Paul O’Toole APEX

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Paul O’Toole

Position: Professor of Microbial Genomics
Principle Investigator, APC Microbiome Institute UCC
Founder and Research Leader, 4D Pharma Cork Ltd.
Professional New Zealand Microbiological Society
memberships: American Society for Microbiology
Society for General Microbiology, UK

Education: BA (Mod), Ph.D. Dept. Microbiology, Trinity College Dublin.

Career development: Post-doctoral training in Lund, Sweden; Victoria BC, Canada
Lecturer and Senior Lecturer in Massey University, New Zealand
Sabbatical visitor, GSK Pharma, Philadelphia USA
UCC since July 2002.

Research themes: Gut commensal bacteria in health and disease
Paul O’Toole is Professor of Microbial Genomics at University College Cork, Ireland. His main research theme is the genomics and metagenomics of gastrointestinal bacteria in humans with emphasis on commensal species. He runs several major projects that examine the composition and function of the gut microbiota, its reaction to habitual diet, and its relationship to health, functional gastrointestinal disorders, ageing and cancer. The ultimate aim of these investigations is to understand host-microbiome interactions, especially in the context of multi-factorial disease. He co-ordinated the ELDERMET project ( that established diet-microbiota health interactions in the elderly, and he leads a project called ELDERFOOD that is investigating novel foods for healthy aging targeting the microbiome. He is a Principal Investigator in the APC Microbiome Institute (, in which he leads projects on microbiota as a modulator of disease risk in aging and colorectal cancer. He is a co-founder of Tucana Health Ltd., now operating as 4D Pharma Cork Ltd., which is developing microbiome profiling as an adjunct to health management and development of Live Biotherapeutics. His lab is supported by Science Foundation Ireland, Dept. Agriculture Fisheries and Marine, Health Research Board, and the EU.
Methods & goals: Bacterial genomics and comparative genomics
Microbiota composition and function using next-gen. sequencing
Microbiota alterations and cancer, loss of cognitive function
Culturing and studying the gut microbiota
Modulating the microbiota using diet
Archaea and cardiovascular disease
Faecal microbiota transplantation
Sample papers: (Please see: for full list)

1. Claesson, M.J., I. B. Jeffery, S. Conde, S. E. Power, E. M. O’Connor, S. Cusack, H. Harris, M. Coakley, B. Lakshminarayanan, O. O’Sullivan, G. F. Fitzgerald, J. Deane, M. O’Connor, N. Harnedy, K. O’Connor, D. O’Mahony, D. van Sinderen, M. Wallace, L. Brennan, C. Stanton, J R. Marchesi, A. P. Fitzgerald, F. Shanahan, C. Hill, R. P. Ross, and P. W. O’Toole. 2012. Gut microbiota composition correlates with diet and health in the elderly. Nature 488: 178-184.
2. O’Toole, P.W. and I.B. Jeffery. 2015. Gut microbiota and aging. Science 350: 214-5.
3. Sun Z, Harris HM, McCann A, Guo C, Argimón S, Zhang W, Yang X, Jeffery IB, Cooney JC, Kagawa TF, Liu W, Song Y, Salvetti E, Wrobel A, Rasinkangas P, Parkhill J, Rea MC, O’Sullivan O, Ritari J, Douillard FP, Ross R, Yang R, Briner AE, Felis GE, de Vos WM, Barrangou R, Klaenhammer TR, Caufield PW, Cui Y, Zhang H, and O’Toole PW. 2015. Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nature Communications Sep 29;6:8322.
4. B. Flemer, D. B. Lynch, J.M.R. Brown, I. B. Jeffery, F. J. Ryan, M. J. Claesson, M. O’Riordain, F. Shanahan, & P. W. O’Toole. 2017. Tumour-associated and non-tumour-associated microbiota in colorectal cancer. Gut 66(4):633-643.

Contact details:  E-mail: Tel: +353 21 4903997
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