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Pauline Scanlon


I am a multi-disciplinary researcher focused on applying hypothesis driven approaches to study the ecology and evolution of the human gut microbiome. I have a BSc. in Plant and Microbial Biotechnology (2002) and a PhD in Medicine (2007) from University College Cork, Ireland (UCC). As part of my research training to date I have worked at a number of internationally renowned Universities (Wageningen University (2003-2004) and University of Oxford (2008-2012). In 2013 I returned to Ireland after successfully securing a Marie Curie- Skłodowska Fellowship to work at Moorepark, Teagasc, and in 2016 I established my own laboratory group at APC Microbiome Ireland, funded by a prestigious Royal Society-Science Foundation Ireland University Research Fellowship, which was extended in 2021 for a further three years. In 2017 I was appointed as a lecturer at the School of Microbiology, UCC. To date, I have established numerous international (Prof. Rob Knight (UC San Diego), Prof. Maria Dominguez-Bello (Rutgers, NY), Prof. Alex Hall (ETH Zurich)) and national (Prof. Paul Cotter (Moorepark, Teagasc), Prof. Colin Hill (APC Microbiome Ireland, UCC)) collaborations, and my research has been published in many high-impact world leading journals e.g. Cell Host and Microbe, Trends in Microbiology, Trends in Parasitology, Ecology Letters, ISME and Molecular Biology and Evolution.

I am currently developing a number of research themes in my laboratory, and a primary focus is to study the effects of different chemicals, such as antibiotics, and xenobiotics that contaminate the food chain (e.g. pesticides and herbicides), on the ecology and evolution of the human gut microbiome. This research specifically addresses how the ecological and evolutionary response of the gut microbiota to chemical exposure varies by chemical class and concentration, and what member species are most adversely affected. Crucially this research also addresses if and how resistance evolves in response to chemical selection, and if exposure to one specific chemical (e.g. herbicide or pesticide) can also select for generalist cross-resistance to other chemicals e.g. antibiotics. In addition to providing much needed fundamental understanding of how potentially lethal selection pressures impact the diversity and function of the gut microbiome, this research tackles key societal, environmental, and public health challenges and has important practical implications for antibiotic stewardship as well as the production of safe foods.

Research Interests

Research Theme: Microbes to Molecules 

SDGs:  SDG 3 Good Health and Well Being and SDG 2 Zero Hunger (e.g. access to safe food). (Research tackles both AMR and SFS).

Research key words: Gut microbiome, anti-microbial resistance, safe food, antibiotics, herbicides, pesticides, xenobiotics, cross-resistance, microbial evolution, microbial ecology, Anthropocene




APC Microbiome Ireland, Biosciences Building, University College Cork, Ireland,