteroidetes bacteria within the gut microbiome could potentially dictate the composition and therefore the functional potential of the gut microbiome. Finally, I also explore the function of a specialized bacterial secretion system, called the type VI secretion system (T6SS), in a gut commensal to understand its effect on naturally co-existing strains. I also perform an extensive literature review and speculate on the ecological and evolutionary factors that determine the observed presence-absence pattern of T6SS across bactreria taxa.