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MRC DiMeN Doctoral Training Partnership: Understanding the gut microbial “interactome” for therapy of enteric virus infection.

MRC DiMeN Doctoral Training Partnership

, , Dr Andrew Filby Wednesday, January 27, 2021 Competition Funded PhD Project (Students Worldwide)
Leeds United Kingdom Microbiology Molecular Biology Nanotechnology Nutrition Structural Biology Virology

About the Project

The human intestinal microbiota is estimated to exceed 1014 cells and is composed of hundreds of bacterial species containing >100-times more genomic information than the human genome. Invading enteric viruses such as norovirus, the leading cause of acute viral gastroenteritis worldwide, must interact with this complex mixture and so encounter co-factors which may influence pathogenesis. Whilst some species of bacteria within the microbiota are believed to be protective against infection others are thought to promote infection. 

This project aims to test this hypothesis by studying the complex interaction between the gut microbiota and incoming viral pathogens. In doing so we aim to answer questions such as, to which bacterial species do enteric viruses attach in a normal healthy microbiota, what are the molecular bases of these interactions and how do they protect against infection? Understanding these questions could help discover future therapies to tackle gastroenteric virus infections. 

This interdisciplinary project includes groups at Universities of Leeds and Newcastle and will build upon our existing workflows using cutting edge methodologies on virus imaging and structural biology. Using purified fluorescently-labelled enteric viruses (e.g. norovirus, astrovirus) we will for the first time study the interaction with gut microbes using an in vitro mammalian gut model. Samples will be taken and analysed using state-of-the-art nano-cytometry/sorting technology. This approach will pave the way for molecular and structural studies to dissect the molecular basis of the viral-microbial interactions. 

Dr Morgan Herod | The Astbury Centre for Structural Molecular Biology (

Dr Morgan Herod | School of Molecular and Cellular Biology | University of Leeds

Morgan Herod Lab (@MRHerodDR) / Twitter

Dr Caroline Chilton | School of Medicine | University of Leeds

Staff Profile - Flow Cytometry Core Facility - Newcastle University (

This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.

We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.

Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here:

Further information on the programme and how to apply can be found on our website: 

Funding Notes

Studentships are funded by the Medical Research Council (MRC) for 3.5yrs. Funding will cover UK tuition fees and stipend only. We aim to support the most outstanding applicants from outside the UK and are able to offer a limited number of bursaries that will enable full studentships to be awarded to international applicants. These full studentships will only be awarded to exceptional quality candidates, due to the competitive nature of this scheme. Please read additional guidance here: View Website
Studentships commence: 1st October 2021
Good luck!


Snowden JS, Hurdiss DL, Adeyemi OO, Ranson NA, Herod MR, Stonehouse NJ. 2020. Dynamics in the murine norovirus capsid revealed by high-resolution cryo-EM. PLOS Biology.
Moura IB, Normington C, Ewin D, Clark E, Wilcox MH, Buckley AM, Chilton CH. 2020. Method comparison for the direct enumeration of bacterial species using a chemostat model of the human colon. BMC Microbiology.
Lippeveld M, Knill C, Ladlow E, Fuller A, Michaelis LJ, Saeys Y, Filby Andrew, Peralta D. 2019. Classification of human white blood cells using machine learning for stain-free imaging flow cytometry. Cytometry A.

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