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Paul D. Cotter

Research Officer

Research Interests

Dr Cotter's research focuses on the microbiology of food (including beneficial, spoilage and pathogenic microbes) and the gastrointestinal tract (using state-of-the-art DNA-based approaches to examine these microbes, with a view to maintaining/establishing a healthy gut flora through dietary interventions). Dr Cotter is also experienced in the investigation of food-grade antimicrobial peptide (‘bacteriocins’), which can be employed to enhanced food safety and improve human and animal health, and in research of stress resistance and virulence factors employed by health-benefiting as well as disease-causing bacteria.

Dr Cotter has been the recipient of €3 million in funding from Science Foundation Ireland, Enterprise Ireland, the Dept of Agriculture, Fisheries and Food, the Health Research Board, the Irish Research Council for Science, Engineering and Technology and the Teagasc Vision Programme.


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

2001 PhD Molecular Biology, University College Cork (UCC), Ireland

  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.