Paul O'Toole

Prof. Paul O’Toole

ELDERMET Project Coordinator
Department of Microbiology, University College Cork


Paul O’Toole graduated with BA (Mod) Microbiology (1984) and PhD (1987) from Trinity College Dublin, in microbial molecular genetics. He has extensive experience in bacterial genetics and gut microbiology, having spent 14 years outside Ireland working in Univ. Lund (Sweden), Univ. Victoria (Canada), Massey University (New Zealand), and GlaxoSmithKline (Philadelphia).Since 2002, he has led the Lactobacillus genomics programme at UCC, where he is a Senior Lecturer in Genetics at the Department of Microbiology, and the co-ordinator of the B.Sc. Genetics degree. As well as co-ordinating ELDERMET, he is a member of the International Co-ordination Board of the MetaHIT consortium, which is an EU-supported FP7 project for metagenomic analysis of healthy, obese and diabetic adults in Europe.

His research programme in bacterial genomics at UCC is funded by Dept. Agriculture Fisheries and Food, Science Foundation Ireland, Enterprise Ireland, and the Irish Research Council for Science, Engineering and Technology.


Ted Dinan

Prof. Ted Dinan

Department of Psychiatry, University College Cork


Ted Dinan is Professor of Psychiatry at University College Cork. He was previously Chair of Clinical Neurosciences and Professor of Psychological Medicine at St. Bartholomew’s Hospital, London. Prior to that, he was a Senior Lecturer in Psychiatry at Trinity College Dublin.He has worked in research laboratories on both sides of the Atlantic and has a PhD in Pharmacology from the University of London. He is a Fellow of the Royal Colleges of Physicians and Psychiatrists and a Fellow of the American College of Physicians. His main research interests are in the biology of depression and functional bowel disorders and in this context he has made significant contributions to the literature on the regulation of the hypothalamic-pituitary-adrenal axis in situations of stress with particular emphasis on the role of vasopressin.

In 1995 was awarded the Melvin Ramsey Prize for this research into the biology of stress. His current research is funded by Science Foundation Ireland, the Health Research Board and the Wellcome Trust. He has published over 180 papers and numerous books on the pharmacology and neurobiology of affective disorders. He is on the Editorial Boards of several journals including the Journal of Affective Disorders, Human Psychopharmacology, Psychoneuroendocrinology and Stress and Health.

Gerald Fitzgerald

Prof. Gerald Fitzgerald

Department of Microbiology, University College Cork


Gerald Fitzgerald has published extensively in areas spanning fundamental and applied research of lactic bacteria (including probiotic bacteria). His research activities have resulted in the completion of more than 60 postgraduate theses over the past 20 years.Prof. Fitzgerald has co-authored a number of patents relating to the commercial application of lactic acid bacteria. He has extensive experience in the leadership and management of large, multipartner projects (funded by PRTLI, EU, Department of Fisheries and Food, Enterprise Ireland) and he is currently the Interim Director of the EUR 22m National Functional Food Research Centre (NFFRC).

Prof Fitzgerald is a member of the Alimentary Pharmabiotic Centre where he serves as Deputy Director. In addition, he is Director of the Biotransfer Unit which is responsible for the commercialisation of life science research in UCC. Thus, he has significant links to the Irish and International food industry, particularly in the areas of functional ingredients. He is a key instigator of the UCC Food and Health initiative which has been flagged as the number one strategic research priority in the current PRTLI 4 round of funding.

Tony Fitzgerald

Dr. Tony Fitzgerald

Department of Epidemiology & Public Health, University College Cork


Dr. Tony Fitzgerald is a Lecturer in Medical Statistics in the department of Epidemiology & Public Health and a Senior Statistician at the National Suicide Research Foundation (NSRF). He obtained a Masters in Mathematical Sciences from UCC in 1985 and a Sc.D. in Medical Statistics from the Harvard School of Public Health in 2000.His primary area of interest is in the development and evaluation of risk prediction systems that will allow clinicians to better identify high risk patients. Future research at the NSRF will examine associations between socio-economic changes and rates of suicidal behaviour and depression and evaluate the effectiveness of various health promotion schemes.

From 1988-1995 Tony worked in the University of London (Guy’s & St. Thomas’s) as Research Statistician and subsequently Lecturer in Medical Statistics. On returning to Ireland in 2000 he worked as a Research Statistician at the Royal College of Surgeons in Ireland (RCSI). Most recently he worked as Statistical Consultant at the Haughton Institute providing collaborative support to researchers in the Adelaide & Meath and St. James’s Hospitals. He is a member of the Steering Committee of the pan-European HeartCORE study to develop electronic and interactive risk prediction models that are tailored to local risk factor data and national mortality statistics.

Colin Hill

Prof. Colin Hill

Department of Microbiology, University College Cork


Professor Colin Hill is Associate Professor of Microbial Food Safety in the Departments of Microbiology and Food & Nutritional Sciences. He received his Ph.D. in Microbiology at UCC and went to North Carolina State University as a Research Fellow, working on the genetics of bacterial viruses.On returning to Ireland and to UCC, he started a research programme in food safety, primarily working on the molecular biology of bacteria of importance in foods. More recently his work has focused on the identification of bioactive compounds derived from bacterial and food sources.

Professor Hill was appointed by the Minister for Heath to the Scientific Committee of the Food Safety Authority of Ireland and has served in that capacity since 2001, was selected for a Scientific Panel of the European Food Safety Authority and was one of four scientists appointed to advise the Minister for Agriculture during the Foot and Mouth crisis in 2002.

He has published over 190 scientific papers, is an inventor on 10 patents, and has raised over €10 million in research funding in the last 10 years.He was awarded a D.Sc on the basis of published work in 2005. He is a Science Foundation Ireland Investigator since 2002 (renewed in 2006), and is a Principal Investigator in the Alimentary Pharmabiotic Centre.

Julian Marchesi

Dr. Julian Marchesi

School of Biosciences, University of Cardiff


Dr. Marchesi graduated from Cardiff University with a PhD in biochemistry (1992) and moved to work on the impact of genetically modified microbes on natural ecosystems. At this point he developed an interest in the contribution of uncultured microbes to the maintenance and function of ecosystems i.e. molecular microbial ecology.He followed his first post-doctoral position with a second position in Cardiff using molecular biological methods to investigate the deep biosphere ecosystem which exists below the sea-floor and developed molecular methods to investigate methanogens in this ecosystem. From this position he successfully secured a Wellcome Trust Fellowship to extend his molecular microbial ecology interest and investigate, with culture independent methods, the diversity and distribution of genes involved in biodegradation of priority pollutants.

After a short time investigating the deep biosphere he successfully obtained a Lectureship in the Department of Microbiology where he is assembling a team to investigate the human gut ecosystem in health and disease. His group is comprised of 6 post-docs, 4 PhD students and a technician who are using a variety of culture independent methods to analysis the gastrointestinal microbiota and its role in the maintenance and function of the host’s health. The main thrust is the use of functional metagenomic methods to determine the core functions in the human gut.

His group has developed novel approaches to investigate the role that microbes play in the human gut, in particular methods aimed at understanding the role of mobile genetic elements in gut function. Recently he has started to investigate, using metagenomic methods, the potential of marine sponge associated bacteria to provide novel bioactive agents and their application to the gut.

Recently he was awarded, in collaboration with Prof. Alan Dobson a Beaufort Marine Biodiscovery grant to expand this area of research. He has extensive experience in the area of metagenomics and molecular microbial ecology.

Denis O'Mahony

Dr. Denis O’Mahony

Department of Medicine, University College Cork


Dr. Denis O’Mahony is an academic clinician in the field of Gerontology, and consultant physician in Geriatric Medicine at Cork University Hospital and St. Finbarr’s Hospital, Cork since 1999. He also holds an appointment with University College Cork as Senior Lecturer in the Department of Medicine. His previous post was Senior Lecturer in Geriatric Medicine at the University of Birmingham where he was appointed in 1995.He is current chairman of the Elderly Services Division at Cork University Hospital. His other current activities include Dean of Examinations for the Royal College of Physicians of Ireland for the Cork Teaching Hospitals and co-ordinator of Specialist Registrar training in the South Munster SpR Training Scheme in Geriatric Medicine/General Internal Medicine.

Dr. O’Mahony is a former Secretary of the Irish Gerontological Society and was principal organiser of the IGS 50th anniversary conference in UCC in September, 2002. He is a current member of the British Geriatrics Society, the American Geriatrics Society, the British Association of Stroke Physicians and the British Society for Heart Failure. He is also a member of the Irish Heart Foundation Council on Stroke. His current research interests include age-related endothelial dysfunction and inappropriate prescribing in old age.

Paul Ross

Prof. Paul Ross

Moorepark Food Research Centre, Fermoy, Co. Cork


Professor Paul Ross is Head of Biotechnology at the Teagasc, Moorepark Food Research Centre (MFRC), Teagasc and a Principal Investigator in the Alimentary Pharmabiotic Centre (APC) at National University of Ireland, Cork.Paul graduated with a B.Sc. (Hons.) in Microbiology/Biochemistry in 1984 and with a PhD in Microbiology in 1989, both from NUI, Cork. He took up a post-doctoral fellowship at the Dept. of Biochemistry, Wake Forest University Medical Centre, Winston-Salem, NC, USA. While there, he was promoted to the position of Assistant Professor and was a founding faculty member of their Molecular Genetics Programme.

His main interests, while in the US, were the study of unusual flavoprotein oxidases from enterococci including NADH peroxidise. He returned to Ireland in 1993 to take up a Senior Research Officer position at Teagasc, Moorepark to lead the research programme on Dairy Biotechnology. In 1997, he was appointed as Head of the Dairy Quality Department and then further promoted to Senior Principle Research Officer in 2001.

Paul is now Head of the newly constructed Biotechnology Centre at Moorepark. His main research interests are in antimicrobial peptides and anti-infectives, probiotics, milk bioactives bacteriocins, probiotics, gut microbiology and functional foods. He has published 191 peer-reviewed publications and is an inventor on 13 patents. In addition, he has supervised 38 post graduates (including 19 Ph.D.s and 19 Masters). He also has coordinated or been a (co-)principle investigator on numerous national, EU and National Institute Health (US) grants.

Prof. P. Ross currently stands on National (Food Safety Authority of Ireland) and International (EFSA) committees dealing with GMOs and novel foods. He also is a member of the Executive Management Group of the Alimentary Pharmabiotic Centre, a virtual Centre between University College Cork and Teagasc (~ 100 scientists) devoted to the study of intestinal flora and their impact on human health. He is also on the Editorial Board of Applied and Environmental Microbiology.

In 2007, Paul received the William Haines Award in dairy Science from the California Dairy Research Foundation.

Fergus Shanahan

Prof. Fergus Shanahan

Department of Medicine, University College Cork & Alimentary Pharmabiotic Centre, University College Cork


Professor Fergus Shanahan received an honours medical degree from the National University of Ireland, Dublin in 1977. After internship and medical residency at the Mater Hospital, Dublin he did fellowships in clinical immunology at McMaster University in Ontario, Canada (1981-1983) and in gastroenterology at the University of California, Los Angeles (UCLA) (1983-1985). He was awarded Fellowships from each of four Colleges of Physicians (Ireland, United Kingdom, Canada and the USA).After finishing his training in gastroenterology at UCLA he was appointed Assistant Professor and subsequently Associate Professor of Medicine at the UCLA Centre for Health Sciences. In 1993 he took up his appointment as Professor and Chair of the Department of Medicine, University College Cork, National University of Ireland, Cork and consultant physician/ gastroenterologist, Cork University Hospital.

He is currently Director of the Alimentary Pharmabiotic Centre UCC, a research centre funded by Science Foundation Ireland and industry, and Director of the Biosciences Institute, UCC.

Catherine Stanton

Prof. Catherine Stanton

Moorepark Food Research Centre, Fermoy, Co. Cork


Prof. Catherine Stanton graduated with B.Sc (Hons) in Nutrition/Food Chemistry in 1983 and with M.Sc in Nutrition in 1986, both from University College, Cork. She did her PhD at Bournemouth University, UK in Biochemistry, graduating in 1988. After her PhD, she joined Johnson & Johnson UK, and later took a Postdoctoral Fellowship in the Department of Medicine, Wake Forest, University Medical Centre, Winston-Salem, NC, USA for 4 years, working on post-translational modifications of vitamin K dependent proteins, involved in blood clotting.In 1994, she joined Teagasc and over the past 14 years has built up the research programme on functional dairy foods. Her research interests include probiotics, microbial biogenic metabolite production, bioactive lipids, CLA/bioactive peptides and the nutritional aspects of dairy/functional foods. Prof. Stanton is an author of over 100 peer-reviewed papers. She is a Principal Investigator with the Alimentary Pharmabiotic Centre and on the ELDERMET project, with responsibilities for the lipid assays and metabolomics.
Douwe van Sinderen

Dr. Douwe van Sinderen

Department of Microbiology, University College Cork


Dr. Douwe van Sinderen is a senior lecturer in Microbiology, UCC, and has previously been involved in several FIRM projects (or its predecessor the NCFRP), such as 97/R&D/D/131 and 01/R&D/C/159, and is currently involved in 06/R&D/C/506. Furthermore, he is currently in receipt of various grants funded through SFI, EI, IRCSET and industry, and has been involved in several EU projects, either as participants or coordinator.Douwe van Sinderen’s research group currently consists of 16 scientists, who work on various themes that include the molecular biology of lactic acid bacteria and their infecting bacteriophage, and comparative and functional genomics of bifidobacteria. Part of his research group is involved in the SFI-funded Alimentary Pharmabiotic Centre, where he together with Dr. Paul O’Toole leads the Genomics and Bioinformatics research programme, which has allowed the establishment of a bioinformatics and genomics suite.


Eileen O'Herlihy

Dr. Eileen O’Herlihy

ELDERMET Project Manager

Eileen is Project and Clinical Trials Manager for the ELDERMET project. She has a B.Sc. in Plant Science (1995) and PhD in Plant Science (2002) from University College Cork. Since then she has worked on the following research projects:1999-2001: Researcher on EU Project FAIR5 PL97-3889: Health certification of rosaceous species based on disease-indexing of in vitro plants: validation of diagnostics and diagnostic strategies.
2002-2004: Research Project Manager on Enterprise Ireland Innovation Partnership, IP/2001/041: Mutation breeding in Phytophthora resistance pineapple (Ananas comosus).
2005-2008: Research Project Manager on Enterprise Ireland Innovation Partnership IP/2005/247: The Selection of Black Sigatoka (Mycosphaerella fijiensis) Resistant Banana (Musa acuminata) Mutants In Vitro in preparation for field trialling.
2009-2012: Research Project Manager of EU FP7 Grant Agreement No. 227522: Valorizing Andean microbial diversity through sustainable intensification of potato-based farming systems
2011: Enterprise Ireland Innovation Voucher R13990 IV-2010-3121 with CleanGrow Ltd.: Biofouling and its effects on CleanGrow multi-ion probesEileen also holds a Certificate in Quality Assurance and a Dip. in Quality Management.
Ian Jeffery

Dr. Ian Jeffery

Dr. Ian Jeffery completed his BSc in biochemistry in UCC. He went on to do a PhD in UCD where he completed his thesis on “Application and Evaluation of Data Analysis Methods for Gene Expression Microarrays”. He remained in Dublin during his early post-doc years working on gene expression regulation in microarray datasets and also participating in scientific collaborations with pharmaceutical company Servier and later with Lorraine Brennan working on diabetes and metabolic syndrome.Ian moved to Cork in 2010 and currently works as a senior Post-doc in the Paul O’Toole lab applying and adapting data analysis techniques to 16S high throughput sequencing datasets. His main research interests are the ELDERMET metagenomics project and the association between IBS and the microbiome.
Jennifer Deane

Ms. Jennifer Deane

Jennifer Deane graduated in 2008 from UCC with an honours degree in Genetics B.Sc. Her final project focused on the molecular population genetics of salmon in the south-east of Ireland. Jennifer was then employed by UCC Zoology department for four months as a research assistant with the Molecular Fisheries lab led by Prof. Tom Cross. In April 2009 Jennifer joined Dr. Paul O’Toole lab as a research assistant with APC, UCC as part of a project investigating bacterial profiles of IBS patients in comparison with healthy subjects using pyrosequencing.In April 2011 she joined the ELERMET team. Her main duties are faecal DNA extractions, amplification of the 16S gene through PCR for sequencing, analysis of cytokines in serum and plasma samples and cortisol analysis in saliva samples. Jennifer’s research interests include Microbiology and bacterial composition of the gastrointestinal tract influencing health and disease.
Guillaume Borrel

Dr. Guillaume Borrel

Dr. Guillaume Borrel graduated with a Masters in Biodiversity & Functioning of Ecosystems in 2007 and a PhD in 2011 from the Université Blaise Pascal in Clermont-Ferrand, France. His doctoral thesis dealt with the archaeal diversity and the contribution of microorganisms to methane cycling in freshwater lake environments. One of his investigations focused on a putative new order of methanogens, occurring in lake water columns, which was previously discovered in the human gut of elderly people.In 2011 his interest for this yet uncharacterized archaeal lineage led him to a postdoctoral position with the team of Dr. Jean-Francois Brugère at Université d’Auvergne (Clermont-Ferrand). There, his work consisted in cultivating a representative of this lineage from elderly gut, then to sequence and analyse its genome, in collaboration with the team of Prof. Paul O’Toole. Guillaume joined the ELDERMET project as a postdoctoral researcher in 2013 to investigate the interactions between methanogens, elderly gut microbiota and health.
Anne-Marie Cusack

Ms. Anne-Marie Cusack

Anne-Marie qualified as a general nurse at CUH and practiced in the areas of general nursing, care of the elderly, learning disabilities and nursing management. She was awarded a Masters in Public Health and Epidemiology from UCC in 2012.In February 2013 Anne-Marie joined the ELDERMET team from the Irish Blood Transfusion Service where she worked as a clinical nurse manager. She has considerable experience in patient care and also working with the elderly having been employed in different care facilities. Her role in the project as a research nurse will be based in St. Finbarr’s Hospital and her duties will include subject recruitment, sample and data collection.
Aisling Murphy

Ms. Aisling Murphy

Aisling graduated with a BSc in General Nursing and has worked in the areas of Surgical and Medical nursing in CUH, Intellectual Disability and has extensive experience in Care of the Elderly. Aisling took a break from nursing in ’08 to work in the Sales field in Danone Nutrition with Nutricia. Responsible for sales and promotion of Oral Nutritional Products in the community, she developed a keen interest in the link between diet and health.Aisling joined the ELDERMET team in August 2013 as a Clinical Research Nurse, from a Care of the Elderly ward. She is based in St. Finbarr’s Hospital and is involved in subject recruitment, sample and data collection.
Mairead Coakley

Ms. Mairéad Coakley

Mairéad graduated with a B.Sc. (Hons) in Microbiology in 1994 from NUI, Cork and with a M.Sc. in 1996, which was undertaken at Teagasc, Moorepark and NUI, Cork. She joined the R&D Centre at Diageo, St. James’ Gate, Dublin where she worked as a Research Officer for 5 years. Work with Diageo included yeast strain identification and differentiation, fermentation, yeast management, product development and process development. While at Diageo Mairéad completed the Institute of Brewing (London) AME examinations.In 2001, she joined Teagasc as a Research Officer and has worked on projects relating to the health promoting fatty acid, conjugated linoleic acid (CLA). Mairéad currently works on the ELDERMET project, based in the Food BioSciences Dept. at the Teagasc Food Research Centre, Moorepark. She is involved in tasks relating to microbiology and fatty acid analysis.
Dr. Marcus Claesson

Dr. Marcus Claesson

Dr. Marcus Claesson did his undergraduate as a BSc in Chemical and Physics Engineering at Chalmers University of Technology in Gothenburg, Sweden. He soon discovered that chemical engineering was not his cup of tea, and made a drastic change towards the MSc programme in Bioinformatics at the same university. Following his MSc Thesis project at AstraZeneca Mölndal, he worked for a year at the start-up biotechnology company AngioGenetics, assisting their research in angiogenesis by setting up and managing databases of mouse cDNA sequences. This was interrupted by the opportunity to start a PhD for Dr. Douwe van Sinderen at the Microbiology Department at University College Cork.The main part of the PhD project was dedicated to sequence, assemble and analyse a commensal Lactobacillus strain, where the major outcome was the discovery of a mega-plasmid, with a size never seen in any other lactic acid bacteria.

Once completed, Marcus worked for nine months at the campus-based biotechnology company Alimentary Health, data mining bifidobacteria for beneficial probiotic traits. This was followed by a longer postdoctoral position in Dr. Paul O’Toole’s lab in the Microbiology Department, where Marcus is now focusing on the bioinformatics involved in the ELDERMET metagenomics project, aiming to sequence the gut-bacteria of hundreds of elderly Irish citizens. As such, next-generation sequencing plays a crucial roll in producing vast amounts of sequence data.

Dr. Orla O'Sullivan

Dr. Orla O’Sullivan

Dr. Orla O’Sullivan is a Research Officer in the Department of Biotechnology at the Moorepark Food Research Centre (MFRC), Teagasc. Dr. O’Sullivan graduated with a B.Sc. (Hons.) in Biochemistry in 2000 and with a PhD in Bioinformatics in 2004 both from National University Ireland, Cork.She took up a post-doctoral fellowship at the Conway Institute of Biomolecular and Biomedical Research at University College Dublin in 2004 investigating methods of improving the accuracy of multiple sequence alignment programs thought the use of weighting schemes and three dimensional protein structures. Orla spent times as a lecturer and senior demonstrator in the Department of Biochemistry in NUI, Cork in 2005, lecturing in such areas as molecular biology, cell signally and bioinformatics.

She joined Teagasc in 2006 as a bioinformatics research officer. Her main areas of research are genome sequencing and annotation, comparative genomics, homology modelling and structure prediction, protein-peptide binding and bioactive discovery. She has 9 peer-reviewed publications as well as 3 conference papers.

Orla joined the ELDERMET Project team in January 2008 and will be responsible for all bioinformatic tasks in the project, including the establishment of a dedicated bioinformatics platform for analyzing microbial communities and metagenomic data, analysis of the microbial composition data generated and analysis of the metabolomic data.

Mary Rea

Dr. Mary Rea

Mary Rea is a graduate of University College Cork where she was conferred with a BSc (Hons) and subsequently with an MSc in Microbiology. She worked as a research assistant on a Medical Research Council grant studying the transport of drugs across membranes in the Clinical Chemistry Department in St. Finbarr’s Hospital and later took up a position for three years as research officer with An Foras Taluntais in Moorepark in Fermoy. During that time, her work involved studying Staphylococcus aureus of mastitis origin with particular reference to isolation methods and toxin production.Following a career break she rejoined An Foras Taluntais (now known as Teagasc) in 1988, where she has worked on a wide variety of projects including milk quality, modelling the growth of Listeria monocytogenes in dairy foods, biodiversity of lactic acid bacteria in artisan dairy products, citrate metabolism in enterococci, amino acid catabolism in lactic acid bacteria and genotyping smear cheese bacteria to track strain diversity in smear cheeses during ripening.

More recently she has been part of The Cork Bacteriocin Group and works with scientists in the Alimentary Pharmabiotic Centre based in the Food Biosciences Department, Teagasc Food Research Centre, Moorepark where her research has focused on gut microbiology and bacteriocins most specifically isolating and characterising Clostridium difficile strains from clinical samples and screening for, and characterising novel antimicrobial peptides with activity against C. difficile and other gut pathogens. She was awarded a PhD in Microbiology from University College Cork in 2011 for her work on the isolation and characterisation of thuricin CD, a novel anti-C. difficile bacteriocin.

In addition to presenting various conference papers, she has published in the area of milk quality, cheese microbiology, food safety, gut microbiology and bacteriocins and is listed as an inventor on two patents. Within the ELDERMET project she is responsible for the isolation and characterisation of C. difficile strains cultured from faecal samples.