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Nicola Holden

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Recent publications

Staff picture: Nicola Holden
Cell and Molecular Sciences
+44 (0)844 928 5428 (*)

The James Hutton Institute
Dundee DD2 5DA
Scotland UK

My research interest lies in the interactions between bacteria and their plant hosts. The research is primarily focused on food-borne bacteria, but also covers opportunistic plant pathogens because of the many similarities in the types of interactions; transmission of the bacteria through the wider environment and the plant host response.

Figure 1: (A) Colonisation of spinach roots by E. coli O157:H7 (in green).Pathogenic enterobacteria Escherichia coli, Salmonella enterica and Klebsiella pneumoniae are normally associated with animal reservoirs. However, a significant proportion of food poisoning outbreaks are attributable to fresh produce (fresh fruit and vegetables). We have good evidence to show that the bacteria are not transported by the plant in an inert manner, rather they interact with plant hosts at a molecular level and are able to replicate both on external and internal plant tissue. Comparative genomics has shown that enteric human pathogens are closely related to enteric plants pathogens, in particular Pectobacterium spp. (formerly Erwinia) (sequenced by Ian Toth and colleagues: Bell et al., 2004 PNAS 101:11105). The comparison allows identification of key genes that are involved in interactions with plants, at the first step of adherence and the subsequent steps of invasion and persistence.

(B) Close-up of systemic tissue of the same spinach root showing bacteria within xylem vessels.The research on food-borne pathogens investigates bacterial factors required for different stages of colonisation, as well as the plant response. We also investigate transmission of bacteria in agricultural systems, from soil amendments to harvested crops. Projects with plant pathogenic bacteria are on-going to find alternative treatment options to current bactericides. The over-all aim of the research is to gain a better understanding of the mechanisms that govern bacteria-plant interactions, with the goal of reducing human illness and plant disease.

Current research interests 

Externally funded research projects

  • Identification and characterisation of EHEC adherence factors that interact with plant tissue. Funded by the BBSRC, Oct 2011 – Sept 2014
  • Transcriptome analysis of enterohaemorrhagic Escherichia coli in planta. Jointly funded by the James Hutton Institute and the University of Reading, Oct 2011 - Sept 2014
  • Defining the interactions between plant cell walls and bacterial surface factors. Funded by the Leverhulme Trust, Feb 2012 – Jan 2015

Other projects funded by RESAS investigate aspects of the plant host response to zoonotic bacteria as well as the population genetics of plant and environmental isolates of Escherichia coli.

Past research 

Previous research has focused on the regulation of bacterial factors that enable them to adapt to different hosts and environments.


  • At the James Hutton Institute with partners in Environmental and Biochemical Sciences and in Controlling Weeds, Pests and Diseases research theme.
  • Professor David L. Gally; Dr Maurice P. Gallagher (University of Edinburgh)
  • Dr Thamarai Schneiders (University of Belfast)
  • Professor Dale Walters (SAC)
  • Dr Rob Jackson (University of Reading)
  • Dr Ruth Zadocks (Moredun Research Institute)


  • Downie, H., Holden, N.Otten, W., Spiers, A.J., Valentine, T.A. and Dupuy, L.X. 2012. Transparent soil for imaging the rhizosphere. PLoS ONE 7(9):e44276.
  • Wright, K.M., Chapman, S., McGeachy, K., Humphris, S., Campbell, E., Toth, I.K. and Holden,N.J. 2013. The endophytic lifestyle of Escherichia coli O157:H7: quantification and internal localization in roots. Phytopathology 103(4), 333-340.
  • Pritchard, L., Holden N.J., Bielaszewska, M., Karch, H. & Toth, I.K. 2012. Alignment-free design of highly discriminatory diagnostic primer sets for Escherichia coli O104:H4 outbreak strains. PLoS ONE 7: e34498.
  • Holden N.J., Pritchard, L, Wright, K.M. & Toth, I. 2012. Mechanisms of plant colonisation by human pathogenic enterobacteria. In Molecular Microbial Ecology of the Rhizosphere (de Bruijn F, eds.). Wiley-Blackwell.
  • Holden, N.J. 2012. Adherence, biofilm and motility characteristics of plant associated Salmonella enterica. Crop Protection of Northern Britain 2012 Conference Proceedings.
  • Holden, N.J., Toth, I.K., Newton, A., Walters, D. 2012. The use of plant elicitors in the control of bacterial infection in field vegetables. Crop Protection of Northern Britain 2012 Conference Proceedings.
  • Holden, N.J. 2010. Plants as reservoirs for human enteric pathogens. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources 5, 1-11.
  • Holden, N., Pritchard, L. and Toth, I. 2009. Colonization outwith the colon: plants as an alternative environmental reservoir for human pathogenic enterobacteria. FEMS Microbiological Reviews 33(4), 689-703.. (doi:10.1111/j.1574-6976.2008.00153.x)
  • Rosser, T., Dransfield, T.,  Allison, L., Hanson, M., Holden, N., Evans, J., Naylor, S., LaRagione, R., Low, J.C. and Gally, D.L. 2008. Pathogenic potential of emergent sorbitol-fermenting Escherichia coli O157:NM. Infection and Immunity. (doi:10.1128/IAI.01180-01108)
  • Totsika, M., Beatson, S.A., Holden, N., Gally, D.L. 2008. Regulatory interplay between pap operons in uropathogenic Escherichia coli. Molecular Microbiology 67, 996-1011.
  • Nart, P., Holden, N., McAteer, S.P., Wang, D., Flockhart, A.F., Naylor, S.W., Low, J.C., Gally, D.L., Huntley, J.F. 2008. Mucosal antibody responses of colonized cattle to Escherichia coli O157-secreted proteins, flagellin, outer membrane proteins and lipopolysaccharide. FEMS immunology and medical microbiology 52, 59-68.
  • Holden, N., Blomfield, I.C., Uhlin, B-E., Totsika, M., Kulasekara, D.H., Gally, D.L. 2007. Comparative analysis of FimB and FimE recombinase activity. Microbiology 153, 4138-4149
  • Holden, N., Totsika, M., Dixon, L., Catherwood, K., Gally, D.L. 2007. Regulation of P-fimbrial phase variation frequencies in Escherichia coli CFT073. Infection and Immunity 75, 3325-34.
  • Low, A.S., Dziva, F., Torres, A.G., Martinez, J.L., Rosser, T., Naylor, S., Spears, K., Holden, N., Mahajan, A., Findlay, J., Sales, J., Smith, D.G., Low, J.C., Stevens, M.P., Gally, D.L. 2006. Cloning, expression, and characterization of fimbrial operon F9 from enterohemorrhagic Escherichia coli O157:H7. Infection and Immunity 74, 2233-44.
  • Holden, N.J., Totsika, M., Mahler, E., Roe, A.J., Catherwood, K., Lindner, K., Dobrindt, U., Gally, D.L. 2006. Demonstration of regulatory cross-talk between P fimbriae and type 1 fimbriae in uropathogenic Escherichia coli. Microbiology 152, 1143-53.
  • Low, A.S., Holden, N., Rosser, T., Roe, A.J., Constantinidou, C., Hobman, J.L., Smith, D.G., Low, J.C., Gally, D.L. 2006. Analysis of fimbrial gene clusters and their expression in enterohaemorrhagic Escherichia coli O157:H7. Environmental Microbiology 8, 1033-47.
  • Holden, N.J., Gally, D.L. 2004. Switches, cross-talk and memory in Escherichia coli adherence. Journal of Medical Microbiology 53, 585-93.

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  • Phone: +44 (0)844 928 5428
  • Craigiebuckler Aberdeen AB15 8QH Scotland
  • Invergowrie Dundee DD2 5DA Scotland
A Scottish charitable company limited by guarantee. Registered in Scotland No SC374831.
Registered office: The James Hutton Institute, Invergowrie Dundee DD2 5DA. Charity No SCO41796

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The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.