Ashleigh Holmes
Ashleigh’s research interests are in microbial pathogenicity and attachment to the rhizosphere. She has investigated the molecular mechanisms of Enterohaemorrhagic Escherichia coli O157:H7 attachment to plant tissues and changes in its gene expression during plant colonization. Now, she is applying her experience to understanding the molecular mechanisms of Pectobacterium atroscepticum pathogenicity and colonisation on potato and other plant species. She is also interested in the plant response to bacteria and if they can distinguish microbial friend from foe.
Current research interests
Current projects include RESAS supported research (2022-2027 Strategic Research Programme: JHI-A1-1 Epidemiology of Key Pests and Diseases; JHI-A1-2 Integrated Crop Protection) to inform on the epidemiology, and methods for the control of, potato blackleg caused by Pectobacterium atrosepticum in Scotland.
Working in collaboration with industry, we are investigating the application of biocontrol (Innovate UK Farming Innovation Pathways project IUK10005717) and other soil amendments (RESAS JHI-D3-1 Healthy Soils For A Green Recovery) to investigate impacts to blackleg disease progression as well as neighbouring soil and rhizosphere microbial communities (microbiomes).
Past research
2016-2022: Scottish Government Rural Affairs, Food and the Environment (RAFE) Strategic Research Deliverables: Animal Disease Epidemiology; Disease Threats in the Environment; and Food Safety.
Dec 2018 - Nov 2020: PDRA on Innovate UK project: Targeted innovation in the seed potato industry to improve productivity and quality.
May 2016 – March 2018 PDRA on Innovate UK project: Biocontrol of food-borne pathogens, Escherichia coli and Salmonella enterica, on horticultural produce.
Oct 2011 – Sept 2014 PDRA on BBSRC funded project: Identification and characterisation of EHEC adherence factors that interact with plant tissue.
Bibliography
- Waters, N.R.; Abram, F.; Brennan, F.; Holmes, A.; Pritchard, L. (2020) Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool., Access Microbiology, 2(9), Article No. 000143.
- Holmes, A.; Pritchard, L.; Hedley, P.; Morris, J.; McAteer, S.P.; Gally, D.L.; Holden, N.J. (2020) Dataset of Escherichia coli O157:H7 genes enriched in adherence to spinach root tissue., Data in Brief, 31, Article No. 105769.
- Holmes, A.; Pritchard, L.; Hedley, P.; Morris, J.; McAteer, S.P.; Gally, D.L.; Holden, N.J. (2020) A high-throughput genomic screen identifies a role for the plasmid-borne type II secretion system of Escherichia coli O157:H7 (Sakai) in plant-microbe interactions., Genomics, 112, 4242-4253.
- Holmes, A.; Rossez, Y.; Wright, K.M.; Hedley, P.E.; Morris, J.; Willats, W.G.T.; Holden, N.J. (2020) Esherichia coli O157:H7 F9 fimbriae recognize plant xyloglucan and elicit a response in Arabidopsis thaliana., International Journal of Molecular Sciences, 21, Article No. 9720.
- Waters, N.R.; Abram, F.; Brennan, F.; Holmes, A.; Pritchard, L. (2018) riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions., Nucleic Acids Research, 46. Article No. e68.
- Holmes, A.; Stanley-Wall, N.; Newton, A.; Holden, N.J. (2018) Can plant growth-promoting rhizobacteria be used to control bacterial pathogens on horticultural produce?, Crop Protection in Northern Britain 2018: The Dundee Conference, Environmental Management and Crop Production, Apex City Quay Hotel, Dundee, 27-28 February 2018. Conference Proceedings, 59-64.
- Wright, K.M.; Crozier, L.; Marshall, J.; Merget, B.; Holmes, A.; Holden, N.J. (2017) Differences in internalisation and growth of Escherichia coli O157:H7 within the apoplast of edible plants, spinach and lettuce, compared with the model species Nicotiana benthamiana., Microbial Biotechnology, 10, 555-569.
- Waters, N.R.; Abram, F.; Brennan, F.; Holmes, A.; Pritchard, L. (2017) riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions., bioRxiv, Article No. 159798.
- Rossez, Y.; Wolfson, E.B.; Holmes, A.; Gally, D.L.; Holden, N.J. (2015) Bacterial flagella: twist and stick, or dodge across the Kingdoms., PLoS Pathogens, 11, Article No. e1004483.
- Holden, N.J.; Holmes, A.; Rossez, Y. (2015) The molecular interactions between human pathogenic bacteria and plants., In: Murillo, J., Vinatzer, B.A., Jackson, R.W. & Arnold, D.L. (eds.). Bacteria-Plant Interactions: Advanced Research and Future Trends, Caister Academic Press, pp139-166.
- Holmes, A.; Birse, L.; Jackson, R.W.; Holden, N.J. (2014) An optimised method for the extraction of bacterial mRNA from plant roots infected with Escherichia coli O157:H7., Frontiers in Microbiology, 5, Article No. 286.
- Rossez, Y.; Holmes, A.; Lodberg-Pedersen, H.; Birse, L.; Marshall, J.; Willats, W.G.T.; Toth, I.K.; Holden, N.J. (2014) Escherichia coli common pilus (ECP) targets arabinosyl residues in plant cell walls to mediate adhesion to fresh produce plants., Journal of Biological Chemistry, 289, 34349-34365.
- Bewley, M.A.; Naughton, M.; Preston, J.; Mitchell, A.; Holmes, A.; Marriott, H.M.; Read, R.C.; Mitchell, T.J.; Whyte, M.K.B.; Dockrell, D.H. (2014) Pneumolysin activates macrophage lysosomal membrane permeabilization and executes apoptosis by distinct mechanisms without membrane pore formation., mBio, 5, Article No. e01710-14.
- Rossez, Y.; Holmes, A.; Wolfson, W.B.; Gally, D.L.; Mahjan, A.; Pedersen, H.L.; Willats, W.G.T.; Toth, I.K.; Holden, N. (2014) Flagella interact with ionic plant lipids to mediate adherence of pathogenic Escherichia coli to fresh produce plants., Environmental Microbiology, 16, 2181-2195.
- Waters, N.R.; Abram, F.; Brennan, F.; Holmes, A.; Pritchard, L. (2020) Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool., Access Microbiology, 2(9), Article No. 000143.
- Holmes, A.; Pritchard, L.; Hedley, P.; Morris, J.; McAteer, S.P.; Gally, D.L.; Holden, N.J. (2020) Dataset of Escherichia coli O157:H7 genes enriched in adherence to spinach root tissue., Data in Brief, 31, Article No. 105769.
- Holmes, A.; Pritchard, L.; Hedley, P.; Morris, J.; McAteer, S.P.; Gally, D.L.; Holden, N.J. (2020) A high-throughput genomic screen identifies a role for the plasmid-borne type II secretion system of Escherichia coli O157:H7 (Sakai) in plant-microbe interactions., Genomics, 112, 4242-4253.
- Holmes, A.; Rossez, Y.; Wright, K.M.; Hedley, P.E.; Morris, J.; Willats, W.G.T.; Holden, N.J. (2020) Esherichia coli O157:H7 F9 fimbriae recognize plant xyloglucan and elicit a response in Arabidopsis thaliana., International Journal of Molecular Sciences, 21, Article No. 9720.
- Waters, N.R.; Abram, F.; Brennan, F.; Holmes, A.; Pritchard, L. (2018) riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions., Nucleic Acids Research, 46. Article No. e68.
- Wright, K.M.; Crozier, L.; Marshall, J.; Merget, B.; Holmes, A.; Holden, N.J. (2017) Differences in internalisation and growth of Escherichia coli O157:H7 within the apoplast of edible plants, spinach and lettuce, compared with the model species Nicotiana benthamiana., Microbial Biotechnology, 10, 555-569.
- Waters, N.R.; Abram, F.; Brennan, F.; Holmes, A.; Pritchard, L. (2017) riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions., bioRxiv, Article No. 159798.
- Rossez, Y.; Wolfson, E.B.; Holmes, A.; Gally, D.L.; Holden, N.J. (2015) Bacterial flagella: twist and stick, or dodge across the Kingdoms., PLoS Pathogens, 11, Article No. e1004483.
- Holmes, A.; Birse, L.; Jackson, R.W.; Holden, N.J. (2014) An optimised method for the extraction of bacterial mRNA from plant roots infected with Escherichia coli O157:H7., Frontiers in Microbiology, 5, Article No. 286.
- Rossez, Y.; Holmes, A.; Lodberg-Pedersen, H.; Birse, L.; Marshall, J.; Willats, W.G.T.; Toth, I.K.; Holden, N.J. (2014) Escherichia coli common pilus (ECP) targets arabinosyl residues in plant cell walls to mediate adhesion to fresh produce plants., Journal of Biological Chemistry, 289, 34349-34365.
- Bewley, M.A.; Naughton, M.; Preston, J.; Mitchell, A.; Holmes, A.; Marriott, H.M.; Read, R.C.; Mitchell, T.J.; Whyte, M.K.B.; Dockrell, D.H. (2014) Pneumolysin activates macrophage lysosomal membrane permeabilization and executes apoptosis by distinct mechanisms without membrane pore formation., mBio, 5, Article No. e01710-14.
- Rossez, Y.; Holmes, A.; Wolfson, W.B.; Gally, D.L.; Mahjan, A.; Pedersen, H.L.; Willats, W.G.T.; Toth, I.K.; Holden, N. (2014) Flagella interact with ionic plant lipids to mediate adherence of pathogenic Escherichia coli to fresh produce plants., Environmental Microbiology, 16, 2181-2195.
- Holden, N.J.; Holmes, A.; Rossez, Y. (2015) The molecular interactions between human pathogenic bacteria and plants., In: Murillo, J., Vinatzer, B.A., Jackson, R.W. & Arnold, D.L. (eds.). Bacteria-Plant Interactions: Advanced Research and Future Trends, Caister Academic Press, pp139-166.
- Holmes, A.; Stanley-Wall, N.; Newton, A.; Holden, N.J. (2018) Can plant growth-promoting rhizobacteria be used to control bacterial pathogens on horticultural produce?, Crop Protection in Northern Britain 2018: The Dundee Conference, Environmental Management and Crop Production, Apex City Quay Hotel, Dundee, 27-28 February 2018. Conference Proceedings, 59-64.
- Holmes, A.; Jones, S.; Watts, L.; Humphris, S.; Cheetham, A.; Toth, I. (2022) Can microbiome profiles be used as an indicator of soil health to investigate the impacts from compaction and potato cropping, 3rd Plant Microbiome Symposium 2022, 24-26 May 2022, Dundee
- Holmes, A.; Wright, K.; Marshall, J.; Holden, N. (2019) The lush life: Escherichia coli O157 colonising the apoplast., MPMI 2019, XVIII Congress, Glasgow, 14-18 July 2019. Molecular Plant-Microbe Interactions, 32, 109. (Poster).
- Holmes, A.; Rossez, Y.; Hedley, P.; Morris, J.; Gally, D.; Holden, N.J. (2018) I’ll stick to the salad: mechanisms of VTEC adherence to fresh leafy produce., Microbiology Society Annual General Meeting, International Conference Centre (ICC), Birmingham, 10-13 April 2018. Poster Abstract Book, P490.
- Wright, K.; Marshall, J.; Holmes, A.; Holden, N.J. (2018) Entertaining with E coli O157., Frontiers in BioImaging Meeting, Glasgow, 27-28 June 2018. Abstract.
- Holmes, A.; Newton, A.; Stanley-Wall, N.R.; Holden, N.J. (2018) Can plant growth-promoting rhizobacteria be used to control bacterial pathogens on horticultural produce?, Crop Protection in Northern Britain 2018: The Dundee Conference, Environmental Management and Crop Production, Apex City Quay Hotel, Dundee, 27-28 February 2018. Conference Proceedings, pp59-64.
- Holmes, A.; Kalamara, M.; Stanley-Wall, N.R.; Holden, N.J. (2017) Can fresh produce be protected from colonisation by human pathogens through the application of plant growth promoting rhizobacteria (PGPR) as biocontrol?, 7th Congress of European Microbiologists (FEMS 2017), Valencia, Spain, 9-13 July 2017, Abstract No 189.
- Holmes, A.; Kalamara, M.; Stanley-Wall, N.R.; Holden, N.J. (2017) Can plant growth promoting rhizobacteria (PGPR) be applied as biocontrol to protect fresh produce from colonisation by human pathogens?, Microbiology Society Annual General Meeting, Edinburgh, 10-13 April 2017. Abstract No.475.
- Holmes, A.; Hedley, P.; Morris, J.; Rossez, Y.; Toth, I.; Holden, N.J. (2017) There’s something hairy going on: Understanding the defence response of plants to Escherichia coli O157:H7., Microbiology Society Annual General Meeting, Edinburgh, 3-6 April 2017.
- Wright, K.M.; Crozier, L.; Marshall, J.; Merget, B.; Holmes, A.; Holden, N.J. (2017) Differences in internalisation and growth of Escherichia coli O157_H7 within the apoplast of edible plants, spinach and lettuce, compared with the model species Nicotiana benthamiana., Microbiology Society Annual Meeting, Edinburgh, 3-6 April 2017. (Poster)
- Holmes, A.; Hedley, P.; Morris, J.; Holden, N.J. (2016) Understanding the defence response of plants to Escherichia coli O157:H7., Young Microbiologists Symposium on Microbe Signalling, Organisation and Pathogenesis, Apex Hotel, Dundee, 29-30 June 2016. Poster session I. No. 5.
- Wright, K.M.; Marshall, J.; Holmes, A.; Holden, N.J. (2016) E coli O157:H7 - Watch out for the salad as well as the undercooked beefburger!, Young Microbiologists Symposium on Microbe Signalling, Organisation and Pathogenesis 2016, Apex City Quay Hotel, Dundee, 29-30 June 2016.
- Holden, N.; Birse, L.; Marshall, J.; Rossez, Y.; Holmes, A. (2013) Molecular interactions between food-borne bacteria and plant hosts., EMBO/EMBL Symposia, New Approaches and Concepts in Microbiology, Heidelberg, Germany, 14-16 October 2013.
- Rossez, Y.; Holmes, A.; Ahl, L.I.; Pedersen, H.L.; Willats, W.G.T.; Toth, I.; Holden, N. (2012) Role of bacterial surface factors in adherence of enteric bacteria to plant polysaccharide., Glycobiology, 22, 1638.
