Developing mechanistic hypotheses for the action of therapeutic diets in the treatment of Crohns disease (QUINCE_E22MMB)

Applications Close: 17 January 2022

Salary: MRC stipend

Contract Length: 4 years

Crohn’s disease (CD) is an incapacitating inflammatory disease of the gut. Dietary therapy is one of the most effective treatments for CD with the advantage of reduced side effects compared to drugs such as steroids. The exact aetiology of Crohn’s is not yet understood but the microbiome is strongly implicated almost certainly through an interaction with the immune system.

We have analysed extensive faecal metagenome and metabolome data sets from human subjects undergoing trials conducted by our collaborators at the University of Glasgow with both the standard dietary therapy for paediatric Crohn’s, exclusive enteral nutrition (EEN), and an ordinary foods alternative, CD-Treat. The latter has the potential to revolutionise the treatment of CD by providing a cheap convenient and safe treatment option. This analysis has revealed potential mechanistic hypotheses for the dietary therapy.

The aim of this project is to test these hypotheses using artificial colon systems. We will conduct experiments simulating the action of therapeutic diets using the QIB colon model starting from faecal inocula, generate integrated ‘omic time series data sets from colon model experiments and compare results of analysis of artificial colon time series with existing clinical trial data. If we can understand the mechanism for the treatment action of the diets then we can improve remission rates through microbiome modulation prior to or after treatment.

This studentship would suit an individual with a strong microbiology background, with an interest in medical applications of the microbiome and a willingness to learn both novel molecular biology and bioinformatics.

The Microbes, Microbiomes and Bioinformatics (MMB) Doctoral Training Partnership (DTP) is open to UK and international candidates with an undergraduate degree relevant to the scope of the programme for entry in October 2022 and offers postgraduates the opportunity to undertake a 4-year PhD research project funded by the UKRI Medical Research Council to advance the training of students in microbiology, with an emphasis on microbial bioinformatics.

The distinctive training offered by the programme aims to ensure that students feel comfortable running sophisticated computer analyses alongside laboratory work whilst enhancing problem-based learning in microbial bioinformatics and professional development and research skills through a comprehensive training programme. All students will undertake a Professional Placement lasting up to 12 weeks.

This project has been shortlisted for funding by the MMB DTP programme. Interviews for shortlisted candidates will take place on Tuesday 15 February or Wednesday 16 February 2022.

This MMB DTP is committed to equality, diversity, widening participation and inclusion in all areas of the programme. We encourage enquiries and applications from all sections of the community, regardless of gender, ethnicity, disability, age, sexual orientation, and transgender status. We value an aptitude for computer-based analysis, curiosity, and independence of thought, plus a commitment to work across the boundaries between the laboratory and bioinformatics to deliver high-impact research. We welcome applicants from low- and middle-income countries.

You can find more information on eligibility and how to apply on the Partnerships in doctoral training page.

Primary Supervisor: Dr Christopher Quince – christopher.quince@earlham.ac.uk
Secondary Supervisor: Prof Arjan Narbad (QIB)