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

• Microbiome & Mucosal Immunity
• Molecular mechanisms underpinning interactions between the gut microbiome and the gut mucosal barrier

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