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  SWBio DTP PhD project: Host adaptation and transmission of the important pathogen Klebsiella pneumoniae

   Department of Life Sciences

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  Prof Edward 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 SWBio DTP is funded by BBSRC and involves a partnership of world-renown universities, research institutes and industry across the South West and Wales. This partnership represents a distinctive group of bioscientists with established international, national and regional networks and widely recognised research excellence. We aim to provide students with outstanding interdisciplinary research training.

Studentships are available for entry in October 2023.

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

Supervisory Team:

Lead supervisor: Prof Edward Feil, University of Bath, Department of Life Sciences, Milner Centre for Evolution (email: [Email Address Removed])  

Co-supervisors: Prof Kristen Reyher (University of Bristol), Dr Lauren Cowley (University of Bath) and Prof Andrew Dowsey (University of Bristol)

The Project:

The global Covid-19 pandemic emerged due to the ability of a pathogen to jump from an animal host into a human, a process known as “spillover”. This phenomenon is becoming more likely as climate change and other anthropogenic impacts result in habitat loss and other ecological disturbances. However, once a pathogen has switched from an animal to a human host, it is likely to be maladapted and show poor potential for onward human-to-human transmission. This is because each host species presents specific challenges to new pathogens, including immune defences and competition from resident microflora. 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 on the conditions under which specialisms are likely to evolve.

This project will address these questions with a focus on the important bacterial pathogen Klebsiella pneumoniae. This species is a notorious pathogen in hospitals globally due to the emergence of strains that are resistant to multiple antibiotics. However, it is also an ecological generalist that can not only infect humans, but also multiple domesticated and wild animal and plant species. Recent studies using whole genome sequencing 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 analyses of large genome datasets, combined with laboratory experiments. The project will consider host specific factors including diet, immunology, the gut environment and the presence of competing bacterial species.

Expertise on bioinformatics will be provided by the primary supervisor, Prof Edward Feil, with additional support from Dr Lauren Cowley, at the Milner Centre for Evolution at the University of Bath. Complimentary expertise in veterinary science and infectious disease dynamics in agricultural settings will be provided by the second supervisor, Prof Kristen Reyher, with additional statistical support from Prof Andrew Dowsey.

Project keywords: adaptation, genomics, infectious disease, agriculture, bioinformatics.


 Applicants should 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. Applicants with a Lower Second Class degree will be considered if they also have Masters degree or have significant relevant non-academic experience.

In addition, due to the strong mathematical component of the taught course in the first year and the quantitative emphasis in our projects, a minimum of a grade B in A-level Maths or an equivalent qualification/experience* is required.

* Physics A-level (grade B and above) or units in your degree with a significant mathematical component, e.g. maths, statistics, bioinformatics.

Applicants must ensure they highlight their Maths background within their application and to upload any supporting evidence.

If English is not your first language, you will need to have achieved Academic IELTS 6.5 overall (with no less than 6.5 in any of the four skills). Find details of other acceptable tests and further information on our website.

Enquiries and Applications:

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

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

When completing the form, please identify your application as being for the SWBio DTP studentship competition in Section 3 Finance (question 2) and quote the project title and lead supervisor’s name in the ‘Your research interests’ section.  You may apply for more than one project within the same application but you should upload a separate (clearly labelled) personal statement for each one, outlining your interest and suitability for that particular project.

See our website for more information about applying for a PhD at Bath.

Equality, Diversity and Inclusion:

We want to support diverse and inclusive work environments. We therefore welcome applications from individuals regardless of their race, ethnicity, sexual orientation, religion, age, gender or disability status.

If you have circumstances that you feel we should be aware of that have affected your educational attainment, then please feel free to tell us about it in your application form. The best way to do this is a short paragraph at the end of your personal statement.

Biological Sciences (4) Mathematics (25) Veterinary Sciences (35)

Funding Notes

Candidates may be considered for SWBio DTP studentship tenable for 4 years. Funding covers tuition fees, a stipend (£17,668 p/a in 2022/23) plus an allowance for research/training costs, fieldwork, conference attendance and a 3-month placement. Studentships are open to both Home and International students; however, International applicants should note that funding does NOT cover the cost of a student visa, healthcare surcharge and other costs of moving to the UK. In line with guidance from UK Research and Innovation (UKRI), the number of awards available to International candidates will be limited to 30% of the total.


Thorpe et al A large-scale population snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission of strains between clinical and non-clinical settings 2022 Nature Microbiology (in press).

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