PhD Studentship: Rapid Metagenomic Strain Profiling of Inflammatory Bowel Disease (IBD) Patients via Nanopore Sequencing

at University of East Anglia
Published March 24, 2023
Location Norwich, United Kingdom
Category Machine Learning  
Job Type Scholarship  


What influence can our gut bacteria exert on our immune system? Can we identify the bacterial genes responsible for this?

This 4-year PhD project will explore changes in the gut microbiome of patients with Inflammatory Bowel Disease (IBD), combine high-resolution metagenomics with 3rd generation sequencing, develop experimental and bioinformatic protocols to distinguish specific gut bacterial strains that can be associated to IBD, and explore their potential impact on the human host. Partnering with Oxford Nanopore Technologies, this project will long-term enable clinical gut community profiling to help patients faster.

During the PhD, the successful candidate will learn about high-resolution metagenomics, advanced sequencing techniques, bacteria in the human gut and statistically working with clinical cohorts. Knowledge and/or willingness to learn about computational machine learning, metagenomics, DNA sequencing, the human gut microbiome and describing dysbiotic microbiomes will be of advantage. Some exposure to statistics and programming languages (either R, python, Perl, C++, or equivalent) will be expected. Specialised skills will be taught and developed through mentorship and collaborations. Visiting international conferences and training courses as well as exchanges with international collaborators will be part of student training.

The project will be supervised by Dr Falk Hildebrand, Prof. Justin O’Grady (representing Oxford Nanopore), Prof. Nathalie Juge, and Dr Tamas Korcsmaros, and will be based at the Quadram Institute in the Norwich Research Park. The Hildebrand Group uses metagenomics to research the diversity, community interactions, and evolution of microbes in communities, developing bioinformatic solutions to complex microbial questions. Norwich hosts a vibrant and active research community, large student community and multiple startups. It is a mid-sized historical, medieval city with an active social scene, situated near the Norfolk coast.

This iCASE studentship within the Microbes, Microbiomes and Bioinformatics (MMB) Doctoral Training Partnership (DTP) is open to UK candidates with relevant undergraduate degrees for entry in October 2023 and offers the opportunity to undertake a 4-year PhD research project funded 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. The student will undertake a placement with the non-academic partner totalling 3-18 months.

Interviews for shortlisted candidates will take place on Wednesday 17 May 2023.

The MRC 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:

Primary Supervisor: Dr Falk Hildebrand

Funding Details

This project is awarded with a 4-year studentship including:

  • Maintenance stipend according to the MRC stipend scale
  • University tuition fee payment
  • Research and training costs

Studentship funding does not normally cover costs associated with visa or health surcharges or additional costs associated with entry to, and living in, the UK.