Function and evolution of strains in the gut microbiota

The commensal intestinal bacteria, or microbiota, are intricately involved in human health. The predominant phyla in adult humans are the Bacteroidota and the Bacillota, the latter being represented mainly by bacteria from the class Clostridia. Shifts in the relative abundances of Clostridia are associated with a variety of disease outcomes, though it is unclear if there are specific Clostridia that largely control disease progression or if there are features shared amongst multiple lineages that collectively dictate microbiota functions. Our approach examines the genetic determinants of microbiota function with the hypothesis that a subset of metabolic pathways influence critical microbiota functions. To support this hypothesis, genomic sequences from Clostridia isolated by our laboratories were compared to identify non-conserved genes. In one set of isolates identified as Paraclostridium bifermentans, a commensal bacterium with pathogenic potential, we observed the disparate presence of genes encoding sorbitol catabolism. Sorbitol can be diet or host-derived and supports pathogenesis of enteric bacteria. In Aim 1, the transcriptional regulation of P. bifermentans sorbitol catabolic genes and the effects of sorbitol utilization on competition with the anaerobic pathogen, Clostridioides difficile, will be elucidated. Furthermore, analysis of multiple P. bifermentans strains suggests that sorbitol metabolism aids in niche establishment and ecotype stabilization. How strains of anaerobic, spore-forming bacteria, which constitute a significant portion of the gut microbiota, evolve to occupy distinct niches to co-exist in the same host has not been examined. In Aim 2, an evolution model will be established to highlight the intrinsic and environmental forces that shape P. bifermentans ecotype abundance. Using sorbitol catabolism in P. bifermentans as a model system, we hypothesize that gene duplication events, a more common form of mutation compared to better recognized single nucleotide polymorphisms, will enhance growth and competitiveness against pathogens while reinforcing strain co-existence. This study is significant because it will uncover metabolic genes encoded by the gut microbiota that may better predict health outcomes compared to associations with bacterial species. Additionally, the mechanisms that govern strain evolution, which has only been studied in aerobic bacteria and eukaryotic yeast, will start to be unraveled for the first time for an anaerobic, spore-forming bacterium, advancing our understanding of how the gut microbiota establishes, recovers, and changes. This project aligns with the developmental and cellular processes branch of NIGMS to elucidate the fundamental factors that control cell responses and microbiome composition. Project Number: 1R15GM160989-01 | Fiscal Year: 2025 | NIH Institute/Center: National Institute of General Medical Sciences (NIGMS) | Principal Investigator: Christopher Lopez (+1 co-PI) | Institution: CALIFORNIA STATE UNIVERSITY SACRAMENTO, SACRAMENTO, CA | Award Amount: $532,500 | Activity Code: R15 | Study Section: Special Emphasis Panel[ZRG1 CDB-N (81)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11219093