UC San Diego

The physiological processes associated with microbiomes represent the biology of individual microbial cells and their interactions with other cells. Moreover, the interactions between microbes are not static, but represent dynamic processes that are subject to ecological and evolutionary changes. One of the main drivers of rapid evolution in microbial species is the process of horizontal gene transfer, often mediated by mobile genetic elements. Few systems or tools exist that allow the study of this process in microbiomes. In this thesis, we review experimental methods to study horizontal gene transfer, as well as catalog computational methods to sequence and filter for mobile elements, including integrative and conjugative elements, plasmids, and viruses. We next leverage long read DNA sequencing to lay the groundwork for a complex in vitro washed cheese rind microbiome model. With our microbiome model and computational methods, we are able to 1) probe natural microbiomes in kefirs and cheese rinds to better understand the breadth and novelty of mobile elements and 2) begin to understand how different community members play a role in the evolution of species and mobility of plasmids within a genus. Our work in the identification, characterization, and tracking of mobile elements in microbiomes enhances our understanding of the unique and niche-adaptive genes carried by these fermenting microbes. Finally, we explore the potential clinical and industrial applications of long read and proximity ligation.