On August 17, 2018, Juliana Soto-Giron presented the oral defense of her PhD thesis, entitled,"From Genomes to Metagenomes: Big Data Analysis of Microbes Related to Public Health." Committee Members: Dr. Konstantinos T. Konstantinidis, Advisor (School of Civil and Environmental Engineering) Dr. King Jordan (School of Biological Sciences) Dr. Brian Hammer (School of Biological Sciences) Dr. Frank Stewart (School of Biological Sciences) Dr. Karen Levy (Rollins School of Public Health, Emory University) Abstract: Bacterial infections represent a major public health concern mainly in young children in the developing world and in immunocompromised individuals. Despite recent developments in clinical microbiology, our understanding of the molecular and ecological mechanisms underlying the pathogen-host-environment interplay, remains incomplete. In this work, we applied cutting-edge laboratory and bioinformatics techniques to profile microbial communities that might pose a risk for human health. Our objectives were to: (1) characterize the composition of microbial communities growing on hospital showerheads using shotgun metagenomics, (2) evaluate the response of the gut microbiome to acute diarrhea episodes along a rural-to-urban gradient in Northern Ecuador, and (3) detect and quantify recent gene transfer events among closely related genomes as the underlying mechanism of response and adaptation. The results showed, among other things, that showerhead biofilms could often serve as reservoirs for opportunistic pathogens, rural and urban gut microbiomes showed a differential response during diarrhea episodes, and recent genetic exchange is spatial and functional biased, it can be rampant, and is largely driven by selection pressures (e.g., antibiotic treatment). Therefore, these findings advance our knowledge on the diversity and dynamics of microbial communities and their potential links to public health.