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 some 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 Safe & Improved Foods challenge-driven research centre
- 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
Current:
- 2020-2025: BBSRC BBR “The UK Crop Microbiome Cryobank”. Ryan, Holden (Co-I), Mauchline, Malone (£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, Rees, Shutter (£30K, 3 years)
- 2021-2022: SFN+ "Genome-guided detection of non-O157 STEC". Holden, Winn, Dallman (£10K, 9 months)
- 2021-2022: SFN+ "Circular urban vertical farming - Data, models and optimisation of waste flows". Ball, Holden, Jensen, Kanu, Xau (£10K, 9 months)
Previous (selected):
- 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, Holden (Co-I), et al. (€1.66M, 5 years)
- 2019: NBIC “Listeria biofilms”. Holden, Anacail Ltd (£80K, 1 year)
- 2019-2020: IBiolC “Antimicrobial coatings and matrices”. Love, Holden, et al (£101K, 1 year)
- 2017-2018: Innovate-UK “In-pack ozone”. Holden, Anacail Ltd. (£38K, 1 year)
- 2016-2018: RESAS Innovation fund “Biocontrol”. Holden, partners (FSS, SERL, Kettle) (£132K)
- 2014-2016: FSA “Internalisation”. Holden (£350K)
- 2013-2016: HDC “Plant defence elicitors”. Holden, et al (£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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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: SRUC-b6-1 Understanding The Diversity Of Stec And Its Relationship With Human Pathogenic Potential
Tongue, S. (PI), Webster, C. (CoI), Baughan, J. (CoI), Henry, M. (CoI), Holden, N. (CoI), Denniston, J. (CoI) & Nale, J. (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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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 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: Environmental Microbiome. 20, 1, p. 108 12 p., 108.Research output: Contribution to journal › Article › peer-review
Open AccessFile6 Downloads (Pure) -
Microbe-plant interactions of Escherichia coli and Salmonella
Holden, N. & Barak, J., 2 Jul 2025, (First published) In: EcoSal Plus. p. eesp00182023Research output: Contribution to journal › Review article › peer-review
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Pectobacterium atrosepticum SCRI1043 flagella mediate adherence to potato plants indirectly through motility
Holmes, A., Humphris, S., Marshall, J., Rossez, Y., Toth, I. & Holden, N. J., 2025, In: Microbiology (Reading, England). 171, 7, 10 p., 001588.Research output: Contribution to journal › Article › peer-review
Open AccessFile2 Downloads (Pure) -
Scottish One Health AMR Register (SOHAR): Updated research insights
Cameron, A., Mooney, R., Avery, L., Connolly, J., Holden, N., Hursthouse, A. & Henriquez-Mui, F., 11 Aug 2025, Centre of Expertise for Waters.Research output: Book/Report/Policy Brief/Technical Brief › Research report
Open AccessFile13 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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A Microbiome Approach for Healthy Soils – Lessons Learned from Across the Globe
Holden, N. (Speaker)
30 May 2024Activity: Talk, evidence or presentation types › Invited talk
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Microbes 4 Climate (External organisation)
Holden, N. (External advisory group)
Feb 2024 → Jan 2029Activity: Membership types › Membership of advisory group
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Food Standards Agency (External organisation)
Holden, N. (Member)
1 Jan 2023 → 1 Jan 2026Activity: Membership types › Membership of committee
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AMR National Action Plan (2024-2029): Animal Health, Plant Health, Food and the Environment Outcomes Workshop
Holden, N. (Speaker)
28 Mar 2023Activity: Talk, evidence or presentation types › Evidence to committees
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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Equipment
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Molecular Biology Suite
Holden, N. (Manager)
Food Security Challenge CentreFacility/equipment: Facility