Title: "Diversity Beneath the Surface: Comparative Genomics and Metabolic Modeling Reveal Hidden Variation in Freshwater E. coli Populations"

Abstract: Escherichia coli is a commensal and pathogen of animals and a foundational model organism in microbiology. It is used worldwide as a fecal indicator bacterium for food and water quality monitoring, and its detection directly informs public health communication and regulatory actions, including beach and recreational water closures. However, growing evidence indicates that some E. coli populations are adapted to secondary, non-host environments such as soil and freshwater. Through long-term monitoring of the Macatawa watershed supporting community-led environmental remediation, we isolated over 12,000 freshwater E. coli strains and generated whole-genome sequences for more than 500 isolates. Using an integrated framework of comparative genomics, experimental metabolic profiling, and genome-scale metabolic modeling, we characterized freshwater populations relative to host-associated strains. We show that phenotypic metabolic diversity in freshwater isolates is associated with distinct genomic architectures and mutations. These results provide evidence for the existence of endemic E. coli populations persisting in surface waters, demonstrate opportunities to improve genome-scale metabolic model performance, and support the use of alternative fecal indicator organisms for more accurate public health monitoring.

Bio: Dr. Aaron Best is the Visscher Professor of Genetics and Director of the Global Water Research Institute at Hope College. He has a Ph.D. in Microbiology from the University of Illinois Urbana-Champaign and has over 20 years of experience in academia with research focused on microbial genomics/ecology as applied to environmental and drinking water quality. In addition, he works with non-governmental organizations to design and assess drinking water quality provision projects in communities around the world. During the COVID-19 pandemic, Dr. Best rapidly established a wastewater monitoring program used for real-time decision-making for leaders in health departments, institutions of higher learning and manufacturing, including monitoring of communities throughout West Michigan as part of the MDHHS statewide monitoring program.