Research Overview

The core research theme of the BIOMERIT Research Centre (BRC) is Environment and Health. This thematic area encompasses the broad study of Microbial-Host Interactions, principally in relation to Functional Genomics and signalling of Prokaryotes applied to Microbial Pathogenesis and Environmental & Marine Biotechnology. This thematic research incorporates a number of related programmes under the leadership of two Principle Investigators (P.I.) within the BRC, Prof. Fergal O’Gara (Director) and Dr. Max Dow and in collaboration with associated P.I.s Dr. John Morrissey (Microbiology Department) and Prof. Alan Dobson (Microbiology Dept. / Environmental Research Institute, ERI).

ENVIRONMENT and HEALTH - Thematic Research Areas:

  • Microbe - Host Interactions
  • Functional Genomics in Gram-negative Bacteria
  • Pathogenicity
  • Environmental / Molecular Ecology
  • Bacterial Signalling and  Pathogenesis (Max Dow P.I.)

Collaborative Programmes:

  • Fungal Genomics and Signalling (John Morrissey P.I., - Microbiology Dept.)
  • Marine Biodiscovery (Alan Dobson P.I., - ERI)

Research in the BRC is fully funded from external agencies including the Dept. of Agriculture, Fisheries and Food (DAFF), the Dept. of the Marine (DOM), The Environmental Protection Agency (EPA), The Higher Education Authority (HEA), the Health Research Board (HRB), the Irish Research Council for Science, Engineering & Technology (IRCSET), Science Foundation Ireland (SFI), the European Union (EU) and National and International industry.

Overview of Research Strategy and Programmes in the BRC
Basic and translational research carried out in Prof. O’Gara’s group in the BRC utilises a Systems Microbiology approach within the thematic area of Environment and Health and is structured around three core programmes, Microbial – Host Interactions, Functional Genomics in Gram negative bacteria and Environmental & Marine Biotechnology. In practice, there is considerable overlap, both in concepts and in methodology, and researchers actively collaborate across the programmes. In addition, there is a strong interest in the applications of the research in biotechnological and biomedical fields with relevant industrial collaborations developed (Fig. 1).

Research Themes

The ability of microbes to sense and adapt to their changing environments through molecular signalling is the basis of many microbe-host interactions and a Systems Biology approach to the integrated analysis of this signalling is a unifying theme in our research programmes. In general the models we use are Pseudomonas fluorescens, a beneficial species associated with the plant rhizosphere, and Pseudomonas aeruginosa, an opportunistic pathogen of immune-compromised humans.  More recently Marine Biodiscovery has emerged as a central theme of our Environmental research whereby we utilize the diverse bacterial populations associated with marine sponges to study microbial signaling and identify bacteria/compounds of industrial / medical significance.

Within the Functional Genomics programme, we investigate sensory and regulatory networks, including post-transcriptional regulation, controlling the production of secondary metabolites and virulence factors, QS and PQS signal molecule production, Type III and VI secretion systems, antibiotic resistance, motility and biofilm formation in human and rhizosphere important microorganisms. The impact of altered membrane composition in response to environmental stress signals in Pseudomonas species is also studied in the programme.  In addition to classical molecular techniques, extensive use is made of genomic and proteomic technologies to facilitate our research in this area. 

The major focus in the Environmental & Marine Biotechnology programme is on the complex signalling between bacteria, fungi and plants in the plant rhizosphere and in biodiversity in marine biotechnology. This signalling has profound implications for plant disease and microbial biodiversity.  Several biotechnology projects in the areas of Biofertilization, Biocontrol and Biodiversity are pursued as part of this research programme.  Furthermore, a Marine Biodiscovery programme, in collaboration with Prof. Alan Dobson (ERI) and Dr. John Morrissey (Microbiology Dept.), is presently funded by the Dept. of the Marine Beaufort Marine Research Award scheme, and DAFF (Discovery + Application of Novel Bioactive Substances from Marine Sponges for the Control of Major Food Pathogens). This biodiscovery programme utilizes both culture based methods and metagenomic libraries from marine sponges to identify and characterise novel signaling systems and industrially or medically significant bioactive compounds.


The origins of our Biomedical Programme lie with studies on the interaction between P. aeruginosa and the lungs of people with Cystic Fibrosis (CF). Molecular signalling and virulence related functions in P. aeruginosa, including antibiotic resistance and Type Three secretion of exotoxins, which contribute to a diseased state, are intricately regulated in response to changing host environments, including oxygen gradients within the lungs of CF patients. How these pathogenic traits are regulated in the host environment, and their impact on host cells are important components of the research work.  It is significant, however, that the host cells also contribute to the milieu of signals, and increasingly, we are exploring the host-cell contribution to the interaction. In order to enhance our studies of microbial pathogenesis a Zebra Fish model system and holding facility has recently been established in the BRC. This facility was funded by a EU TOK initiative (TRAMWAYS) in collaboration with Prof. Dobson and Dr. Morrissey.

Biomerit Research Centre

Professor Fergal O'Gara, 3rd Floor, Biosciences Bldg & 4th Floor, Microbiology Dept., University College Cork, Cork, Ireland