Gut Health Theme
The Rowett Institute
University of Aberdeen
AB25 2ZD, UK
I am a microbiologist by training with specific research interests in the bacteria that inhabit the gastrointestinal tract of mammalian hosts.
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 of humans and animals, and how these factors may contribute to host health.
- PhD Gut Microbiology2006 - University of Dundee
- BSc (Hons) Microbiology2001 - University of Aberdeen
Memberships and Affiliations
- Internal Memberships
University of Aberdeen Foresterhill Biological Safety Committee member – 2022 to Present.
- External Memberships
Microbiome (2013 – 2017) [Editorial Board member then Associate Editor]
Microbial Genomics (2015 – present) [Senior Editor to Jan. 2022, then Editor]
Grant Panel Member:
The Deutsche Forschungsgemeinschaft (German Research Foundation) (x2)
BBSRC Tools and Resources Development Fund
BBSRC Institute Assessment Exercise
BBSRC Responsive Mode Committee A (x5)
European Commission Joint Programming Initiative
Committee/Advisory Board Member:
ComMet – Community Network in Metagenomics (BBSRC funded initiative), 2014-2018.
EnteroBiotix Ltd – Independent Scientific & Medical Advisory Board member, 2015-2020.
BBSRC Microbiome Expert Working Group, 28/9/16 and 15/11/16.
BBSRC Pool of Experts (Microbiome), 2018-2021.
Core Membership of BBSRC Research Committee A, 1/1/2022 to 31/3/2025.
KTN Microbiome Biobanking Group, 2021-2022.
Prizes and Awards
Clarivate (Web of Science) highly cited researcher: 2019, 2020, 2021 and 2022.
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 of humans and animals.
Our research specialisms are based on the Higher Education Classification of Subjects (HECoS) which is HESA open data, published under the Creative Commons Attribution 4.0 International licence.
Much of our current research interests are in identifying key functional groups of bacteria within the intestinal microbiota of humans and animals. Although intestinal microbiotas are extremely complex entities, 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. We are also interested the role that host diet plays in the prevalence and activities of these key functional gut bacterial groups.
In addition, we study the role that the intestinal microbiota plays in inhibiting pathogenic microbes. We use the Rowett Institute's extensive collection of gut bacteria to screen for individual strains that show activity against a range of important pathogens of humans and animals. We are also members of the EU-funded FunHoMic network, as part of which we are particularly interested in identifying specific microbes, and mechanisms, involved in antagonistic activity against the fungal pathogen 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 are carrying out 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 gut bacteria, which is a critical step towards developing microbiota-based therapeutics for use in humans and animals.
Andrew Farquharson – Research Assistant
Dr Galiana Lo - Research Associate
Dr Anouschka Ramsteijn - Research Fellow
Dr Tim Snelling - Honorary Research Fellow
Nate Cole - PhD Student
Sharon Johnson - MSc Student
Previous Group Members:
Gillian Donachie - April 2014 to March 2021
Dr Indrani Mukhopadhya - Oct 2020 to Nov 2022
Dr Paul Sheridan - May 2015 to Nov 2017
Dr Dominic Partridge - Feb 2019 to Dec 2020
Elena Conti - PhD Student
Liviana Ricci - PhD Student
Visiting PhD Students:
Kristýna Mezerová (Palacký University Olomouc) – Aug to Nov 2018
Irene Gil Sánchez (Instituto de Investigación en Ciencias de La Alimentación) – April to July 2017
Laura Gardener – Jan 2020 to July 2020
Noburo Kato – March 2019 to July 2019
Debbie Bain – April 2018 to July 2018
Davide Fraccascia – April 2017 to July 2017
Galiana Lo – April 2017 to July 2017
Ambre Chapuis – April 2016 to July 2016
Nika Ivanovova – April 2015 to July 2015
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.
Funding and Grants
Selected Ongoing Projects:
2022-2027 Harnessing the gut microbiome to strengthen livestock resilience against carriage and infection by pathogens. Scottish Government's Rural and Environmental Science and Analysis Service (RESAS). [PI].
2022-2027 Incorporation of whole ecosystem approaches to reduce transmission of foodborne pathogens and antimicrobial resistance. RESAS. [Co-I: Karen Scott is PI].
2022-2026 Developing delivery strategies for next generation probiotics and microbiome therapeutics. RESAS PhD Studentship. [Co-I: Karen Scott is PI].
2019-2024 Action Against Stunting Hub. UKRI GCRF. [Co-I: Claire Heffernan is PI].
2020-2023 EnteroBiotix KTP. Innovate UK/Enterobiotix. [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].
Selected Past Funding:
2014-2022 Supported by core institutional funding for the Rowett Institute. RESAS. [PI].
2017 - 2021 MECNUT: Impact of dietary exposure to emulsifiers on the intestinal mucosa - implications for inflammatory bowel disease and metabolic syndrome. MRC. [Co-I: Barry Campbell was 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]
2016-2019 Microbiome and metagenomic study of the rumen microbial population and their microbial enzyme genes. RESAS. [PI]
2015-2017 Exploiting the microbiome to prevent and treat human diseases. Chr. Hansen. [Co-PI with Harry Flint]
2015 Impact of the gut microbiota and diet upon Candida colonisation and infection. Wellcome Trust ISSF@Aberdeen Seed Corn award. [Co-I: Al Brown was PI].
2011-2014 Immunological and microbiological effects of fecal transplantation in chronic pouchitis. Broad Foundation. [Co-I: Ailsa Hart was PI]
2010-2014 Microbial community ecology of chronic respiratory infections. NERC 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 Consortium. Core – The Digestive Disorders Foundation. [Co-I: Charlie Lees was PI].
- Molecular Nutrition, RR5502
- Introduction to Microbiology, MC5008
- Genes and Immunity, MB5526
- Clinical Nutrition for Disease Prevention, PU5541
- Challenges in Global Nutrition, PU5547
- Honours Microbiology, MC4014
- Molecular Microbiology, MC3504
- Mothur Workshop (Bioinformatics training workshop)
Associate Fellow of the Higher Education Authority – June 2015 to Present
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Modulating the early-life gut microbiota using pro-, pre-, and synbiotics to improve gut health, child development, and growthNutrition ReviewsContributions to Journals: Articles
- [ONLINE] DOI: https://doi.org/10.1093/nutrit/nuad050
Links between diet, intestinal anaerobes, microbial metabolites and healthBiomedicines, vol. 11, no. 5, 1338Contributions to Journals: Articles
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studiesNature, vol. 613, pp. 639–649Contributions to Journals: Articles
- [ONLINE] DOI: https://doi.org/10.1038/s41586-022-05546-8
Impact of changes at the Candida albicans cell surface upon immunogenicity and colonisation in the gastrointestinal tractThe Cell Surface, vol. 8, 100084Contributions to Journals: Articles
Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiomeAnimal Microbiome, vol. 4, 57Contributions to Journals: Articles
Human gut bifidobacteria inhibit the growth of the opportunistic fungal pathogen Candida albicansFEMS Microbiology Ecology, vol. 98, no. 10, fiac095Contributions to Journals: Articles
Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with latrine fill-up rateFrontiers in Microbiology, vol. 13, 960747Contributions to Journals: Articles
Survival strategies and metabolic interactions between Ruminococcus gauvreauii and Ruminococcoides bili, isolated from human bileMicrobiology spectrum, e0277621Contributions to Journals: Articles
Microbial lactate utilisation and the stability of the gut microbiomeGut Microbiome, vol. 3, e3Contributions to Journals: Articles
Higher total faecal short chain fatty concentrations correlate with increasing proportions of butyrate and decreasing proportions of branched chain fatty acids across multiple human studiesGut Microbiome, vol. 3, e2Contributions to Journals: Articles