Microbes carry out essential ecosystem services that are important for human health. How will microbial communities evolve in response to environmental change, antibiotics or phage therapy?

 

We want to understand microbial evolution so that we can predict the evolutionary outcomes of environmental change, use microbiome engineering to manage microbial communities and design strategies that slow down the evolution of antibiotic resistance.

We study the genetics and mechanisms of adaptation. Our approach is to grow populations of bacteriophage, bacteria and fungi for 1000s of generations in a variety of environments, observing evolution as it happens. With the tools of whole genome sequencing, statistics and genetic engineering we figure out the rules of how new mutations can shape a better adapted organism. In particular we are interested how horizontal gene transfer changes the rules of evolution in prokaryotes and speeds the evolution of antibiotic resistance. The species we use for these studies are H. pylori, E. coli and Klebsiella.  We are also interested how co-evolution (evolution with multiple different species) can change the speed and mechanisms of evolution. We use E. coli, P. fluorescens, L. plantarum, S. cerevisiae and C. albicans for these studies. Finally, we study host range expansion and the impact that bacteriophage has on microbial communities using Escherichia bacteriophage isolated from the environment.

Lab News

April 2022 Congratulations Dr. Nguyen!

An has graduated and published a new paper (here in PNAS) after developing and mastering (among other things) a really cool, large-scale sequencing-based fitness assay in H. pylori.

March 2022 Congratulations Dr. Sant!

Duhita has graduated after bringing phage evolution to the lab and mastering a new sequence-based tracking of a microbial community -  more coming soon.

 

Feb 2022 Congratulations Dr. Barber!

Jake just graduated- he has changed our understanding of how having a microbial community around changes the outcomes of evolution. Check out his second and latest paper here in ISME

August 2021 Congratulations Dr Woods!

Laura is the first Ph.D graduate of the lab and her first contributions to experimental evolution will have a big impact on how we will look at horizontal gene transfer, more work coming soon.

March 2021. Two new papers from the group: Duhitas study of Phage evolution in the context of multiple potential hosts, out in Nature Ecology and Evolution, Jake's efforts to get E. coli and S. cerevisiae to get along (Coexistence from competition out in ISME)

October 2020- We have been trying for some time to carry out evolution experiments with HGT- still a major challenge in microbial experimental evolution, and we think we have found the perfect system. Check out our paper, out now in PNAS: Horizontal gene transfer potentiates adaptation by reducing selective constraints on the spread of genetic variation

A new paper in February 2020 in Nature Ecology and Evolution

Sex alters molecular evolution in diploid experimental populations of S. cerevisiae

DOI https://doi.org/10.1038/s41559-020-1101-1 

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