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(BBSRC DTP) Understanding and predicting how bacteriophages structure the microbiome

Faculty of Biology, Medicine and Health

Manchester United Kingdom Applied Mathematics Bioinformatics Data Analysis Ecology Evolution Genetics Microbiology Other Other Radiology

About the Project

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.

David Guttman lab web page:

Entry Requirements:
Applicants must have obtained, or be about to obtain, at least an upper second class honours degree (or equivalent) in a relevant subject.

UK applicants interested in this project should make direct contact with the Principal Supervisor to arrange to discuss the project further as soon as possible. International applicants (including EU nationals) must ensure they meet the academic eligibility criteria (including English Language) as outlined before contacting potential supervisors to express an interest in their project. Eligibility can be checked via the University Country Specific information page (

If your country is not listed you must contact the Doctoral Academy Admissions Team providing a detailed CV (to include academic qualifications – stating degree classification(s) and dates awarded) and relevant transcripts.

Following the review of your qualifications and with support from potential supervisor(s), you will be informed whether you can submit a formal online application.

To be considered for this project you MUST submit a formal online application form - full details on how to apply can be found on the BBSRC DTP website

Funding Notes

Funding will cover UK tuition fees/stipend only. The University of Manchester aims to support the most outstanding applicants from outside the UK. We are able to offer a limited number of scholarships that will enable full studentships to be awarded to international applicants. These full studentships will only be awarded to exceptional quality candidates, due to the competitive nature of this scheme.

Equality, diversity and inclusion is fundamental to the success of The University of Manchester, and is at the heart of all of our activities. The full Equality, diversity and inclusion statement can be found on the website View Website


Coyte KZ, Schluter J, Foster KR. The ecology of the microbiome: Networks, competition, and stability. Science. 2015;350(6261):663-666. doi:10.1126/science.aad2602

Davies EV, James CE, Williams D, et al. Temperate phages both mediate and drive adaptive evolution in pathogen biofilms. Proc Natl Acad Sci U S A. 2016;113(29):8266-8271. doi:10.1073/pnas.1520056113

Foster KR, Schluter J, Coyte KZ, Rakoff-Nahoum S. The evolution of the host microbiome as an ecosystem on a leash. Nature. 2017;548(7665):43-51. doi:10.1038/nature23292

Koskella B, Brockhurst MA. Bacteria-phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol Rev. 2014;38(5):916-931. doi:10.1111/1574-6976.12072

Layeghifard M, Li H, Wang PW, et al. Microbiome networks and change-point analysis reveal key community changes associated with cystic fibrosis pulmonary exacerbations. NPJ Biofilms Microbiomes. 2019;5:4. Published 2019 Jan 21. doi:10.1038/s41522-018-0077-y

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