Academic Staff

Academic Staff Research Interests and Expertise

John Atkins

  • Translational recoding including programmed ribosomal frameshifting, translational bypassing and codon redefinition
  • Stop codons specifying a standard amino acid (readthrough), UGA specifying selenocysteine, uncommon start codons and the StopGo utilized in Foot and Mouth Disease virus expression
  • Deep earth life and RNA World issues 

Hilary Browne

  • Ecology and evolution of intestinal spore-forming bacteria
  • Genomic functional characterisation of gut microbes
  • Gut microbiome phylogenomics  

Marcus Claesson

  • Bioinformatics
  • Metagenomics and metatranscriptomics
  • Culture-independent approaches to understanding Inflammatory Bowel Disease

David Clarke

  • Bacteria-host interactions
  • Biofilm formation
  • Signaling in bacteria

Sinéad Corr

  • Molecular mechanisms underpinning interactions between the gut microbiome, the gut mucosal barrier and immunity
  • The Gut Microbiome and its metabolites in health and inflammation
  • Dietary and environmental sources of new immune-modulators, anti-microbials and therapeutics

Alan Dobson

  • Applied Microbiology
  • Environmental Biotechnology
  • Marine Biotechnology
  • Physiology and genetics of bacteria and fungi from marine and terrestrial Environments
  • Functional Metagenomics
  • Food Mycology/Genetics of Mycotoxigenic fungi
  • Eukaryotic microbes/Cell Biology

Gerald Fitzgerald

  • Biochemistry, physiology and genetics of Lactic Acid Bacteria
  • Probiotic cultures - fundamental analysis and applications in foods
  • Genomics of Bifidobacterium
  • Bacteriophage resistance in Lactococcus: fundamental analysis of resistance systems and their application in the construction of phage resistant cultures
  • Molecular genetics of bacteriophage of Lactococcus
  • Antimicrobials of Lactic Acid Bacteria as biopreservatives of foods

Cormac Gahan

  • Development of live bacterial vaccine and DNA delivery vectors
  • Understanding microbial pathogenesis (Listeria monocytogenes & Clostridium difficile)
  • Culture-independent approaches to understanding the gut microbiota
  • Microbe-host signaling and bile degradation in the human GI tract

Colin Hill

  • Infectious pathogens
  • The gut microbiome
  • Bacteriocins (applied and fundamental aspects)
  • Bacteriophage (applied and fundamental aspects)
  • Probiotics as anti-infectives

John MacSharry

  • Host-microbe interactions
  • Mucosal immune sampling and response in the gut and the lungs 

Jennifer Mahony

  • Bacteriophage-host interactions in lactic acid bacteria and other food-associated bacteria
  • Bacteriophage-resistance systems
  • Functional genomics of lactic acid bacteria
  • Industrial microbiology

Ruth Massey

  • Microbial pathogenicity
  • Staphylococcus aureus toxin production and immune evasion
  • Streptococcus pneumoniae virulence
  • Functional genomics and GWAS
  • Clinical metagenomics
  • Molecular diagnostics development

John Morrissey

  • Yeast Biotechnology
  • Microbial signalling
  • Microbe-host interactions
  • Fungal pathogenesis
  • Environmental and Marine Biotechnology 

Nicky O'Boyle  

  • Host-pathogen interactions
  • Regulation of gene expression in response to environmental metabolites
  • Chiral amino acid sensing and signal transduction
  • Development and application of in vitro and in vivo infection models
  • Exploring the relationship between metabolism and virulence
  • Understanding the molecular basis of microbial community structure and interbacterial signalling

Fergal O’Gara

  • Microbial Genetics and Genomics
  • Microbe-host Interactions Applied to Environment and Health Sectors
  • Microbial Pathogenesis
  • Molecular Biology of Plant-Microbe Interactions
  • Molecular Microbial Ecology of Microbes

 Niall O'Leary

  • Environmental Biotechnology 
  • Microbial Bioconversions for Resource Sustainability
  • Waste/Wastewater bioremediation
  • Global regulation of microbial pathways for pollutant catabolism

Liam O'Mahony

  • Mechanisms of Immune Tolerance
  • Allergy and Asthma
  • Innate Immune Recognition of Bacterial Structures

Paul O’Toole

  • Genomics of host interaction mechanisms in gastrointestinal bacteria
  • Composition and function of the human gut microbiota

Mike Prentice

  • Bacterial genomics, especially Yersinia sp
  • Bacterial Microcompartments
  • Horizontal gene transfer in bacteria (phage mediated)

Gaurav Rajauria 

  • Industrial Biotechnology, Microbial Fermentation
  • Valorisation of Marine Biomass, Agriculture / Food / Urban Waste and Side Streams
  • Resource Efficiency, Zero Waste Cascading Biorefinery Development
  • Advanced Food Processing / Extraction Technologies, Pretreatment Technologies
  • Bioprocessing, Bioactive Mining
  • Alternative Proteins and Biochemicals for Biobased Economy
  • Isolation, Purification and Characterisation

F. Jerry Reen

  • Small molecule signalling in microbial communities
  • Chemico-biological therapeutics
  • (Post)Transcriptional regulatory systems

 Paul Ross

  • Food Biotechnology 
  • Gut microbiota
  • Novel antimicrobials, including bacteriocins and bacteriophage
  • Probiotics and starter cultures

Francisco Vitor Santos da Silva

  • Industrial bioprocesses, mathematical modelling, and data science
  • Chemical and biochemical process development and scale-up
  • Hybrid modelling techniques
  • New and sustainable processes in the areas of food, chemical, and pharmaceutical production

Martina Scallan

  • Virus-host cell interactions: intracellular molecular communication between virus and cell components determining infection outcome.
  • Viruses as vectors for therapeutic gene delivery.
  • Gastrointestinal viruses and gut epithelial cells and the influence of probiotic bacteria on virus-epithelial cell interactions.
  • Neurotropic viruses and cells of the central nervous system

Pauline Scanlan

  • Ecology and evolution of the gut microbiome
  • Prevalence, diversity and function of gut microbial eukarya (Fungi and Protists e.g. Blastocystis)
  • Bacteriophages
  • Host-parasite coevolution
  • Chronic Disease

Andrey Shkoporov

  • Bacteriophages in the human microbiome (the phageome)
  • Phage-host interactions, phage life cycles
  • Gut microbiome in the Inflammatory Bowel Disease
  • Anaerobic bacteriology
  • Taxonomy and nomenclature of gut bacteria and bacteriophages

Douwe van Sinderen

  • Global gene regulation in bacteria through environmental sensing systems
  • Molecular biology of bacteriophage infecting lactic acid bacteria
  • Genomics and systems biology of lactic acid bacteria and bifidobacteria
  • Metabolic engineering of lactic acid bacteria
  • Probiotic functionality of bifidobacteria

Jens Walter

  • Evolutionary ecology of gut microbes
  • Community ecology of host-associated microbiomes
  • Human nutrition and the gut microbiome
  • Translation of basic microbiome science into therapeutic and nutritional strategies

School of Microbiology

Scoil na Micribhitheolaíochta

Microbiology Office, Room FSB452, 4th Floor Food Science & Technology Building, University College Cork, Cork T12 Y337