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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

  • Ferrocino I, Rantsiou K, McClure R, Kostic T, de Souza RSC, Lange L, FitzGerald J, Kriaa A, Cotter PD, Maguin E, Schelkle B, Schloter M, Berg G, Sessitsch A, Cocolin L. 2023. The need for an integrated multi-OMICs approach in microbiome science in the food system. MicrobiomeSupport Consortium. Comprehensive Reviews in Food Science and Food Safety. doi: 10.1111/1541-4337.13103. PMID: 36636774.
  • Jalanka J, Gunn D, Singh G, Krishnasamy S, Lingaya M, Crispie F, Finnegan L, Cotter PD, James L, Nowak A, Major G, Spiller RC. 2023. Postinfective bowel dysfunction following Campylobacter enteritis is characterised by reduced microbiota diversity and impaired microbiota recovery. Gut. 72(3):451-459. doi: 10.1136/gutjnl-2021-326828. PMID: 36171082.
  • Walsh AM, Leech J, Huttenhower C, Delhomme-Nguyen H, Crispie F, Chervaux C, Cotter PD. 2023. Integrated molecular approaches for fermented food microbiome research. FEMS Microbiology Reviews. 47(2) fuad001. doi: 10.1093/femsre/fuad001.
  • Bourrie BCT, Forgie AJ, Ju T, Richard C, Cotter PD, Willing BP. 2022. Consumption of the cell-free or heat-treated fractions of a pitched kefir confers some but not all positive impacts of the corresponding whole kefir. Frontiers in Microbiology. 13:1056526. doi: 10.3389/fmicb.2022.1056526. PMID: 36504827.
  • Mukherjee A, Gómez-Sala B, O'Connor EM, Kenny JG, Cotter PD. 2022. Global regulatory frameworks for fermented foods: A review. Frontiers in Nutrition. 9:902642. doi: 10.3389/fnut.2022.902642.
  • Obafemi YD, Oranusi SU, Ajanaku KO, Akinduti PA, Leech J, Cotter PD. 2022. African fermented foods: overview, emerging benefits, and novel approaches to microbiome profiling. NPJ Science of Food. 6(1):15. doi: 1038/s41538-022-00130-w.
  • Walsh LH, Coakley M, Walsh AM, O'Toole PW, Cotter PD. 2022. Bioinformatic approaches for studying the microbiome of fermented food. CriticalReviews in Microbiology. 26:1-33. doi: 10.1080/1040841X.2022.2132850. PMID: 36287644.
  • Yap M, Ercolini D, Álvarez-Ordóñez A, O'Toole PW, O'Sullivan O, Cotter PD. 2022. Next-Generation food research: use of meta-omic approaches for characterizing microbial communities along the food chain. Annual Review of Food Science and Technology. 13:361-384. doi: 10.1146/annurev-food-052720-010751. PMID: 34678075.
  • Yap M, Ercolini D, Álvarez-Ordóñez A, O'Toole PW, O'Sullivan O, Cotter PD. 2022. Next-generation food research: use of meta-omic approaches for characterizing microbial communities along the food chain. Annual Review of Food Science and Technology. 13:361-384. doi: 10.1146/annurev-food-052720-010751. PMID: 34678075.
  • Bourrie BCT, Ju T, Fouhse JM, Forgie AJ, Sergi C, Cotter PD, Willing BP. 2021. Kefir microbial composition is a deciding factor in the physiological impact of kefir in a mouse model of obesity. British Journal of Nutrition. 125(2):129-138. doi: 10.1017/S0007114520002743. PMID: 32684173.
  • 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. 2021. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nature Reviews Gastroenterology & Hepatology. 18(3):196-208. doi: 10.1038/s41575-020-00390-5. PMID: 33398112.
  • McHugh AJ, Yap M, Crispie F, Feehily C, Hill C, Cotter PD. 2021. Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples. NPJ Science of Food. 5(1):4. doi: 10.1038/s41538-021-00087-2.
  • Mirzayi C, Renson A, 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. 2021. Reporting guidelines for human microbiome research: the STORMS checklist. Nature Medicine. 27(11):1885-1892. doi: 1038/s41591-021-01552-x.
  • 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. 2021. Protein quality and quantity influence the effect of dietary fat on weight gain and tissue partitioning via host-microbiota changes. Cell Reports. 35(6):109093. doi: 1016/j.celrep.2021.109093.
  • van de Wouw M, Moloney GM, Gual-Grau A, Spichak S, Olavarría-Ramírez L, Fitzgerald P, Morillas E, Ritz NL, Jaggar M, Cowan CSM, Crispie F, Donoso F, Halitzki E, Neto MC, Sichetti M, Golubeva AV, Fitzgerald RS, Claesson MJ, Cotter PD, O’Leary OF, Dinan TG, Cryan, JF. 2021. Microbiota from young mice counteracts selective age-associated behavioral deficits. Nature Aging. 1, 666–676. doi: 10.1038/s43587-021-00093-9.
  • Alexa Oniciuc EA, Walsh CJ, Coughlan LM, Awad A, Simon CA, Ruiz L, Crispie F, Cotter PD, Alvarez-Ordóñez A. 2020. Dairy products and dairy-processing environments as a reservoir of antibiotic resistance and quorum-quenching determinants as revealed through functional metagenomics. mSystems. 5(1):e00723-19. doi: 10.1128/mSystems.00723-19. PMID:
  • Feehily C, Crosby D, Walsh CJ, Lawton EM, Higgins S, McAuliffe FM, Cotter PD. 2020. Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth. NPJ Biofilms Microbiomes. 6(1):50. doi: 10.1038/s41522-020-00162-8. PMID: 33184260.
  • Leech J, Cabrera-Rubio R, Walsh AM, Macori G, Walsh CJ, Barton W, Finnegan L, Crispie F, O'Sullivan O, Claesson MJ, Cotter PD. 2020. Fermented-food metagenomics reveals substrate-associated differences in taxonomy and health-associated and antibiotic resistance determinants. mSystems. 5(6):e00522-20. doi: 10.1128/mSystems.00522-20. PMID: 33172966.
  • McHugh AJ, Feehily C, Fenelon MA, Gleeson D, Hill C, Cotter PD. 2020. Tracking the dairy microbiota from farm bulk tank to skimmed milk powder. mSystems. 5(2):e00226-20. doi: 10.1128/mSystems.00226-20.
  • Pasolli E, De Filippis F, Mauriello IE, Cumbo F, Walsh AM, Leech J, Cotter PD, Segata N, Ercolini D. 2020. Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nature Communications. 11(1):2610. doi: 10.1038/s41467-020-16438-8. PMID: 32451391.
  • Villarreal-Soto SA, Bouajila J, Pace M, Leech J, Cotter PD, Souchard JP, Taillandier P, Beaufort S. 2020. Metabolome-microbiome signatures in the fermented beverage, Kombucha. International Journal of Food Microbiology. 333:108778. doi: 10.1016/j.ijfoodmicro.2020.108778. PMID: 32731153.
  • Walsh AM, Macori G, Kilcawley KN, Cotter PD. 2020. Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality. Nature Food. 1(8):500-510. doi: 1038/s43016-020-0129-3.
  • Walsh CJ, Healy S, O'Toole PW, Murphy EF, Cotter PD. 2020. The probiotic  caseiLC-XCAL™ improves metabolic health in a diet-induced obesity mouse model without altering the microbiome. Gut Microbes. 12(1):1704141. doi: 10.1080/19490976.2020.1747330. PMID: 32403964.
  • Barton W, Penney NC, Cronin O, Garcia-Perez I, Molloy MG, Holmes E, Shanahan F, Cotter PD, O'Sullivan O. 2018. The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level. Gut. 67(4):625-633. doi: 1136/gutjnl-2016-313627. PMID: 28360096.
  • Walsh AM, Crispie F, O’Sullivan O, Finnegan L, Claesson MJ, Cotter PD. 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.