Bacterial Regulation of Acid Resistance and Amino Acid Metabolism

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. Project Number: 1R15GM163283-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of General Medical Sciences (NIGMS) | Principal Investigator: Benjamin Koestler | Institution: WESTERN MICHIGAN UNIVERSITY, KALAMAZOO, MI | Award Amount: $532,909 | Activity Code: R15 | Study Section: Special Emphasis Panel[ZRG1 MGG-J (80)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11290916