Microbial Evolution Through Viral Gene Flow in Natural Populations

Recent research has unearthed regions of the genome that are capable of moving rapidly between cells, creating a sea of dramatic and unpredictable genetic changes. These mobile genetic elements (MGEs) are particularly exploited by infectious bacteria, which evade antibiotics through rapid evolution driven by MGEs. While the scientific response to infectious disease has focused on identifying new ways to target and kill bacteria, antimicrobial resistance, virulence, and many other properties of pathogens are evolutionary problems driven by mobile elements. An evidence-based predictive understanding of the forces of evolution that lead to the emergence and spread of these traits is needed in order to stop them. Whitaker’s project will create models of MGEs and their evolutionary roles within a human system, and compare and refine those models against longitudinal data in order to capture and better understand this crucial evolutionary process.

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Affiliated Investigators

Rachel Whitaker, Ph.D.

University of Illinois, Urbana-Champaign

Intimate and specific host-microbe symbiotic associations join microbes into the fabric of every ecosystem. The Whitaker lab focuses on the ecology and evolutionary biology of microorganisms in dynamic environments, including the human microbiome.  Whitaker uses genomic tools in simple natural environments to study microbial population dynamics and how they are shaped by interactions with mobile genetic elements.  Recent work has focused on interactions mediated by CRISPR-Cas: the exquisitely sensitive, sequence-specific immune system in Bacteria and Archaea.  The Whitaker lab has identified key signatures of the recent evolutionary history of microbes and viruses from population genomic data.  Recent work has demonstrated that virus infections can benefit their hosts through conditional mutualism and has enhanced understanding of both positive and negative impacts of viral infection.  Work in the Whitaker lab seeks to integrate molecular microbiology with evolutionary understanding of natural variation to better understand ongoing evolutionary processes in the microbial world.

Dr. Whitaker is an associate professor in the Department of Microbiology and Leader of the Infection Genomics for One Health (IGOH) Theme at the Carl R. Woese Institute for Genomic Biology at the University of Illinois at Urbana-Champaign.  Dr. Whitaker earned her Bachelor of Arts with a double major in Biology and the Science in Society Program at Wesleyan University in Middletown, CT. Whitaker received her Ph.D. in microbiology at the University of California, Berkeley with Dr. John Taylor, learning evolutionary principles, population genetics, and genomics.  A NASA graduate research fellowship enabled Whitaker to develop a new model system in the Archaea Sulfolobus, examining natural population structure and gene flow.  Whitaker’s postdoctoral research was in the laboratory of Dr. Jillian Banfield at Berkeley.  In 2018 she begins as co-director of the Microbial Diversity course at the Marine Biological Laboratories in Woods Hole.