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The Rowett Institute

Professor Alan Walker

Professor Alan Walker
Professor Alan Walker
Professor Alan Walker

Personal Chair

About
Email Address
alan.walker@abdn.ac.uk
Telephone Number
+44 (0)1224 438739
Office Address
5.050 The Rowett Institute
Foresterhill Campus
Foresterhill
AB25 2ZD

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School/Department
School of Medicine, Medical Sciences and Nutrition
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Biography

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 Research Fellow/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.

Qualifications

  • PhD Gut Microbiology 
    2006 - University of Dundee 
  • BSc (Hons) Microbiology 
    2001 - University of Aberdeen 

Memberships and Affiliations

Internal Memberships

University of Aberdeen Foresterhill Biological Safety Committee member – 2022 to Present.

External Memberships

Editorial Roles:

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.

Earlham Institute Scientific Advisory Board, 2024-2027

 

Prizes and Awards

Clarivate (Web of Science) highly cited researcher: 2019, 2020, 2021, 2022 and 2023.

Team member – “Outstanding Research Team”, awarded to the Rowett Gut Microbiology Group, University of Aberdeen Excellence Awards, 2023.

Team member – Runner up, “Nature/Yakult Global Grants for Gut Health Research Group Prize 2023”, awarded to the Rowett Gut Microbiology Group. https://www.guthealth-grants.com/pages/group-prize-announcement

Research

Research Overview

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. 

Current Research

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.

 

Research Team:

Andrew Farquharson – Research Assistant

Dr Anouschka Ramsteijn - Postdoctoral Research Fellow

Dr Tim Snelling - Honorary Research Fellow

Dr Eva Soto-Martin - Postdoctoral Research Fellow

 

 

Previous Group Members:

Research Assistants:

Gillian Donachie - April 2014 to March 2021

Postdocs:

Dr Galiana Lo - Jan 2023 to Dec 2023

Dr Indrani Mukhopadhya - Oct 2020 to Nov 2022

Dr Paul Sheridan - May 2015 to Nov 2017

Dr Dominic Partridge -  Feb 2019 to Dec 2020

PhD Students:

Elena Conti - PhD Student

Liviana Ricci - PhD Student

Nate Cole - PhD Student

Visiting PhD Students:

Margot Delavy (Institut Pasteur) - Mar to Apr 2022

Kristýna Mezerová (Palacký University Olomouc) – Aug to Nov 2018

Irene Gil Sánchez (Instituto de Investigación en Ciencias de La Alimentación) – April to July 2017

MSc Students:

Alison Eastick – May to Aug 2023

Abdulelah Aljadani – May to Aug 2023

Bonface Gichuki - May to Aug 2022

Sharon Johnson - May to Nov 2021

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

Collaborations

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.

 

Supervision

Supervisees

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].

2019-2024       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:

2020-2023       EnteroBiotix KTP. Innovate UK/Enterobiotix. [PI].

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].

 

Teaching

Teaching Responsibilities

  • Joint course co-ordinator: Honours Microbiology, MC4014 (2023-Present). Deputy course co-ordinator from 2020 to 2023.

 

Lectures/Tutorials:

MSc

  • Molecular Nutrition, RR5502
  • Introduction to Microbiology, MC5008
  • Genes and Immunity, MB5526
  • Clinical Nutrition for Disease Prevention, PU5541
  • Challenges in Global Nutrition, PU5547

Undergraduate

  • Honours Microbiology, MC4014
  • Molecular Microbiology, MC3504

Other

  • Mothur Workshop (Bioinformatics training workshop) 

 

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

Publications

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  • Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention

    Cuthbertson, L., Rogers, G. B., Walker, A. W., Oliver, A., Green, L. E., Daniels, T. W. V., Carroll, M. P., Parkhill, J., Bruce, K. D., van der Gast, C. J.
    The ISME Journal, vol. 10, no. 5, pp. 1081-1091
    Contributions to Journals: Articles

  • Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines

    Torondel, B., Ensink, J. H. J., Gundogdu, O., Ijaz, U. Z., Parkhill, J., Abdelahi, F., Nguyen, V., Sudgen, S., Gibson, W., Walker, A. W., Quince, C.
    Microbial Biotechnology, vol. 9, no. 2, pp. 209-223
    Contributions to Journals: Articles

  • Modulation of the human gut microbiota by dietary fibres occurs at the species level

    Chung, W. S. F., Walker, A. W., Louis, P., Parkhill, J., Vermeiren, J., Bosscher, D., Duncan, S. H., Flint, H. J.
    BMC Biology, vol. 14, 3
    Contributions to Journals: Articles

  • The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water

    Karkey, A., Jombart, T., Walker, A. W., Thompson, C. N., Torres, A., Dongol, S., Tran Vu Thieu, N., Pham Thanh, D., Tran Thi Ngoc, D., Voong Vinh, P., Singer, A. C., Parkhill, J., Thwaites, G., Basnyat, B., Ferguson, N., Baker, S.
    PLoS Neglected Tropical Diseases, vol. 10, no. 1, pp. 1-18
    Contributions to Journals: Articles

  • Chemokine (C-C Motif) Receptor 2 Mediates Dendritic Cell Recruitment to the Human Colon but Is Not Responsible for Differences Observed in Dendritic Cell Subsets, Phenotype, and Function Between the Proximal and Distal Colon

    Bernardo, D., Durant, L., Mann, E. R., Bassity, E., Montalvillo, E., Man, R., Vora, R., Reddi, D., Bayiroglu, F., Fernández-Salazar, L., English, N. R., Peake, S. T., Landy, J., Lee, G. H., Malietzis, G., Siaw, Y. H., Murugananthan, A. U., Hendy, P., Sánchez-Recio, E., Phillips, R. K. S., Garrote, J. A., Scott, P., Parkhill, J., Paulsen, M., Hart, A. L., Al-Hassi, H. O., Arranz, E., Walker, A. W., Carding, S. R., Knight, S. C.
    CMGH Cellular and Molecular Gastroenterology and Hepatology, vol. 2, no. 1, pp. 22-39.e5
    Contributions to Journals: Articles

  • Whole Genome Amplification of Single Bacterial Cells

    Scott, P., Walker, A. W.
    Hydrocarbon and Lipid Microbiology Protocols: Isolation and Cultivation. McGenity, T. J., Timmis, K. N., Nogales Fernández, B. (eds.). Humana Press, pp. 29-41, 13 pages
    Chapters in Books, Reports and Conference Proceedings: Chapters

  • The Intestinal Microbiota Contributes to the Ability of Helminths to Modulate Allergic Inflammation

    Zaiss, M. M., Rapin, A., Lebon, L., Dubey, L. K., Mosconi, I., Sarter, K., Piersigilli, A., Menin, L., Walker, A. W., Rougemont, J., Paerewijck, O., Geldhof, P., McCoy, K. D., Macpherson, A. J., Croese, J., Giacomin, P. R., Loukas, A., Junt, T., Marsland, B. J., Harris, N. L.
    Immunity, vol. 43, no. 5, pp. 998-1010
    Contributions to Journals: Articles

  • ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition

    Koslicki, D., Chatterjee, S., Shahrivar, D., Walker, A. W., Francis, S. C., Fraser, L. J., Vehkaperä, M., Lan, Y., Corander, J.
    PloS ONE, vol. 10, no. 10, e0140644
    Contributions to Journals: Articles

  • Variable alterations of the microbiota, without metabolic or immunological change, following faecal microbiota transplantation in patients with chronic pouchitis

    Landy, J., Walker, A. W., Li, J. V., Al-Hassi, H. O., Ronde, E., English, N. R., Mann, E. R., Bernardo, D., McLaughlin, S. D., Parkhill, J., Ciclitira, P. J., Clark, S. K., Knight, S. C., Hart, A. L.
    Scientific Reports, vol. 5, 12955
    Contributions to Journals: Articles

  • Interleukin 6 Increases Production of Cytokines by Colonic Innate Lymphoid Cells in Mice and Patients With Chronic Intestinal Inflammation

    Powell, N., Lo, J. W., Biancheri, P., Vossenkämper, A., Pantazi, E., Walker, A. W., Stolarczyk, E., Ammoscato, F., Goldberg, R., Scott, P., Canavan, J. B., Perucha, E., Garrido-Mesa, N., Irving, P. M., Sanderson, J. D., Hayee, B., Howard, J. K., Parkhill, J., MacDonald, T. T., Lord, G. M.
    Gastroenterology, vol. 149, no. 2, pp. 456-467
    Contributions to Journals: Articles

  • Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses

    Cuthbertson, L., Rogers, G. B., Walker, A. W., Oliver, A., Hoffman, L. R., Carroll, M. P., Parkhill, J., Bruce, K. D., van der Gast, C. J.
    Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society, vol. 14, no. 4, pp. 464-467
    Contributions to Journals: Articles

  • 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

    Walker, A. W., Martin, J. C., Scott, P., Parkhill, J., Flint, H. J., Scott, K. P.
    Microbiome, vol. 3, 26
    Contributions to Journals: Articles

  • TLR Signaling Modulates Side Effects of Anticancer Therapy in the Small Intestine

    Frank, M., Hennenberg, E. M., Eyking, A., Rünzi, M., Gerken, G., Scott, P., Parkhill, J., Walker, A. W., Cario, E.
    The Journal of Immunology, vol. 194, no. 4, pp. 1983-1995
    Contributions to Journals: Articles

  • Microbiota that affect risk for shigellosis in children in low-income countries

    Lindsay, B., Oundo, J., Hossain, M. A., Antonio, M., Tamboura, B., Walker, A. W., Paulson, J. N., Parkhill, J., Omore, R., Faruque, A. S. G., Das, S. K., Ikumapayi, U. N., Adeyemi, M., Sanogo, D., Saha, D., Sow, S., Farag, T. H., Nasrin, D., Li, S., Panchalingam, S., Levine, M. M., Kotloff, K., Magder, L. S., Hungerford, L., Sommerfelt, H., Pop, M., Nataro, J. P., Stine, O. C.
    Emerging Infectious Diseases, vol. 21, no. 2, pp. 242-250
    Contributions to Journals: Articles

  • Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

    Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., Turner, P., Parkhill, J., Loman, N. J., Walker, A. W.
    BMC Biology, vol. 12, no. 1, 87
    Contributions to Journals: Articles

  • The human microbiota and pathogen interactions

    Walker, A. W.
    Molecular Medical Microbiology. Tang, Y., Sussman, M., Liu, D., Poxton, I., Schwartzman, J. (eds.). 2 edition. Academic Press, pp. 347-356, 10 pages
    Chapters in Books, Reports and Conference Proceedings: Chapters

  • Time between Collection and Storage Significantly Influences Bacterial Sequence Composition in Sputum Samples from Cystic Fibrosis Respiratory Infections

    Cuthbertson, L., Rogers, G. B., Walker, A. W., Oliver, A., Hafiz, T., Hoffman, L. R., Carroll, M. P., Parkhill, J., Bruce, K. D., van der Gast, C. J.
    Journal of Clinical Microbiology, vol. 52, no. 8, pp. 3011-3016
    Contributions to Journals: Articles

  • Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

    Pop, M., Walker, A. W., Paulson, J., Lindsay, B., Antonio, M., Hossain, M. A., Oundo, J., Tamboura, B., Mai, V., Astrovskaya, I., Bravo, H., Rance, R., Stares, M., Levine, M. M., Panchalingam, S., Kotloff, K., Ikumapayi, U. N., Ebruke, C., Adeyemi, M., Ahmed, D., Ahmed, F., Alam, M., Amin, R., Siddiqui, S., Ochieng, J. B., Ouma, E., Juma, J., Mailu, E., Omore, R., Morris, J. G., Breiman, R. F., Saha, D., Parkhill, J., Nataro, J. P., Stine, O. C.
    Genome Biology, vol. 15, R76
    Contributions to Journals: Articles

  • Phylogeny, culturing, and metagenomics of the human gut microbiota

    Walker, A. W., Duncan, S. H., Louis, P., Flint, H. J.
    Trends in Microbiology, vol. 22, no. 5, pp. 267-274
    Contributions to Journals: Literature Reviews

  • The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing

    Kennedy, N. A., Walker, A. W., Berry, S. H., Duncan, S. H., Farquarson, F. M., Louis, P., Thomson, J. M., Satsangi, J., Flint, H. J., Parkhill, J., Lees, C. W., Hold, G. L., UK IBD Genetics Consortium
    PloS ONE, vol. 9, no. 2, e88982
    Contributions to Journals: Articles

  • Adding genomic 'foliage' to the tree of life

    Walker, A.
    Nature Reviews Microbiology, vol. 12, no. 2, 78
    Contributions to Journals: Articles

  • Patent human infections with the whipworm, Trichuris trichiura, are not associated with alterations in the faecal microbiota

    Cooper, P., Walker, A. W., Reyes, J., Chico, M., Salter, S. J., Vaca, M., Parkhill, J.
    PloS ONE, vol. 8, no. 10, e76573
    Contributions to Journals: Articles

  • Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection

    Lindsay, B., Pop, M., Antonio, M., Walker, A. W., Mai, V., Ahmed, D., Oundo, J., Tamboura, B., Panchalingam, S., Levine, M. M., Kotloff, K., Li, S., Magder, L. S., Paulson, J. N., Liu, B., Ikumapayi, U., Ebruke, C., Dione, M., Adeyemi, M., Rance, R., Stares, M. D., Ukhanova, M., Barnes, B., Lewis, I., Ahmed, F., Alam, M. T., Amin, R., Siddiqui, S., Ochieng, J. B., Ouma, E., Juma, J., Mailu, E., Omore, R., O'Reilly, C. E., Hannis, J., Manalili, S., Deleon, J., Yasuda, I., Blyn, L., Ranken, R., Li, F., Housley, R., Ecker, D. J., Hossain, M. A., Breiman, R. F., Morris, J. G., McDaniel, T. K., Parkhill, J., Saha, D., Sampath, R., Stine, O. C., Nataro, J. P.
    Journal of Clinical Microbiology, vol. 51, no. 10, pp. 3263-3269
    Contributions to Journals: Articles

  • Fighting obesity with bacteria

    Walker, A. W., Parkhill, J.
    Science, vol. 341, no. 6150, pp. 1069-1070
    Contributions to Journals: Articles

  • Deep-sea striving

    Walker, A.
    Nature Reviews Microbiology, vol. 11, no. 6, 364
    Contributions to Journals: Articles
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