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.
A new paper in February 2020 in Nature Ecology and Evolution
Sex alters molecular evolution in diploid experimental populations of S. cerevisiae
July 27th, 2019
A new review paper published in EMBO report, Microbial Experimental Evolution – a proving ground for evolutionary theory and a tool for discovery.
June 26th, 2019
A new paper published in The ISME Journal (2019), Diverse hydrogen production and consumption pathways influence methane production in ruminants
NHMRC Grant, December 2019
Grant to research the antibiotic resistance network in multi-drug resistant Helicobacter pylori.
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