Vaughn Cooper, Ph.D.

1. Mechanisms of beneficial mutations

We use evolution to understand how microbes work, as a potent genetic screen for mutations that increase fitness in any imaginable environment. These mutations affect genes and systems that often yield the best adaptations and usually teach us new, surprising, fundamental attributes of microbial biology. We continue to investigate why mutations in certain genes are repeatedly selected in evolution experiments or chronic infections and how they work.

2. Evolution during Infections

Microbes often adaptively evolve when establishing infections by escaping components of the immune system and subsequently, antimicrobial treatment. We are interested in how bacterial populations evolve to escape antibiotic and host pressures during infections, with the goal of improving prediction of antimicrobial resistance. We study the evolution of drug resistance and pathogenicity in near real time through in vitro and in vivo experimental evolution using comparative genomics and analyses of longitudinal deep-sequenced populations. Our research questions include: (1) mechanisms of drug resistance and treatment failure, (2) the impact of the biofilm lifestyle on resistance, (3) how host immune state influences resistance evolution, and (4) comparative genomics of multi-drug resistant clinical isolates.

3 Ecological-evolutionary dynamics

Microbes exist within complex communities where both abiotic factors and inter-/intra-species interactions influence evolutionary trajectories. These environmental factors impose selective forces on communities. Likewise, individuals in a community can modify their environment and indirectly influence selective pressures applied to the community. We are interested in understanding such ecological and evolutionary dynamics at a community scale, especially in the context of biofilms, polymicrobial communities, and active bacteriophages.

4 Adaptive dynamics within host-associated microbiomes

Like any disrupted ecosystem, when a host-associated microbiome is far from equilibrium, certain community members may be selected to inhabit vacant niches in which they are relatively maladapted. These lineages may undergo rapid adaptive evolution that can be tracked by longitudinal genome sequencing. We study these processes in a wide range of systems with experts focused on particular diseases or symbioses, including:

in the upper and lower airways of persons with cystic fibrosis,
during establishment of chronic wounds,
during chronic infections of prosthetic joint replacement
during colonization of the infant gut
during symbiosis with the Hawaiian bobtail squid and even among the virome within bacterial cells

5. EvolvingSTEM

We created EvolvingSTEM, a research-education partnership program that uses evolution-in-action to capture the imagination of middle and high school biology students. We partner with classrooms across the US to engage students in an authentic laboratory experience. They evolve populations of Pseudomonas fluorescens under selection for biofilm growth and observe conspicuous changes to colony morphology in as little as one week. Our goals are to (1) increase understanding of key life science topics, including evolution, microbiology, and genetics, (2) provide training in essential biotechnology skills, and (3) inspire an enduring interest in science. Students gain confidence in STEM topics through hands-on experiences and drawing connections from their bench-top experiments to real-life medical applications. In addition, we train teachers to effectively implement our program in their classrooms through an immersive 8-week summer research experience hosted in our laboratory through support from NSF and NIH