We study the ecology and evolution of microbes and their associated host organisms.
Using experimental evolution to study microbial adaptation in real-time

Experimental evolution can be used to study microbial evolution in real-time. The method involves culturing replicate populations of study microbial species in a highly controlled laboratory or natural environment for hundreds to thousands of generations. As microbes have inherently large population sizes and short generation times, they will evolve and adapt rapidly. Microbes can be further cryopreserved indefinitely, which allows direct comparisons between evolved, ancestral and control populations at both phenotypic and genetic levels. We use experimental evolution to understand how bacterial diseases might evolve in response to therapeutic interventions such as antibiotics or phages. Understanding the ecology and evolution of microbial and microbe-host interactions is important in its own right as microbes typically live in multi-species communities called microbiomes.

Using ecological and evolutionary theory to engineer rhizosphere microbiomes in agriculture

Bacterial rhizosphere communities form the first line of defence against invading pathogens. The diversity resistance hypothesis argues that diverse communities are resistant to invasions due to a high number of species interactions and intensified competition for niche space. While this pattern is supported by both theory and experiments, diversity–invasion resistance relationships are more complex often varying from positive to negative.

We have studied diversity-invasion resistance relationships with Ralstonia solanacearum plant pathogen, which is capable of infecting over 200 plant species across 50 families. We have found that increasing the diversity of non-pathogenic rhizosphere bacteria reduces the likelihood of pathogen invasion due to more intensified resource competition and direct inhibition via antibiosis. In addition to bacteria, also phage diversity is important for R. solanacearum suppression in the rhizosphere. Disease outcomes are further affected by functional differences in the initial microbiome composition and abiotic environmental conditions that can determine the strength of interactions between the invading pathogen and the resisting non-pathogenic rhizosphere bacteria.

Phage therapy in clinical and agricultural contexts

Due to the rapid increase in multi-drug resistant bacteria, recent years have seen renewed interest in phage therapy - the use of viruses to specifically kill the disease-causing bacteria. While phage therapy offers many advantages over conventional antibiotics, the rapid evolution of phage resistance might be a problem. Furthermore, it is important to establish that phages are safe for the environment and do not cause collateral damage to commensal and mutualist beneficial bacteria. We have developed model phage therapies against Pseudomonas aeruginosa human opportunistic pathogen and Ralstonia solanacearum – a notorious plant pathogenic bacterium.

Antibiotic resistance evolution in microbial communities

Antibiotics leak constantly into environments due to widespread use in agriculture and human therapy, affecting complex environmental microbiomes. Similarly, while antibiotics are known to affect wider bacterial communities beyond the target pathogen, these effects are seldom studied in the presence of other microbes. This is a clear shortcoming as many infections, such as bacterial infections in Cystic Fibrosis patient lungs, are typically polymicrobial. We are using experimental, bioinformatic and modelling approaches to study the ecological and evolutionary effects of antibiotics in microbial communities.