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SWBio DTP PhD project: Host specialisms in bacterial pathogens

Department of Biology & Biochemistry

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Prof Ed Feil No more applications being accepted Competition Funded PhD Project (Students Worldwide)

About the Project

This project is one of a number that are in competition for funding from the South West Biosciences Doctoral Training Partnership (SWBio DTP)

The DTP offers an interdisciplinary research training programme delivered by a consortium comprising the Universities of Bath, Bristol and Exeter, Cardiff University and Rothamsted Research, alongside six regional associate partners: Marine Biological Association, Plymouth Marine Laboratory, Swansea University, UCB Pharma, University of the West of England and SETsquared Bristol.

All SWBio DTP projects will follow a structured 4-year PhD model, combining traditional project-focussed studies with a taught first year which includes directed rotation projects.

+++ Studentships are available for entry in October 2021 - please see the ’Funding Notes’ below and for information on eligibility +++


Lead supervisor: Prof Edward Feil, University of Bath, Department of Biology & Biochemistry, email [Email Address Removed]
Co-supervisors: Dr Kristen Reyher (Bristol), Prof Sam Sheppard (Bath) and Dr Katy Turner (Bristol)


The global Covid-19 pandemic emerged due to the ability of a pathogenic agent to jump from an animal host into a human, a process known as “spillover”, and this phenomenon is becoming more likely due to climate change and other anthropogenic perturbations on ecosystems and habitats. However, once a pathogen has switched from an animal to a human host, it is likely to be maladapted and show restricted capacity for human-to-human transmission.

The rapid spread of Sars-CoV-2 within the human population therefore represents an exceptional case, and host specific adaptations of pathogens typically shield humans from such large-scale zoonotic outbreaks. Despite the importance of these host specialisms, significant knowledge gaps remain regarding the genetic basis of host adaptation and the ecological or evolutionary conditions under which specialisms are likely to be relaxed or reinforced.

This project will address these questions with a focus on the important bacterial pathogen Klebsiella pneumoniae as a model system. This species, when taken as a whole, is an ecological generalist and can infect humans and multiple domesticated and wild animal species. However, evidence from large-scale genome sequencing generated in our lab has shown that different strains tend to be specialised for particular hosts, such as cows or humans.

This project will pin-point the genetic changes underlying these specialisms through bioinformatics and statistical analysis. These analyses will be combined with laboratory experiments to further characterise the phenotypic differences between strains adapted to different hosts. The phenotypic and genomic analyses will be considered within the context of differences in diet, immunology, gut environment and microbiome between the hosts. Finally, modelling approaches will be used to illuminate how specialisms might evolve or be relaxed at a population scale under differing ecological conditions.

Expertise on comparative genomics and bioinformatics will be provided by the primary supervisor, Prof. Edward Feil, and Prof. Sam Sheppard (Milner Centre). Complimentary expertise in veterinary science and infectious disease dynamics in agricultural settings will be provided by the second supervisor, Dr Kristen Reyher, and modelling supervision will be provided by Dr Katy Turner, both of whom are at the University of Bristol Veterinary School.


Applicants must have obtained, or be about to obtain, a First or Upper Second Class UK Honours degree, or the equivalent qualifications gained outside the UK, in an appropriate area of science or technology.

Informal enquiries are welcomed and should be addressed to the lead supervisor.

Enquiries about the application process should be addressed to [Email Address Removed].

Formal applications should be submitted on the University of Bath’s online application form for a PhD in Biosciences:

Please ensure that you quote the supervisor’s name and project title in the ‘Your research interests’ section. You may apply for more than one project if you wish but you should submit a separate personal statement relevant to each one.

If you are an EU/EEA/Swiss national with settled or pre-settled status in the UK under the EU Settlement Scheme, please upload documentary evidence with your application.

More information about applying for a PhD at Bath may be found on our website

Funding Notes

Studentships cover tuition fees at the ‘Home’ level, research/training costs and a stipend (£15,285 p.a., 2020/21 rate) for 3.5 years.

The main categories of candidates normally eligible for 'Home' fees are:
UK nationals*
Irish nationals living in the UK/Ireland
Applicants with settled or pre-settled* status in the UK under the EU Settlement Scheme
Applicants with indefinite leave to enter/remain in the UK

* must have lived in the UK/EEA/Switzerland continuously since September 2018.

If you do not qualify for ‘Home’ fees, you may be considered for an international student fee discount equivalent to the difference between ‘Home’ and ‘Overseas’ fees.


Bonneaud C, Weinert LA, Kuijper B. Understanding the emergence of bacterial pathogens in novel hosts. Philos Trans R Soc Lond B Biol Sci. 2019 Sep 30;374(1782):20180328. doi: 10.1098/rstb.2018.0328. Epub 2019 Aug 12. PMID: 31401968; PMCID: PMC6711297.

Sheppard SK, Guttman DS, Fitzgerald JR. Population genomics of bacterial host adaptation. Nat Rev Genet. 2018 Sep;19(9):549-565. doi: 10.1038/s41576-018-0032-z. PMID: 29973680.
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