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Paul D. Cotter

Head of Food Biosciences Department

Research Interests

  • Microbiology of foods (especially fermented foods) and the role of microbes in health, spoilage and disease.
  • Microbiology of the gut and its modulation by diet and exercise.
  • Food grade antimicrobials to control spoilage and pathogenic bacteria.
  • Next generation DNA sequencing technologies.

Current Projects


1996 B.Sc. (Hons) 1st class Microbiology, University College Cork (UCC), Ireland (Graduated in 1st position)

2001 Ph.D. Molecular Biology, University College Cork (UCC), Ireland


2018 Senior Principal Research Officer, Teagasc Food Research Centre

2016 Head of Food Biosciences Department, Teagasc Food Research Centre

2009 Principal Research Officer, Teagasc Food Research Centre

2009 Manager of Teagasc Next Gen DNA Sequencing platform

2009 PI, APC Microbiome Institute

2007–09 Lecturer Microbiology Dept., UCC

2002–06 Post-Doc/Senior Research Fellow UCC

  1. Cotter P.D., R.P. Ross and C. Hill. 2013. Bacteriocins – a viable alternative to antibiotics? Nature Rev Microbiol. 11:95-105
  2. Quigley, L., O. O’Sullivan, T.P. Beresford, R.P. Ross, G.F. Fitzgerald and P.D. Cotter*. 2012. High-throughput sequencing detects subpopulations of bacteria not previously associated with artisanal cheeses. Appl Environ Microbiol. 78:5717-5723.
  3. Fouhy, F., R.P. Ross, G.F. Fitzgerald, C. Stanton, P.D. Cotter*. Composition of the early intestinal microbiota; Knowledge, knowledge gaps and the use of high-throughput sequencing to address these gaps. Gut Microbes. 3:203-20
  4. Murphy, E.F.*, P.D Cotter*, A. Hogan, O. O’Sullivan, A. Joyce, F. Fouhy, S.F Clarke, T.M. Marques, P.W. O’Toole, C. Stanton, E.M. Quigley, C. Daly, RP. Ross, R.M O’Doherty, F. Shanahan. 2012. Divergent Metabolic Outcomes Arising from Targeted Manipulation of the Gut Microbiota in the Diet-Induced Obesity. Gut. 62:220-6. * Joint 1st authors.
  5. Dobson, A., P.D. Cotter, R.P. Ross and C. Hill. 2012. Bacteriocin Production as a Probiotic Trait? Appl Environ Microbiol. 78:1-6.
  6. Molloy, E.M., P.D. Cotter*, C. Hill, D.A. Mitchell and R.P. Ross. 2011. Streptolysin S-like virulence factors: the continuing sagA. Nature Rev Microbiol. 9:670
  7. Field, D., C. Hill, P.D. Cotter* and R.P. Ross. 2010. The dawning of a ‘Golden era’ in lantibiotic bioengineering. Mol. Microbiol. 78:1077
  8. Murphy, E.F., P.D. Cotter, S. Healy, T.M Marques, O. O’Sullivan, F. Fouhy, S. Clarke, P.W. O’Toole, E.M. Quigley, C. Stanton, R.P. Ross, R.M. O’Doherty and F. Shanahan. 2010. The composition and energy harvesting capacity of the gut microbiota and their relationship to diet and obesity over time in mouse models. Gut. 59:1635 Rea, M.C., A. Dobson, O. O’Sullivan, F. Crispie, F. Fouhy, P.D. Cotter, F. Shanahan, B. Kiely, C. Hill, R.P. Ross. 2011. Effect of broad and narrow spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon. Proc Natl Acad Sci USA. 108 Suppl 1:4639.
  9. Cotter, P.D.*, L.A. Draper, E.M. Lawton, K.M. Daly, D.S. Groeger, P.G. Casey, R.P. Ross and C. Hill. 2008. Listeriolysin S, a novel peptide haemolysin associated with lineage I Listeria monocytogenes. PLoS Pathogens. 4:e1000144.
  10. Field, D., P. M. O Connor, P.D. Cotter*, C. Hill and R.P. Ross. 2008. The generation of Nisin variants with enhanced activity against specific gram positive pathogens. Mol. Microbiol. 69:218.
  11. Deegan, L., P.D. Cotter, C. Hill, and R.P. Ross. 2006. Bacteriocins; biological tools for biopreservation and shelf-life extension. Int. Dairy J. 16:1058-1071.
  12. Cotter, P.D., P.M. O’Connor, L.A. Draper, E.M. Lawton, L.H. Deegan, C. Hill and R.P. Ross. 2005. Post-translational conversion of L-Serines to D-Alanines is vital for optimal production and activity of the lantibiotic Lacticin 3147. Proc. Natl. Acad. Sci. USA. 102:18584-9
  13. Cotter, P.D., C. Hill and R.P. Ross. 2005. Bacteriocins; developing innate immunity for food. Nat. Rev. Microbiol. 3:777-788.
  14. Cotter, P.D., and C. Hill. 2003. Surviving the acid test: the Gram positive response to low pH. Microbiol. Mol. Biol. Rev.67:429-453.
  15. Cotter, P.D., C.G.M. Gahan, and C. Hill. 2001. A glutamate decarboxylase system protects Listeria monocytogenes in gastric juice. Mol. Microbiol. 40:465-475
  16. Walsh AM, Macori G, Kilcawley KN and Cotter PD. Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality. Nat Food 2020 1; 500–510
  17. Pasolli E, De Filippis F, Mauriello IE, Cumbo F, Walsh AM, Leech J, Cotter PD, Segata N, Ercolini D. Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nat Commun. 2020 May 25;11(1):2610. doi: 10.1038/s41467-020-16438-8
  18. van de Wouw M, Walsh AM, Crispie F, van Leuven L, Lyte JM, Boehme M, Clarke G, Dinan TG, Cotter PD, Cryan JF. Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse.
    Microbiome. 2020 May 18;8(1):67. doi: 10.1186/s40168-020-00846-5. doi: 10.1080/19490976.2019.1613124.
  19. McHugh AJ, Feehily C, Fenelon MA, Gleeson D, Hill C, Cotter PD. Tracking the Dairy Microbiota from Farm Bulk Tank to Skimmed Milk Powder. mSystems. 2020 Apr 7;5(2):e00226-20. doi: 10.1128/mSystems.00226-20.
  20. Alexa Oniciuc EA, Walsh CJ, Coughlan LM, Awad A, Simon CA, Ruiz L, Crispie F, Cotter PD, Alvarez-Ordóñez A. Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional Metagenomics. mSystems. 2020 Feb 18;5(1):e00723-19. doi: 10.1128/mSystems.00723-19.
  21. Walsh, A.M., Crispie, F., O’Sullivan, O., Finnegan, L., Claesson, M.J., Cotter, P.D. (2018) Species classifier choice is a key consideration when analysing low-complexity food microbiome data. Microbiome. 6(1):50. doi: 10.1186/s40168-018-0437-0.