Strain-level dynamics of microbiome transplantation (QUINCE_E25MMB)

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 healthy community is transferred into a patient’s gut to modulate the microbiome is an established treatment for some diseases, e.g. C. difficile infections. It is now being explored 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 this 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 mobile genetic elements (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. This will then be augmented by in vitro simulations of FMT in model colon systems. The result will be an improved understanding of IBD treatment with translational applications.

This ambitious studentship with major potential impact to the treatment of IBD would suit an

individual with strong computational skills and an interest in experimental microbiology. 

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: http://www.uea.ac.uk/phd/mmbdtp