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Evolution Education Trust PhD project: Strain wars and the evolution of opportunistic pathogens

  • Full or part time
  • Application Deadline
    Wednesday, February 05, 2020
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

The University of Bath is inviting applications for this PhD opportunity based at the Milner Centre for Evolution, a unique, cross-faculty research centre bridging biology, health and education. The Centre is dedicated to a broad range of fundamental research questions relating to evolutionary biology; from in deep time to the micro-evolutionary dynamics of a disease outbreak. We have a strong focus on public engagement and outreach. We are located in a dedicated multi-million-pound building that opened on the University campus in September 2018. Visit our website:

Supervisory Team:

Professor Samuel K Sheppard, Milner Centre for Evolution, University of Bath (lead supervisor)
Dr Maisem Laabei, Department of Biology and Biochemistry, University of Bath
Dr Ben Pascoe , Milner Centre for Evolution, University of Bath
Professor Edward Feil, Milner Centre for Evolution, University of Bath
Dr Fintan Moriarty, AO Foundation, Davos, Switzerland

Project Overview:

Many serious diseases (e.g., meningitis, pneumonia, blood/wound infections) are caused by commensal bacteria that are common on the skin or in the guts of healthy people. However, questions remain about what makes good strains go bad. For example: Are all strains equally able to cause disease? What are the disease determinants? Why aren’t pathogenic strains outcompeted in the commensal niche, where pathogenicity genes have no benefit? Using large isolate and genome collections, and state-of-the-art lab and genome analyses this project will identify the pathogenicity genes and evolutionary forces that cause harmless bacteria to become pathogens.

The maintenance of potentially pathogenic sublineages in a commensal community presents a challenge in terms of evolutionary theory. Bacteria adapted to the commensal niche, such as on the skin, will encounter the disease niche (eg bloodstream) relatively infrequently. Therefore there is little opportunity for an evolutionary trade off to develop, and strains in the commensal population that are weighed down by the metabolic cost of maintaining pathogenicity genes should be outcompeted and purged from the commensal niche. This is not the case.

We will use large collections of Staphylococcus aureus and Staphylococcus epidermidis genomes. Novel pangenome-wide association studies will be used to identify genetic determinants of pathogenicity in a subset of commensal strains. We will then use (i) phylogenetics and analysis of recombination to demonstrate the evolutionary scenario by which horizontal gene transfer spreads these elements allowing divergent clones to cause infection, and (ii) machine learning based upon genomic variation to identify high risk strains.


Applicants should have an excellent academic record and hold, or expect to obtain, a First Class or high Upper Second Class UK Honours degree (or the equivalent) in a relevant subject. A master’s level qualification would also be advantageous.

Enquiries and Applications:

All enquiries should be addressed to .

** Candidates are strongly encouraged to discuss projects directly with the lead supervisor before submitting an application.**

Formal applications should be made via the University of Bath’s online application form for a PhD in Biology:

On the application form, please ensure that you quote ‘Evolution Education Trust’ in the Finance section and the supervisor’s name and project title in the ‘Your research interests’ section. Should you wish to be considered for more than one project, quote the projects in order of preference and upload a separate personal statement relevant to each one.

It is essential that your application is complete when you submit it to us. Incomplete applications cannot be considered. You should ensure that you have completed all fields on the application form and supplied the contact details of TWO referees who are available and willing to provide us with a reference when requested (one must be from your most recent place of study). In addition, you should ensure that you have uploaded the following documents:
• a scanned copy of the certificate/s for any degree/s you have been awarded;
• a scanned copy of your degree transcript/s or your interim transcript if you are still studying;
• an up-to-date CV;
• a personal statement explaining your motivation for wishing to study a PhD and your interest in the specific project for which you are applying;
• English language test certificate (if available) for EU candidates.

More information about applying for a PhD at Bath may be found here:

Interviews will take place in Bath on Friday 3 April 2020.

Anticipated start date: 28 September 2020.

Unfortunately, we are NOT able to consider international applicants for this project.

Funding Notes

Candidates applying for this project will be considered for a 3.5-year Evolution Education Trust Studentship which will cover UK/EU tuition fees, a tax-free maintenance allowance at the UKRI Doctoral Stipend rate (£15,009 for 2019/20) and a generous budget for research, training and outreach expenses.

Note: Only UK and EU applicants are eligible for studentship funding.


1. Méric, Mageiros, Pensar, Laabei, Yahara, Pascoe, Kittiwan, Tadee, Post, Lamble, Bowden, Bray, Morgenstern, Jolley, Maiden, Feil, Didelot, Miragaia, de Lencastre, Moriarty, Rohde, Massey, Mack, Corander, Sheppard. (2018) Disease-causing genotypes of the commensal skin bacterium Staphylococcus epidermidis. Nature Communications 9:5034.

2. Berthenet, Yahara, Thorell, Pascoe, Méric, Mikhail, Engstrand, Enroth, Burette, Mégraud, Varon, Atherton, Smith, Wilkinson, Hitchings, Falush, Sheppard. (2018) Helicobacter pylori genome-wide association study shows promise for predicting gastic cancer risk. BMC Biology 16:84

3. Sheppard, Guttman, Fitzgerald. (2018) Population genomics of bacterial host adaptation. Nature Reviews Genetics 1471-0064

4. Méric, Miragaia, de Been, Yahara, Pascoe, Mageiros, Mikhail, Harris, Wilkinson, Rolo, Lamble, Bray, Jolley, Hanage, Bowden, Maiden, Mack, de Lencastre, Feil, Corander, Sheppard (2015) Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis. Genome Biology and Evolution 7(5):1313-1328.

5. Sheppard, Didelot, Meric, Torralbo, Jolley, Kelly, Bentley, Maiden, Parkhill, Falush (2013) Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter. PNAS 110(29):11923-7.

How good is research at University of Bath in Biological Sciences?

FTE Category A staff submitted: 24.50

Research output data provided by the Research Excellence Framework (REF)

Click here to see the results for all UK universities

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