Prof. Paul Cotter

Senior Principal Research Officer & Head of Food Biosciences Department

It is a pleasure to be part of the BioTransform project. I very much look forward to being involved in exciting science with passionate researchers that can have a genuine impact to (Bio)Transform health!

Professional background

Paul graduated from UCC with a BSc and PhD in Microbiology and lectured at CIT and UCC before being appointed as a Principal Research Officer, and then a Senior Principal Research Officer, at Teagasc Food Research Centre, where he also manages the Irish Next Generation Sequencing platform. Paul is now Head of the Food Biosciences Department at Teagasc.

 

Paul Cotter’s research has significantly impacted the field of microbial ecology, particularly in the context of agri-food microbiology and human microbiomes. More specifically, his focus has been on understanding the composition, function, and interactions of microbial communities in environments, such as fermented foods (FFs) and the human gut, including the transfer of microbes from one niche to another (e.g., from mothers to their infants). Paul Cotter’s contributions to the development of a greater understanding of the composition of FFs from across the globe has also facilitated the design and creation of defined communities of FF starters that are optimised with respect to health benefits or other characteristics. He has also extensively studied the impacts of other modulators, including non-FFs and food ingredients, antimicrobials, and other factors, such as exercise, on gut and other human microbiomes and health. Paul’s complementary work with LAB and associated bacteriocins (antimicrobial peptides) has included a focus on the discovery, identification, characterisation and engineering of bacteriocins and their applications of relevance to food preservation and human health. Paul Cotter’s research has resulted in numerous highly cited papers published in high impact journals such as Cell, Nature, Nature Microbiology, Nature Food, Nature Medicine, Nature Aging, Nature Protocols, Nature Communications, Nature Reviews Microbiology, Nature Reviews Gastro and Hepatol, Gut, Proc Natl Acad Sci USA, Microbiome, and others. Overview: >489 peer-reviewed papers; H index 126/100 with >68,281/>39,894 citations (Google Scholar/Web of Science).

Selected publications
  • Breselge S, Skibinska I, Yin X, Brennan L, Kilcawley K, Cotter PD. 2025. The core microbiomes and associated metabolic potential of water kefir as revealed by pan multi-omics. Commun Biol. 2025 Mar 11;8(1):415. doi: 10.1038/s42003-025-07808-3
  • Carlino N, Blanco-Míguez A, Punčochář M, Mengoni C, Pinto F, Tatti A, Manghi P, Armanini F, Avagliano M, Barcenilla C, Breselge S, Cabrera-Rubio R, Calvete-Torre I, Coakley M, Cobo-Díaz JF, De Filippis F, Dey H, Leech J, Klaassens ES, Knobloch S, O’Neil D, Quijada NM, Sabater C, Skírnisdóttir S, Valentino V, Walsh L; MASTER EU Consortium; Alvarez-Ordóñez A, Asnicar F, Fackelmann G, Heidrich V, Margolles A, Marteinsson VT, Rota Stabelli O, Wagner M, Ercolini D, Cotter PD, Segata N, Pasolli E. 2024. Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. Cell. 2024 Aug 16:S0092-8674(24)00833-X. doi: 10.1016/j.cell.2024.07.039.
  • Hartikainen AK, Jalanka J, Lahtinen P, Ponsero AJ, Mertsalmi T, Finnegan L, Crispie F, Cotter PD, Arkkila P, Satokari R. 2024. Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients. NPJ Biofilms Microbiomes. 2024 Aug 28;10(1):73. doi: 10.1038/s41522-024-00549-x. 
  • Finnegan D, Connolly C, Mechoud MA, FitzGerald JA, Beresford T, Mathur H, Brennan L, Cotter PD, Loscher CE. 2024. Novel dairy fermentates have differential effects on key immune responses associated with viral immunity and inflammation in dendritic cells. Foods. 2024 Jul 29;13(15):2392. doi: 10.3390/foods13152392. 
  • Walsh LH, Coakley M, Walsh AM, Crispie F, O’Toole PW, Cotter PD. 2023. Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathways. iScience. 2023 Sep 21;26(10):108004. doi: 10.1016/j.isci.2023.108004.
  • Walsh LH, Walsh AM, Garcia-Perez I, Crispie F, Costabile A, Ellis R, Finlayson J, Finnegan LA, Claesson MJ, Holmes E, Cotter PD. 2023. Comparison of the relative impacts of acute consumption of an inulin-enriched diet, milk kefir or a commercial probiotic product on the human gut microbiome and metabolome. NPJ Sci Food. 2023 Aug 16;7(1):41. doi: 10.1038/s41538-023-00216-z.