Projects per year
Personal profile
Personal profile
Professor in Food Safety
My work is driven by the major challenges facing our food production and public health. Solutions are in exploring the utility and function of microbes, how food is produced, and technological innovations.
Research interests
I am a molecular bacteriologist interested in how microbes, e.g. foodborne pathogens or hazards such as AMR, are transmitted via environmental sources. The technical approaches are in molecular microbiology, genomics and microbiomes. I work with stakeholders in public health and the agri-food industry.
My roles are:
- Lead the Centre for Epidemiology and Planetary Health (CEPH) team
- Lead research into the interactions between human pathogenic bacteria and food products, pre- and post-harvest, to reduce foodborne illness
- Manage Scottish Government strategic research between Scottish research providers
- Supervision of staff, students and visitors; teaching and external examinations
- Committee member for external organisations
Supervision
PhD student (2021-2025) 'Exploring host-microbiota interactions for improved crop health and food safety', joint with University of Dundee
PhD student (2018-2022) 'Impact of ozone on viability of fooborne and food spoilage pathogens on fresh produce', joint with University of Oxford
PhD student (2017-2021) 'Modelling attachement of bacteria to developing roots', joint with University of Warwick and James Hutton Institute
PhD student (2017-2021) 'Benign enhancement of natural defences: BEYOND', joint with University of Sheffield and James Hutton Institute
Projects
- 2025-2027: UKRI-STEC grants on "Structure-informed design of PCR kits for pathogenic E. coli" Winn (multiple, ~ 1 year)
- 2025: Scottish Alliance for Food "Building a knowledge exchange partnership between an academic partner and a sustainable community food growing project" Holden (£5K, 4 months)
- 2023-2025: UKRI "Scottish Government Tackling Infections Bioscience UKRI Policy Fellowship" Holden (PI) (£148K, 18 months)
- 2024: UKRI "Mobilising Scotland's Assets in equitable ways for Epidemic Control (MOSAEC)" Flowers (PI), Holden (£98K, 1 year)
- 2020-2025: BBSRC BBR “The UK Crop Microbiome Cryobank”. Ryan (PI) et al, Holden (£1.9M, 5 years)
- 2021-2025: BBSRC "Sharing expertise to quantify and mitigate GHG in the agriculture and land use sector in Argentina and the UK" Holden (£30K, 3 years)
- 2021-2022: SFN+ "Genome-guided detection of non-O157 STEC". Holden (£10K, 9 months)
- 2021-2022: SFN+ "Circular urban vertical farming - Data, models and optimisation of waste flows". Ball (PI) (£10K, 9 months)
- 2021: SEFARI Gateway "Scoping review for a Scottish AMR activity dashboard". Holden (£17K, 5 months)
- 2018-2021: Innovate-UK “KTP: microbe management”. Holden, IGS Ltd. (£227K, 3 years)
- 2021: Scottish Government "Scottish One Health AMR Register". Holden (£30K, 4 months)
- 2016-2021: ERC “SENSOILS”. Dupuy (€1.66M, 5 years)
- 2019: NBIC “Listeria biofilms”. Holden, Anacail Ltd (£80K, 1 year)
- 2019-2020: IBiolC “Antimicrobial coatings and matrices”. Love (£101K, 1 year)
- 2017-2018: Innovate-UK “In-pack ozone”. Holden, Anacail Ltd. (£38K, 1 year)
- 2016-2018: RESAS Innovation fund “Biocontrol”. Holden (FSS, SERL, Kettle) (£132K)
- 2014-2016: FSA “Internalisation”. Holden (£350K)
- 2013-2016: HDC “Plant defence elicitors”. Holden (£300K)
- 2012-2015: The Leverhulme Trust “Plant cell walls”. Holden (£230K)
- 2011-2014: BBSRC “Surface factors colonise plants” Holden (£556K)
- 2011-2011 & 2010-2012: HDC, elicitor grants Holden (£150K)
Education/Academic qualification
PhD, Cold shock response of Salmonella typhimurium, University of Edinburgh
1995 → 1999
External positions
The James Hutton Institute
2011 → 2020
Scottish Crop Research Institute, Invergowrie
2007 → 2011
Open University Milton Keynes
2002 → 2007
Centre for Infectious Diseases, School of Biomedical Sciences, Edinburgh Medical School, The University of Edinburgh
2000 → 2007
Keywords
- QR180 Immunology
- microbiology
- microbiome
- food safety
- food quality
- Crop/livestock systems
- STEC
- Salmonella
- host interactions
- sequencing
- vertical farm
- sustainability
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Collaborations and top research areas from the last five years
Recent external collaboration on country/territory level. Dive into details by clicking on the dots or
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Flipping the switch on fungal pH adaptation
Fraser, F. (PI), Watson, C. (Other) & Holden, N. (Other)
1/02/26 → 31/12/30
Project: Research
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Assessing Microbiome Functional Traits As Indicators Of Soil Health For Sustainable Agriculture
Watson, C. (Supervisor), Holden, N. (Supervisor) & Horne, J. (PhD Student)
1/10/22 → 30/09/26
Project: PhD project
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RESAS 22-27: SRUC-a2-3 A Systems Understanding Of The Flow Of Amr From Livestock Production To The Environment And Humans: Informing Antimicrobial Stewardship And Optimal Use
Hutchings, M. (PI), Webster, C. (CoI), Tongue, S. (CoI), Baker, E. (CoI), Henry, M. (CoI), Humphry, R. (CoI), Holden, N. (CoI), Rodrigues da Costa, M. (CoI), Smith, L. (CoI), Humphry, R. (CoI) & Lowe, A. (CoI)
Scottish Government: Rural & Environment Science & Analytical Services
1/04/22 → 31/03/27
Project: Research
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RESAS 22-27: SRUC-b6-2 A Systems Understanding Of The Flow Of Amr From Livestock Production To The Environment And Humans: Informing Risk Analyses
Hutchings, M. (PI), Baker, E. (CoI), Galgano, S. (CoI), Pollock, J. (CoI), Holden, N. (CoI), Smith, L. (CoI) & Lowe, A. (CoI)
Scottish Government: Rural & Environment Science & Analytical Services
1/04/22 → 31/03/27
Project: Research
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RESAS 22-27: Jhi-d3-1 Healthy Soils For A Green Recovery
Watson, C. (PI), Bagnall, A. (CoI), Buckingham, S. (CoI), Hargreaves, P. (CoI), Topp, K. (CoI), Walker, R. (CoI), Fraser, F. (CoI), Holden, N. (CoI) & Boyko, R. (CoI)
Scottish Government: Rural & Environment Science & Analytical Services
1/04/22 → 31/03/27
Project: Research
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Bacteriophages vs Escherichia coli: A Targeted Approach to Decontaminate Packaged Meat
Uikey, R., Galgano, S., Lawton, S., Houdijk, J., Hutchings, M., Holden, N. & Nale, J., Apr 2026.Research output: Contribution to conference › Poster
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Host plant selects bacterial rhizosphere microbiome function whereas community structure is determined by soil legacy
Taketani, R. G., Clark, I. M., Yau, P. T. O., Liu, L., Zhang, F., Bak, G. R., Thompson, C. M. A., Bonnin, J. M., Stewart, H., Malone, J. G., Jones, S., Holden, N., Ryan, M. J. & Mauchline, T. H., 28 Mar 2026, (First published) In: ISME Communications. 6, 1, ycag083.Research output: Contribution to journal › Article › peer-review
Open AccessFile1 Link opens in a new tab Citation (Scopus)4 Downloads (Pure) -
A commentary on the 2025 Annual Conference (Liverpool) Session 'Beyond the lab - Turning your research into reality'
Holden, N., Gostic, M. & van Keulen, G., 1 Oct 2025, In: Microbiology (Reading, England). 171, 10, 001614.Research output: Contribution to journal › Comment/debate
Open AccessFile8 Downloads (Pure) -
Human Pathogenic Microorganisms in Fresh Produce Production: Lessons Learned When Plant Science Meets Food Safety
Zhao, X., Van Overbeek, L., Burgess, C. M., Holden, N., Brennan, F., Johannessen, G. S., Allende, A., Höfte, M., Cottyn, B., Pothier, J. F., Schikora, A. & Uyttendaele, M., 31 May 2025, (First published) In: Journal of Food Protection. 88, 7, p. 100551 12 p., 100551.Research output: Contribution to journal › Review article › peer-review
Open AccessFile8 Link opens in a new tab Citations (Scopus)137 Downloads (Pure) -
Introducing the UK Crop Microbiome Cryobank data resource, AgMicrobiomeBase, with case studies and methods on metabarcoding analyses
Yau, P. T., Taketani, R. G., Bonnin, J. M., Stewart, H., Thompson, C. M. A., Clark, I. M., Mauchline, T. H., Malone, J. G., Ryan, M. J., Jones, S. & Holden, N., 21 Aug 2025, (First published) In: Standards in Genomic Sciences. 20, 1, 12 p., 108.Research output: Contribution to journal › Article › peer-review
Open AccessFile3 Link opens in a new tab Citations (Scopus)25 Downloads (Pure)
Datasets
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A dataset of genomes of non-O157 Shigatoxigenic Escherichia coli (STEC) associated with UK clinical disease, wild deer and food items
Holden, N. (Owner), Wynn, M. (Contributor) & Dallman, T. (Contributor), Unknown Publisher, 9 Mar 2023
DOI: 10.58073/SRUC.22240660.v1
Dataset
Activities
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VTEC 2026 conference
Holden, N. (Organiser)
10 May 2026 → 13 May 2026Activity: Participating in or organising an event types › Organising a conference, workshop, ...
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Microbiology Annual Conference 2025 session ‘Beyond the lab – Turning your research into reality’
Holden, N. (Participant)
1 Apr 2025Activity: Participating in or organising an event types › Organising a conference, workshop, ...
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Microbiology (Journal)
Holden, N. (Reviewer)
14 Oct 2025Activity: Publication peer-review and editorial work types › Publication Peer-review
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PHA4GE Conference & IPSN Global Partners Forum 2025
Holden, N. (Participant)
25 Oct 2025 → 29 Oct 2025Activity: Participating in or organising an event types › Participating in a conference, workshop, ...
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Scottish collective microbiology capability workshop
Holden, N. (Participant)
5 Jun 2025Activity: Participating in or organising an event types › Participating in a conference, workshop, ...
Press/Media
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Science Media Centre: Expert reaction to UKHSA E. coli advice amid rise in cases
6/06/24
1 Media contribution
Press/Media
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Construction of world-leading UK Crop Microbiome Cryobank now complete
31/10/23
1 Media contribution
Press/Media
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Farmers Weekly Question Time
2/03/23 → 8/03/23
1 item of Media coverage, 1 Media contribution
Press/Media
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