Understanding and predicting how bacteriophages structure the microbiome

Background: Microbiomes play important roles in human health and nutrition. The performance of these functions is expected to be higher in more diverse microbiomes. Thus, the ecological stability of microbiomes - particularly their ability to recover from perturbations like antibiotic treatment - is believed to be an important predictor of their healthy function. To control and improve the benefits of microbiomes to human health we first need to understand the ecological and evolutionary rules that govern their structure and stability (Foster et al. 2017). Bacteriophages, viruses that infect bacteria, are universal in bacterial communities, driving their ecology and evolution (Koskella & Brockhurst 2014), but how bacteriophages affect the structure and stability of human microbiomes is currently unknown.

Project: In this project we will explore how bacteriophages influence the structure and stability of human airway microbiome communities. Specifically, we will use a combination of ecological theory (Coyte et al. 2015) and simplified experimental communities (Davies et al. 2015) to predict and test the impact of bacteriophages on the structure and stability of microbiome communities with or without antibiotic perturbation. Then, we will use metagenomics to track the longitudinal dynamics of bacteriophages and bacteria within human airways (Layeghifard et al. 2019), testing our predictions in a real-world and clinically-relevant context. This research will advance understanding of the ecology and evolution of the human microbiome. This is vital for improving microbiome function (e.g. though microbiome restoration and transplants) and understanding the broader impacts of antimicrobial treatments (e.g. antibiotics and phage therapy) on human health.

Training and supervision: This project offers a broad interdisciplinary training, including mathematical and computational modelling, microbiology, experimental evolution, evolutionary biology, genomics and bioinformatics. The supervisory team provides expertise in ecological theory for microbiomes (Katherine Coyte, UoManchester), experimental approaches to understanding microbial ecology and evolution (Michael Brockhurst, UoManchester), and genomics methods and bioinformatics (David Guttman, UoToronto). The project will be based at UoManchester with a 12-month placement at UoToronto enabling you to experience diverse research environments. You will be part of vibrant research labs alongside postdocs, technicians and students working on related projects investigating microbial evolution and ecology, offering an exciting and supportive training environment.