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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. Walsh AM, Macori G, Kilcawley KN and Cotter PD. Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality. Nature Food 2020 1; 500–510
  2. 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. Nature Commun. 2020 May 25;11(1):2610. doi: 10.1038/s41467-020-16438-8
  3. Marco ML, Sanders ME, Gänzle M, Arrieta MC, Cotter PD, De Vuyst L, Hill C, Holzapfel W, Lebeer S, Merenstein D, Reid G, Wolfe BE, Hutkins R. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nature Rev Gastroenterol Hepatol. 2021 Mar;18(3):196-208.
  4. Mirzayi C, Renson A; Genomic Standards Consortium; Massive Analysis and Quality Control Society, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, Beghini F, Bergstrom K, Bhatt A, Bisanz JE, Braun J, Bravo HC, Buck GA, Bushman F, Casero D, Clarke G, Collado MC, Cotter PD, Cryan JF, Demmer RT, Devkota S, Elinav E, Escobar JS, Fettweis J, Finn RD, Fodor AA, Forslund S, Franke A, Furlanello C, Gilbert J, Grice E, Haibe-Kains B, Handley S, Herd P, Holmes S, Jacobs JP, Karstens L, Knight R, Knights D, Koren O, Kwon DS, Langille M, Lindsay B, McGovern D, McHardy AC, McWeeney S, Mueller NT, Nezi L, Olm M, Palm N, Pasolli E, Raes J, Redinbo MR, Rühlemann M, Balfour Sartor R, Schloss PD, Schriml L, Segal E, Shardell M, Sharpton T, Smirnova E, Sokol H, Sonnenburg JL, Srinivasan S, Thingholm LB, Turnbaugh PJ, Upadhyay V, Walls RL, Wilmes P, Yamada T, Zeller G, Zhang M, Zhao N, Zhao L, Bao W, Culhane A, Devanarayan V, Dopazo J, Fan X, Fischer M, Jones W, Kusko R, Mason CE, Mercer TR, Sansone SA, Scherer A, Shi L, Thakkar S, Tong W, Wolfinger R, Hunter C, Segata N, Huttenhower C, Dowd JB, Jones HE, Waldron L. Reporting guidelines for human microbiome research: the STORMS checklist. Nature Med. 2021 Nov;27(11):1885-1892.
  5. Boehme, M., Katherine E. Guzzetta, Thomaz F. S. Bastiaanssen, Marcel van de Wouw, Gerard M. Moloney, Andreu Gual-Grau, Simon Spichak, Loreto Olavarría-Ramírez, Patrick Fitzgerald, Enrique Morillas, Nathaniel L. Ritz, Minal Jaggar, Caitlin S. M. Cowan, Fiona Crispie, Francisco Donoso, Evelyn Halitzki, Marta C. Neto, Marzia Sichetti, Anna V. Golubeva, Rachel S. Fitzgerald, Marcus J. Claesson, Paul D. Cotter, Olivia F. O’Leary, Timothy G. Dinan & John F. Cryan. Microbiota from young mice counteracts selective age-associated behavioral deficits. Nature Aging 2021; 1:666–676.
  6. 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.
  7. Feehily C, Crosby D, Walsh CJ, Lawton EM, Higgins S, McAuliffe FM, Cotter PD. Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth. NPJ Biofilms Microbiomes. 2020 Nov 12;6(1):50. doi: 10.1038/s41522-020-00162-8
  8. Nychyk O, Barton W, Rudolf AM, Boscaini S, Walsh A, Bastiaanssen TFS, Giblin L, Cormican P, Chen L, Piotrowicz Y, Derous D, Fanning Á, Yin X, Grant J, Melgar S, Brennan L, Mitchell SE, Cryan JF, Wang J, Cotter PD, Speakman JR, Nilaweera KN. Protein quality and quantity influence the effect of dietary fat on weight gain and tissue partitioning via host-microbiota changes. Cell Rep. 2021 May 11;35(6):109093. doi: 10.1016/j.celrep.2021.109093.
  9. 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.
  10. 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.
  11. McHugh AJ, Yap M, Crispie F, Feehily C, Hill C, Cotter PD. Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples. NPJ Sci Food. 2021 Feb 15;5(1):4. doi: 10.1038/s41538-021-00087-2.
  12. 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.