Robert Whelan

Thesis title: The oral-gut microbiome axis in Crohn's disease: understanding the interplay between the oral and gut microbiota in disease susceptibility and progression

MRC Precision Medicine DTP

Year of study: 1

Contact details



Centre for Inflammation Research | Queen’s Medical Research Institute
Edinburgh BioQuarter | 47 Little France Crescent | Edinburgh

Post code
EH16 4TJ


In 2021, Robert completed his MSc in Biology at Leiden University in the Netherlands. Specialising in Molecular Genetics and Biotechnology, he undertook two research projects within the Animal Sciences and Health/Bioinformatics and Genomics clusters, collaborating with research teams at Radboud University, Nijmegen and KU Leuven in Belgium. The first used the zebrafish as a model system to investigate the glucocorticoid receptor and innate immune cell migration during the inflammatory response, the results of which were published. A later project focused on the taxonomic and functional profiling of zebrafish intestinal microbiome using metagenomic approaches and next-generation sequencing datasets. Today, Robert bridges these areas, combining his research interests in human disease, inflammation, and the gut microbiome and applying them to his present PhD project.


MSc Biology specialising in Molecular Genetics and Biotechnology, Leiden University

Research summary

Inflammatory Bowel Diseases (IBD) are chronic immune-mediated conditions affecting the gastrointestinal tract. They are common, with a global prevalence approaching 20-30 million individuals by 2025.   

The gut microbiome is a critical factor in the development of IBD and there are now several approaches aimed at manipulating the gut flora as therapy including faecal transplantation, probiotics and selective expansion of beneficial bacteria populations using spore technologies. However, we do not yet have the precision medicine tools to refine our understanding of the complex gut microbiome and its interconnection with IBD disease activity to improve the way we choose and tailor microbial-based treatments.   

Emerging evidence suggests that inflammation may begin in the oral cavity and spread to the gut as pathobionts move between those body sites, hence there is a need to investigate the oral-gut microbiome axis in IBD.  

Robert – alongside PI’s with bioinformatics, clinical and IBD expertise – aims to characterise the metagenome to determine if the complexities of the gut microbiome can be refined and reduced based on oral microbiome data to allow for a simple, quicker and more acceptable form of microbiome analysis that can be carried out in the widest IBD setting. Together, they will use strain-level metagenomics to look at the cross-talk between the oral and gut microbiota in IBD, and functional metagenomics to look at functional correlates with disease progression, outcome, and mucosal healing.

Early Life Glucocorticoid Exposure Modulates Immune Function in Zebrafish (Danio rerio) Larvae

Front. Immunol., 29 April 2020