Bacterial regulation of acid resistance and amino acid metabolism

The National Institute of General Medical Sciences awarded Western Michigan University $532,909 on February 15, 2026, under the Biomedical Research and Research Training program (CFDA 93.859, Project Grant R15GM163283) to investigate bacterial acid resistance and amino acid metabolism in gastrointestinal pathogens.

The research examines how the bacterial second messenger c-di-GMP regulates both amino acid metabolism and acid resistance in E. coli and Shigella, with particular focus on isoleucine-mediated acid resistance, a mechanism not previously reported in the literature. The study will investigate how isoleucine contributes to acid stress survival, how c-di-GMP signaling regulates these pathways across the two organisms, and how pathoadaptation influences these mechanisms. The project will employ methodologies accessible to undergraduate researchers, who will execute the proposed experiments. Findings are expected to generalize across other gastrointestinal bacteria that use amino acid metabolism for acid stress survival, with implications for food supply chain protection, symbiotic bacterial promotion, and pathogen control.

Work is performed in Kalamazoo, Michigan, with a period of performance extending from the award date through January 31, 2029.

Abstract

Bacteria have successfully colonized almost every niche on this planet, and their success is driven in large part by their ability to adapt to and survive environmental challenges. One example is excessive protons (or acidity, low PH), which can damage lipids, nucleic acids, and proteins. Bacteria that colonize the human body contend with many different PH gradients, especially in the gastrointestinal system. One way that bacteria survive this stress is by using amino acid catabolism to DE-acidify their environment. We discovered that the bacterial second messenger c-DI-GMP regulates both amino acid metabolism and acid resistance in the gastrointestinal bacteria e. Coli and shigella. One of these amino acids is isoleucine, and we have found that e. Coli, but not shigella, catabolizes isoleucine to resist acid stress. Bacterial isoleucine-mediated acid resistance has not been previously reported. In this application, we will investigate how isoleucine contributes to acid resistance, how c- DI-GMP regulates acid resistance in these two organisms, and how these pathways are impacted by the evolutionary process of pathoadaptation. Methodologies proposed here are accessible for undergraduate researchers, who will complete the experiments outlined in this proposal. Because many bacteria use amino acid metabolism to resist acid stress, and because c-DI-GMP signaling is so widely conserved, findings from this study will be widely generalizable for other gastrointestinal bacteria. Understanding how gastrointestinal bacteria adapt to PH stress is critical for many aspects of human health, including protecting our food supply chain, promoting symbiotic bacteria, and controlling human pathogens.