Date of Award

Summer 2023

Document Type

Open Access Thesis


Biological Sciences

First Advisor

Melissa Ellermann


The gastrointestinal tract is home to trillions of microbes that collectively influence host physiology, immunity, nutrient metabolism, and infectious disease. The overgrowth of naturally-occurring Escherichia coli in the gut is a common signifier of microbiome dysfunction and occurs in many chronic diseases including obesity. Recent studies have shown that higher fat intake is associated with increased gut E. coli growth. However, it remains unknown whether gut E. coli utilize lipids such as long chain fatty acids (LCFAs) as carbon sources to colonize the mammalian gut. Therefore, the central objective of my dissertation was to utilize bacterial genetics and various mouse models to determine whether LCFA metabolism impacts E. coli colonization within the gut. Using a well-established DNA recombineering technique, we generated E. coli mutants lacking fatty acid degradation (fad) genes. We inactivated fadL, which imports LCFAs; fadD, which initiates cellular consumption of LCFAs; and fade, which catalyzes the first step of LCFA catabolism. Additionally, we inactivated fadR, a transcription factor that senses intracellular LCFA pools and regulates lipid metabolism in E. coli. Our results show that the LCFA catabolism pathway is active in a commensal E. coli gut isolate within defined in vitro growth conditions. Furthermore, E. coli fad mutants were unable to grow when the LCFA oleate was supplied as the sole carbon source. In a germ-free mouse model, all E. coli fad mutants showed no altered growth phenotypes in the gut. When assessing the competitive fitness of the fad mutants relative to the wild-type strain in mice harboring a microbiome, we observed that LCFA catabolism modestly increases E. coli growth within the gut. Inactivation of lipid sensing via fadR significantly decreased the competitive fitness of E. coli and resulted in the mutant’s exclusion from the gut. Taken together, these findings suggest that LCFA sensing, rather than catabolism, may be more important for modulating E. coli growth in the mammalian gut. Future studies will assess how high fat diets impact the contribution of LCFA catabolism to E. coli gut colonization and will characterize the effects of lipid sensing and metabolism on the E. coli transcriptome within the gut environment.


© 2023, Tessa Carolina Cox

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