Senior Lecturer


Contact Details

work +44 (0)1224 438739
The University of Aberdeen Gut Health Theme
The Rowett Institute
Room 5.050
University of Aberdeen
AB25 2ZD, UK

 Google Scholar Page: https://scholar.google.co.uk/citations?hl=en&user=D3CqfBkAAAAJ


I am a microbiologist by training with specific interests in the bacteria that inhabit the gastrointestinal tract of mammalian hosts, particularly in humans and mice.

After receiving an undergraduate degree in Microbiology from the University of Aberdeen I studied for my PhD at the Rowett Institute and at the University of Dundee, specialising in gut microbiology and the role that intestinal bacteria play in the breakdown of dietary fibre. I then spent eight and a half years at the Wellcome Sanger Institute in Cambridge, a renowned centre for genomics research. While there I used state of the art DNA sequencing facilities to better characterise host-associated microbial communities and shed light on the roles these microbes play both in health and in diseases such Cystic Fibrosis, inflammatory bowel disease and infection with Salmonella spp. and Clostridium difficile.

I am now a Senior Lecturer/Principal Investigator at the Rowett Institute within the University of Aberdeen. In our lab we combine anaerobic microbiology with DNA sequencing technologies in order to examine interactions between host diet and the intestinal microbiota, and how these factors may contribute to host health.


Research Interests

Microbiota research has been revolutionised in recent years by the advent of modern DNA sequencing technologies. These allow large-scale, in-depth studies, greatly expanding our ability to monitor the microbiota and how it responds to host behaviour such as changes in diet. However, traditional microbiology techniques such as anaerobic culture also remain highly relevant, and help us to understand the functional roles that individual members of the microbiota may play in the intestines. In our lab we combine DNA sequence analysis and microbiological approaches to generate novel insights into the intestinal microbiota. 

Current Research

Typical Western diets, rich in refined carbohydrates, fats and proteins and low in fibre, are fundamentally different to those consumed in more agrarian societies, where people tend to consume more fibre-rich diets. Working with collaborators in both the UK and in developing countries we are trying to understand how consuming disparate diets results in the development of different intestinal microbiota compositions, and how this impacts host health.
A better understanding of the health impacts of fibre-rich versus more processed foods should lead to improved dietary advice, and allow us to identify potentially beneficial novel gut bacterial species.
A further research interest is in identifying key functional groups of bacteria within the intestinal microbiota. Although the microbiota is an extremely complex entity, with many species sharing overlapping functional capabilities, it is thought that some deleterious or beneficial activities are limited to a relatively small range of species. In particular, we are interested in microbial contributors to the development of chronic ailments. For example, we are interested in bacterial consumers of lactate, accumulation of which has been linked to chronic diseases such as inflammatory bowel disease, and producers of trimethylamine (TMA), which has been linked to cardiovascular disease.

In addition, we study the role that the intestinal microbiota plays in inhibiting pathogenic microbes. We are part of the EU-funded FunHoMic network, and are particularly interested in identifying the specific microbes, and mechanisms, involved in antagonistic activity against Candida albicans in the colon.

We are also part of GCRF-funded Action Against Stunting Research Hub, which involves partners from many different countries, where we will do research to investigate how the microbes that are present in the intestines of children in low to middle income countries might play a role in their risk of developing stunting.

Ultimately, the unifying goal across all of these projects is to determine key functional groups of bacteria, which is a critical step towards microbiota-based therapeutics.


Research team:

Gillian Donachie – Research Assistant

Dominic Partridge - Research Fellow

Tim Snelling - Honorary Research Fellow

Elena Conti - PhD Student

Liviana Ricci - PhD Student

Nate Cole - PhD Student



We are aided in our work by long standing collaborations with many other international research groups. We also have links to industry, including companies such as Chr. Hansen and Enterobiotix.


Research Grants

Selected Ongoing Projects

2014-2021       Supported by institutional core funding from the Scottish Government’s Rural and Environmental Science and Analysis Service (RESAS).

2016-2019       Microbiome and metagenomic study of the rumen microbial population and their microbial enzyme genes. RESAS. [PI]

2016-2020       Mechanisms underpinning the links between diet, the intestinal microbiota and health. Princess Royal Tenovus Scotland Medical Research Scholarship. [PI]

2016-2020       Uncovering the impact of diet-responsive gut microbes on host health.  RESAS PhD Studentship. [PI]

2017-2020       MECNUT: Impact of dietary exposure to emulsifiers on the intestinal mucosa - implications for inflammatory bowel disease and metabolic syndrome. MRC. [Co-I: Barry Campbell is PI]

2019-2023       FunHoMic: Deciphering the fungus-host-microbiota interplay to improve the management of fungal infections. European Commission. [Co-I: Christophe d'Enfert is PI]

2019-2024       Action Against Stunting Hub. UKRI GCRF. [Co-I: Claire Heffernan is PI]


Selected Past Funding

2015-2017       Exploiting the microbiome to prevent and treat human diseasesChr. Hansen. [Co-PI with Harry Flint]

2015                Impact of the gut microbiota and diet upon Candida colonisation and infectionWellcome Trust ISSF@Aberdeen Seed Corn award. [Co-I: Al Brown was PI].

2011-2014       Immunological and microbiological effects of fecal transplantation in chronic pouchitisBroad Foundation. [Co-I: Ailsa Hart was PI]

2010-2014       Microbial community ecology of chronic respiratory infectionsNERC CASE Studentship. [Co-I: Christopher van der Gast was PI]

2011-2013       The gut microbiota and NOD2 genotype in Crohn’s disease: a pilot study for the UKIBD Microbiota ConsortiumCore – The Digestive Disorders Foundation. [Co-I: Charlie Lees was PI].



Teaching Responsibilities



  • Molecular Nutrition, RR5502
  • Introduction to Microbiology, MC5008
  • Genes and Immunity, MB5526
  • Clinical Nutrition for Disease Prevention, PU5541


  • Honours Microbiology, MC4014
  • Molecular Microbiology, MC3504


  • Mothur Workshop (Bioinformatics training workshop) 


Associate Fellow of the Higher Education Authority – June 2015 to Present

Further Info

Editorial Appointments

Senior Editor - Microbial Genomics