Postgraduate research opportunities

Exploring the role of the gut microbiome and its interaction with food components in patients with Crohn’s disease - an integrated systems biology approach

Crohn’s Disease, targeted mass spectrometry, metabolomics

Number of places



Home fee, Stipend


2 February 2021


3 May 2021


36 Months


Applicants must have obtained, or expect to obtain, a first or 2.1 UK honours degree, or equivalent for degrees obtained outside the UK, in analytical chemistry, biomedical or pharmaceutical sciences.

Project Details

The etiology of Crohn’s Disease remains unknown, with genetic factors alone being unable to explain its rapidly increasing incidence. In Scotland, recent research estimates an increase in all-age inflammatory bowel diseases (IBD) by 4.3% per year, between 2008 and 2018, one of the highest rates in the world.

Currently, there is an unpreceded interest in the role of diet in Crohn’s Disease onset and management; both from patients and their healthcare professionals. Exclusive enteral nutrition (EEN), a nutritionally complete liquid formula, is used as the first-line treatment for active paediatric Crohn’s Disease. EEN induces clinical remission in over 80% of children with active Crohn’s Disease and induces mucosal healing in a higher proportion of patients than treatment with oral steroids.


This research proposal will take advantage of a growing external collaboration with Dr Konstantinos Gerasimidis (School of Medicine, Dentistry and Nursing University of Glasgow) and Shimadzu Corporation, and will explore how EEN treatment influences the metabolic signatures of gut inflammation and by extension disease pathogenesis. We have access to a large number (>500) of well-curated faecal, urinary and blood samples from previous and ongoing clinical research exploring the role of gut microbiome and its interaction with food components, including food additives, in patients with Crohn’s disease.


The successful candidate will have the unique opportunity to integrate student generated metabolomics and targeted mass spectrometry datasets with existing datasets of shotgun metagenomics and meta-transcriptomics performed on exactly the same samples. This will enable us to build a multiomics understanding of disease pathogenesis, the role of dietary influences and underlying mechanisms of dietary therapy.


Techniques used:

  • Un/targeted metabolomics
  • Liquid chromatography mass spectrometry
  • Biological sample preparation
  • r-programming
  • metabolic pathway analysis
  • Integration of multiomics datasets

Funding Details

The studentship will last for 3 years. It will cover the tuition fee for UK/EU candidates, and provide and annual tax-free PhD stipend (approx. £15,000 per annum). Please note that candidates outside the EU will only be eligible if they provide funding for international fees.


Primary Supervisor: Dr Nicholas J W Rattray



Co-Supervisors: Prof Kostas Gerasimidis and Dr Ibrahim Khadra

How to apply

All enquiries and applications should be directed to Dr Nicholas J W Rattray ( Applications will be reviewed when received, and shortlisted candidates will be invited for an interview. The position will remain open until filled.


All applications must be submitted via email (subject line: PhD applicant) as a single pdf file and include the following:

  • A cover letter (max 1 page) explaining your interest and fit to the project
  • A CV (maximum three pages).
  • Names and contact details of TWO references (including email addresses).