PhD Studentship - Strain-level Dynamics of Microbiome Transplantation

Number of Opportunities Available: 1

Primary supervisor – Dr Christopher Quince

The human gut microbiome, the community of organisms living inside the gastrointestinal tract, plays a key role in health and disease. Fecal microbiome transplantation (FMT), where a community from a healthy donor is transferred into a patient’s gut to modulate the microbiome, is an established treatment for some diseases, e.g. C. difficile infections. FMT is now being trialled for a wide variety of conditions where the gut microbiome is implicated, including irritable bowel diseases (IBDs) of which ulcerative colitis (UC) is an example.

The mechanism of FMT, exactly how it shifts the microbiome and what changes are important to clinical response is still poorly understood. In part this is due to the limitations of current methods to study the microbiome which are often restricted to the species level and cannot resolve movements of mobile genetic elements (MGEs) such as phages and plasmids.

In this inter-disciplinary studentship we will develop improved methods for strain-level analysis of FMT data sets that combine the latest long read sequencing technologies with proximity ligation that can allow MGEs to be linked to their host microbes. These methods will be applied to existing data and samples from trials of FMT to treat IBD. The results from these analyses will be validated using in vitro experiments in model colon systems and used to develop mathematical models of FMT. The result will be an improved understanding of IBD treatment with translational applications.

This ambitious studentship would suit an individual with strong computational skills and an interest in experimental microbiology. A variety of first degrees may be appropriate including mathematics, physics, microbiology and computer science. The student will be based within the Quince group at the Earlham Institute which uses cutting-edge computational and experimental methods to study microbiomes: https://www.earlham.ac.uk/scientific-group/quince-group

The Microbes, Microbiomes and Bioinformatics (MMB) Doctoral Training Partnership (DTP) is open to UK and international candidates with relevant undergraduate degrees for entry in October 2025 and offers the opportunity to undertake a fully-funded 4-year PhD research project supported by the UKRI Medical Research Council in microbiology and microbial bioinformatics.

Our unique and comprehensive training programme empowers students to feel comfortable running sophisticated computer analyses alongside laboratory work and emphasises problem-based learning in microbial bioinformatics, professional development and research skills. All MMB DTP students undertake a Professional Placement.

Interviews for shortlisted candidates will take place on Tuesday 20 and Wednesday 21 May 2025.

The MMB DTP is committed to equality, diversity and inclusion. Students are selected without regard to age, disability, gender identity, marriage or civil partnership, pregnancy or maternity, ethnicity, religion or belief, sex or sexual orientation or social background. We value curiosity, independence of thought, plus an aptitude for research that combines laboratory work and bioinformatics.

For information on eligibility and how to apply: www.uea.ac.uk/phd/mmbdtp

Funding Information:

This project is awarded with a 4-year fully-funded studentship including direct payment of tuition fees to the University, stipend for living expenses (2025/26 rate: £20,780) and a Research Training Support Grant for each year of the studentship.

Closing Date: 14/04/2025

Please complete your application via the ‘Apply’ button above.

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