Nutrient-driven bacterial physiology in recalcitrant infections.

Project Summary We currently lack effective therapies for treating chronic infections because most antibiotics were screened for their ability to kill fast-growing, planktonic bacteria. In chronic infections, bacteria are difficult to eradicate because they grow slowly and form biofilms; these physiologies facilitate antibiotic tolerance and resistance to host immune defenses. Our research aims to address this challenge by investigating how the host nutrient environment drives bacteria to adopt these recalcitrant states. Our preliminary studies have identified nutrient availability as a key regulator of the slow growth and biofilm lifestyles, highlighting bacterial metabolism and the host nutrient environment as inroads for controlling these difficult-to-treat states. This research program will build from these findings to determine how nutrient cues direct the physiologies of gram-positive anaerobic cocci (GPAC). GPAC are a diverse group of obligate anaerobic bacteria; their physiologies are distinct from well-studied biofilm-forming bacteria, providing an opportunity to uncover new mechanisms for counteracting antibiotic tolerance and disrupting biofilms. GPAC are prevalent members of the human microbiota and understudied agents of chronic infections. In this proposal, we will determine how the nutrient environment supports or limits GPAC metabolism, investigating how this relationship underpins antibiotic treatment failure. We will also identify how specific nutrient cues regulate biofilm formation or dispersal, and further explore how biofilm regulation has diverged within an important GPAC lineage. Our work integrates a range of techniques to pursue mechanistic studies of GPAC physiology, including quantitative microscopy, experimental evolution, and genetic and omics approaches. We have also developed crucial new tools for studying these non-model bacteria, including genetic manipulation, defined media for manipulating the nutrient environment, and the establishment of an ex vivo wound tissue growth medium to recapitulate the host nutrient environment. In completing these projects, we will reveal how the host nutrient environment regulates bacterial physiologies that enable chronic colonization and recalcitrance to antibiotic therapies. Studying physiologically relevant bacterial states will inspire new therapeutic approaches for combatting chronic infections.