Personal Chair
- About
-
- Email Address
- alan.walker@abdn.ac.uk
- Telephone Number
- +44 (0)1224 438739
- Office Address
- School/Department
- School of Medicine, Medical Sciences and Nutrition
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 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
-
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
- MISS ANN-KRISTIN KAUNE
- MR BRENDAN MACKAY
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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Objections to the proposed reclassification of Eubacterium rectale as Agathobacter rectalis
International Journal of Systematic and Evolutionary Microbiology, vol. 66, no. 5, pp. 2106-2106Contributions to Journals: Letters- [ONLINE] DOI: https://doi.org/10.1099/ijsem.0.000969
Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention
The ISME Journal, vol. 10, no. 5, pp. 1081-1091Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1038/ismej.2015.198
- [OPEN ACCESS] http://aura.abdn.ac.uk/bitstream/2164/5960/1/ismej2015198a.pdf
Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines
Microbial Biotechnology, vol. 9, no. 2, pp. 209-223Contributions to Journals: ArticlesModulation of the human gut microbiota by dietary fibres occurs at the species level
BMC Biology, vol. 14, 3Contributions to Journals: ArticlesThe Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water
PLoS Neglected Tropical Diseases, vol. 10, no. 1, pp. 1-18Contributions to Journals: ArticlesChemokine (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
CMGH Cellular and Molecular Gastroenterology and Hepatology, vol. 2, no. 1, pp. 22-39.e5Contributions to Journals: ArticlesWhole Genome Amplification of Single Bacterial Cells
Hydrocarbon and Lipid Microbiology Protocols: Isolation and Cultivation. McGenity, T. J., Timmis, K. N., Nogales Fernández, B. (eds.). Humana Press, pp. 29-41, 13 pagesChapters in Books, Reports and Conference Proceedings: Chapters- [ONLINE] DOI: https://doi.org/10.1007/8623_2015_152
The Intestinal Microbiota Contributes to the Ability of Helminths to Modulate Allergic Inflammation
Immunity, vol. 43, no. 5, pp. 998-1010Contributions to Journals: ArticlesARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition
PloS ONE, vol. 10, no. 10, e0140644Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1371/journal.pone.0140644
- [OPEN ACCESS] http://aura.abdn.ac.uk/bitstream/2164/5145/1/ARK_PLoSONE_2015.pdf
Variable alterations of the microbiota, without metabolic or immunological change, following faecal microbiota transplantation in patients with chronic pouchitis
Scientific Reports, vol. 5, 12955Contributions to Journals: ArticlesInterleukin 6 Increases Production of Cytokines by Colonic Innate Lymphoid Cells in Mice and Patients With Chronic Intestinal Inflammation
Gastroenterology, vol. 149, no. 2, pp. 456-467Contributions to Journals: ArticlesImplications of multiple freeze-thawing on respiratory samples for culture-independent analyses
Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society, vol. 14, no. 4, pp. 464-467Contributions to Journals: Articles16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice
Microbiome, vol. 3, 26Contributions to Journals: ArticlesTLR Signaling Modulates Side Effects of Anticancer Therapy in the Small Intestine
The Journal of Immunology, vol. 194, no. 4, pp. 1983-1995Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.4049/jimmunol.1402481
Microbiota that affect risk for shigellosis in children in low-income countries
Emerging Infectious Diseases, vol. 21, no. 2, pp. 242-250Contributions to Journals: ArticlesReagent and laboratory contamination can critically impact sequence-based microbiome analyses
BMC Biology, vol. 12, no. 1, 87Contributions to Journals: ArticlesThe human microbiota and pathogen interactions
Molecular Medical Microbiology. Tang, Y., Sussman, M., Liu, D., Poxton, I., Schwartzman, J. (eds.). 2 edition. Academic Press, pp. 347-356, 10 pagesChapters in Books, Reports and Conference Proceedings: ChaptersTime between Collection and Storage Significantly Influences Bacterial Sequence Composition in Sputum Samples from Cystic Fibrosis Respiratory Infections
Journal of Clinical Microbiology, vol. 52, no. 8, pp. 3011-3016Contributions to Journals: ArticlesDiarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition
Genome Biology, vol. 15, R76Contributions to Journals: ArticlesPhylogeny, culturing, and metagenomics of the human gut microbiota
Trends in Microbiology, vol. 22, no. 5, pp. 267-274Contributions to Journals: Literature Reviews- [ONLINE] DOI: https://doi.org/10.1016/j.tim.2014.03.001
The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing
PloS ONE, vol. 9, no. 2, e88982Contributions to Journals: ArticlesAdding genomic 'foliage' to the tree of life
Nature Reviews Microbiology, vol. 12, no. 2, 78Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1038/nrmicro3203
Patent human infections with the whipworm, Trichuris trichiura, are not associated with alterations in the faecal microbiota
PloS ONE, vol. 8, no. 10, e76573Contributions to Journals: ArticlesSurvey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection
Journal of Clinical Microbiology, vol. 51, no. 10, pp. 3263-3269Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1128/JCM.01342-13
Fighting obesity with bacteria
Science, vol. 341, no. 6150, pp. 1069-1070Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1126/science.1243787
Deep-sea striving
Nature Reviews Microbiology, vol. 11, no. 6, 364Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1038/nrmicro3037
Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions
Nature Genetics, vol. 45, no. 4, pp. 450-455Contributions to Journals: ArticlesEnhanced susceptibility to Citrobacter rodentium infection in microRNA-155-deficient mice
Infection and Immunity, vol. 81, no. 3, pp. 723-732Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1128/IAI.00969-12
Therapeutic modulation of intestinal dysbiosis
Pharmacological Research, vol. 69, no. 1, pp. 75-86Contributions to Journals: Literature Reviews- [ONLINE] DOI: https://doi.org/10.1016/j.phrs.2012.09.008
Intestinal colonization resistance
Immunology, vol. 138, no. 1, pp. 1-11Contributions to Journals: Literature Reviews- [ONLINE] DOI: https://doi.org/10.1111/j.1365-2567.2012.03616.x
Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice
PLoS Pathogens, vol. 8, no. 10, e1002995Contributions to Journals: ArticlesThe transcription factor T-bet regulates intestinal inflammation mediated by interleukin-7 receptor+ innate lymphoid cells
Immunity, vol. 37, no. 4, pp. 674-684Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1016/j.immuni.2012.09.008
Fibrinogen-binding and platelet-aggregation activities of a Lactobacillus salivarius septicaemia isolate are mediated by a novel fibrinogen-binding protein
Molecular Microbiology, vol. 85, no. 5, pp. 862-877Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1111/j.1365-2958.2012.08148.x
Bayesian estimation of bacterial community composition from 454 sequencing data
Nucleic Acids Research, vol. 40, no. 12, pp. 5240-5249Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1093/nar/gks227
- [OPEN ACCESS] http://aura.abdn.ac.uk/bitstream/2164/3229/1/NuclAcidsRes2012_BEBaC.pdf
Welcome to the plasmidome
Nature Reviews Microbiology, vol. 10, no. 6, pp. 379Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1038/nrmicro2804
Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae
PNAS, vol. 109, no. 4, pp. 1269-1274Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1073/pnas.1113246109
Intestinal Microbiology and Ecology in Inflammatory Bowel Disease
Crohn's Disease and Ulcerative Colitis. Baumgart, D. C. (ed.). Springer Science+Business Media, pp. 85-95, 11 pagesChapters in Books, Reports and Conference Proceedings: Chapters- [ONLINE] DOI: https://doi.org/10.1007/978-1-4614-0998-4_5
Ileal pouch microbial diversity
Annals of Surgery, vol. 254, no. 4, pp. 669-670Contributions to Journals: Letters- [ONLINE] DOI: https://doi.org/10.1097/SLA.0b013e318230669c
- [ONLINE] View publication in Scopus
Review article: faecal transplantation therapy for gastrointestinal disease
Alimentary Pharmacology & Therapeutics, vol. 34, no. 4, pp. 409-415Contributions to Journals: Literature Reviews- [ONLINE] DOI: https://doi.org/10.1111/j.1365-2036.2011.04737.x
Singled out
Nature Reviews Microbiology, vol. 9, no. 7, pp. 485Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1038/nrmicro2603
Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities
The ISME Journal, vol. 5, no. 5, pp. 780-791Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1038/ismej.2010.175
- [OPEN ACCESS] http://aura.abdn.ac.uk/bitstream/2164/5417/1/CFcoresatelliteISME2010.pdf
Dominant and diet-responsive groups of bacteria within the human colonic microbiota
The ISME Journal, vol. 5, no. 2, pp. 220-230Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1038/ismej.2010.118
High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease
BioMed Central Microbiology, vol. 11, 7Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1186/1471-2180-11-7
- [OPEN ACCESS] http://aura.abdn.ac.uk/bitstream/2164/3228/1/BMCmicro_IBD_2011.pdf
Gut metagenomics goes viral
Nature Reviews Microbiology, vol. 8, no. 12, pp. 841Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1038/nrmicro2476
Special issue: The Human Intestinal Microbiota
Microbiology , vol. 156, no. 11, pp. 3203-3204Contributions to Journals: EditorialsThe bacteriology of pouchitis: a molecular phylogenetic analysis using 16S rRNA gene cloning and sequencing
Annals of Surgery, vol. 252, no. 1, pp. 90-98Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1097/SLA.0b013e3181e3dc8b
Comparing the microbiota of the cystic fibrosis lung and human gut
Gut Microbes, vol. 1, no. 2, pp. 85-93Contributions to Journals: Literature Reviews- [ONLINE] DOI: https://doi.org/10.4161/gmic.1.2.11350
- [OPEN ACCESS] http://aura.abdn.ac.uk/bitstream/2164/3913/3/gmic_2E1_2E2_2E11350.pdf
A glut from the gut: metagenomics takes a giant step foward
Nature Reviews Microbiology, vol. 8, no. 5, pp. 315Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1038/nrmicro2363
Lung infections in cystic fibrosis: deriving clinical insight from microbial complexity
Expert Review of Molecular Diagnostics, vol. 10, no. 2, pp. 187-196Contributions to Journals: Literature Reviews- [ONLINE] DOI: https://doi.org/10.1586/erm.09.81
Probiotics stick it to the man
Nature Reviews Microbiology, vol. 7, no. 12, pp. 843Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1038/nrmicro2271