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Microbiology
Ireland
2026

D-Index & Metrics

Microbiology

D-Index
119
Citations
59762
World Ranking
152
National Ranking
5

Research.com Recognitions

  • 2026 - Research.com Microbiology in Ireland Leader Award
  • 2025 - Research.com Microbiology in Ireland Leader Award
  • 2008 - WH Pierce Prize, The Society for Applied Microbiology

Overview

Paul D. Cotter is affiliated with University College Cork in Ireland. Their research spans multiple domains within biochemistry, genetics, molecular biology, medicine, and agricultural and biological sciences.

They have contributed extensively to the fields of Molecular Biology, Food Science, Physiology, Nutrition and Dietetics, and Infectious Diseases. Their main topics of investigation include:

  • Gut microbiota and health
  • Probiotics and Fermented Foods
  • Diet and metabolism studies
  • Genomics and Phylogenetic Studies
  • Clostridium difficile and Clostridium perfringens research
  • Protein Hydrolysis and Bioactive Peptides
  • Nutrition, Genetics, and Disease

Their recent published papers include:

  • The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods, 2021, Nature Reviews Gastroenterology & Hepatology
  • Gut microbes from the phylogenetically diverse genus Eubacterium and their various contributions to gut health, 2020, Gut Microbes
  • Fermented foods in a global age: East meets West, 2020, Comprehensive Reviews in Food Science and Food Safety
  • Bacteriocins as a new generation of antimicrobials: toxicity aspects and regulations, 2020, FEMS Microbiology Reviews
  • Reporting guidelines for human microbiome research: the STORMS checklist, 2021, Nature Medicine

Paul D. Cotter has collaborated frequently with the following co-authors:

  • Fiona Crispie
  • Douwe van Sinderen
  • Calum J. Walsh
  • Órla O'Sullivan
  • Fionnuala M. McAuliffe

Their work is often published in these venues:

  • Frontiers in Microbiology
  • bioRxiv (Cold Spring Harbor Laboratory)
  • Gut Microbes
  • Faculty Opinions - Post-Publication Peer Review of the Biomedical Literature
  • Scientific Reports

Paul D. Cotter received the WH Pierce Prize awarded by The Society for Applied Microbiology in 2008.

Best Publications

  • Bacteriocins: developing innate immunity for food

    Paul D. Cotter;Colin Hill;R. Paul Ross

  • Ribosomally synthesized and post-translationally modified peptide natural products: Overview and recommendations for a universal nomenclature

    Paul G. Arnison;Mervyn J. Bibb;Gabriele Bierbaum;Albert Alexander Bowers

  • Bacteriocins — a viable alternative to antibiotics?

    Paul D. Cotter;R. Paul Ross;Colin Hill

  • Health benefits of fermented foods: microbiota and beyond

    Maria L. Marco;Dustin Heeney;Sylvie Binda;Christopher J. Cifelli

  • Exercise and associated dietary extremes impact on gut microbial diversity

    Siobhan F Clarke;Siobhan F Clarke;Eileen F Murphy;Orla O'Sullivan;Alice J Lucey

  • Surviving the Acid Test: Responses of Gram-Positive Bacteria to Low pH

    Paul D. Cotter;Colin Hill

  • Nucleic acid-based approaches to investigate microbial-related cheese quality defects

    Daniel J. O'Sullivan;Linda Giblin;Paul L. H. McSweeney;Jeremiah J. Sheehan

  • Composition and energy harvesting capacity of the gut microbiota: relationship to diet, obesity and time in mouse models

    E. F. Murphy;P. D. Cotter;P. D. Cotter;S. Healy;Tatiana M. Marques;Tatiana M. Marques

  • Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ

    Caitriona M. Guinane;Paul D. Cotter

  • Bacteriocins: Biological tools for bio-preservation and shelf-life extension

    Lucy H. Deegan;Paul D. Cotter;Colin Hill;Paul Ross

  • The complex microbiota of raw milk

    Lisa Quigley;Lisa Quigley;Orla O'Sullivan;Catherine Stanton;Tom P. Beresford

  • Gut microbiota depletion from early adolescence in mice: Implications for brain and behaviour.

    Lieve Desbonnet;Gerard Clarke;Alexander Traplin;Orla O’Sullivan

  • Bacteriocin Production: a Probiotic Trait?

    Alleson Dobson;Paul D. Cotter;Paul D. Cotter;R. Paul Ross;R. Paul Ross;Colin Hill

  • The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods

    Maria L. Marco;Mary Ellen Sanders;Michael Gänzle;Marie Claire Arrieta

  • Fermented foods in a global age: East meets West

    Jyoti Prakash Tamang;Paul D. Cotter;Akihito Endo;Nam Soo Han

  • The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level.

    Wiley Barton;Nicholas C Penney;Owen Cronin;Isabel Garcia-Perez

  • Gut microbes from the phylogenetically diverse genus Eubacterium and their various contributions to gut health

    Arghya Mukherjee;Cathy Lordan;Cathy Lordan;R. Paul Ross;Paul D. Cotter;Paul D. Cotter

  • High-Throughput Sequencing Reveals the Incomplete, Short-Term Recovery of Infant Gut Microbiota following Parenteral Antibiotic Treatment with Ampicillin and Gentamicin

    Fiona Fouhy;Caitriona M. Guinane;Seamus Hussey;Rebecca Wall

  • The gut microbiota and its relationship to diet and obesity: New insights

    Siobhan F. Clarke;Eileen F. Murphy;Kanishka Nilaweera;Paul R. Ross

  • The Impact of Food Bioactives on Health: in vitro and ex vivo models

    Kitty Verhoeckx;Paul Cotter;Iván López-Expósito;Charlotte Kleiveland

  • A glutamate decarboxylase system protects Listeria monocytogenes in gastric fluid.

    Paul D. Cotter;Cormac G. M. Gahan;Colin Hill

  • Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples.

    Alan J. Marsh;Alan J. Marsh;Orla O'Sullivan;Colin Hill;R. Paul Ross;R. Paul Ross

Frequent Co-Authors

R. Paul Ross
R. Paul Ross University College Cork
Colin Hill
Colin Hill University College Cork
Orla O'Sullivan
Orla O'Sullivan Teagasc - The Irish Agriculture and Food Development Authority
Paula M. O'Connor
Paula M. O'Connor Teagasc - The Irish Agriculture and Food Development Authority
Catherine Stanton
Catherine Stanton Teagasc - The Irish Agriculture and Food Development Authority
Mary C. Rea
Mary C. Rea Teagasc - The Irish Agriculture and Food Development Authority
Fergus Shanahan
Fergus Shanahan National University of Ireland
Gerald F. Fitzgerald
Gerald F. Fitzgerald University College Cork
John F. Cryan
John F. Cryan University College Cork
Paul W. O'Toole
Paul W. O'Toole University College Cork

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