Evolutionary Genetics
We study how genetic variation in microbes leads to evolutionary change over time, mostly by examining how microbes can adapt—or not adapt—to environmental challenges via the evolutionary mechanism of natural selection.
Much of this research harnesses the power of studying microbial experimental evolution (“evolution-in-action”) in well-controlled laboratory environments, using bacteria, bacteriophages, and viruses of eukaryotes as models. Some of our studies examine genomics, population structure, and communities of microbes evolving in the wild.
Ecology and Evolution of Infectious Diseases
Our research concerns the ecological and evolutionary drivers that impact transmission dynamics of infectious disease agents, particularly emerging antibiotic-resistant bacteria, directly transmissible viruses, and vector-borne viruses.
Often, we examine these microbes in the laboratory using experimental evolution, and via mathematical, theoretical, and computational studies. Also, our spatiotemporal analyses of natural environment, microbiome, and clinical samples reveal how evolutionary mechanisms influence the genetic variation and phenotypic traits in populations and communities of evolving pathogens.
Evolutionary Medicine
We use “evolution-thinking” to enable an integrated understanding of human biology and medicine. These studies often focus on trade-offs: evolutionary changes in one trait that improve fitness while causing other trait(s) to decrease fitness, such as greater disease vulnerability.
Our evolutionary medicine studies are interdisciplinary, involving mathematics, theory, lab experiments, and publicly available datasets, as well as bridges between evolutionary biology and biotechnology. For example, we develop phage therapy—bacteria-specific viruses used to treat human infections—that kills target bacteria while selecting for evolved phage-resistance that compromises virulence and pathogenicity.
Microbe-Animal Symbiosis in Aquatic Systems
We increasingly study symbiotic interactions between host animals and microbiome community members, especially bacteria and bacteriophages. Symbiosis includes both positive interactions (mutualism) as well as negative associations (parasitism) between organisms. Our current work examines spatiotemporal analyses of changes in gut and skin microbiome composition in aquatic vertebrates, such as captive beluga whales and ray fish, with collaborators at Mystic Aquarium in Connecticut and Aquarium of the Bay in California.
These projects examine how antibiotic-resistant bacteria spread within and among host-animal microbiomes, potentially threatening rare species conservation and rehabilitation efforts. We also study how lytic phage composition of host viromes can benefit vertebrate and invertebrate (shellfish) host animals by targeting bacterial pathogen invaders.