Session A

Microbial ecology: Starters, adjunct and indigenous microbiota

Analysis of cheese microbiomes highlights contributions to multiple aspects of quality.

Prof Paul Cotter (PhD), Head of Food Biosciences, Teagasc Food Research Centre Moorepark, Cork, Ireland
Prof Paul Cotter is the Head of Food Biosciences at Teagasc and a Principal Investigator with the large Irish Research Centres, APC Microbiome Ireland, Vistamilk and Food for Health Ireland. He also co-ordinates an EU H2020 Innovation Action relating to microbiomes and the food chain, MASTER (€10.9 mi budget). Paulalso heads the Teagasc DNA high throughput sequencing facility. He is a molecular microbiologist, with a particular focus on the microbiology of foods, the food chain and of humans as well as antimicrobial peptides/bacteriocins. Prof Cotter’s laboratory are multiple winners at the Irish Laboratory of the Year Awards, he has received awards from the Society for Applied Microbiology, ESCMID and FEMS, and heads the Applied Microbiology section within Faculty of 1000 (Biology). Prof Cotter is also the author of >350 peer-reviewed publications resulting from research funded by industry as well as funding agencies in Ireland, Europe and the US and was included in the Clarivate list of highly cited researchers for 2018, 2019 and 2020. Paul is also a co-founder and CTO of SeqBiome, a spin-out company that provide custom DNA sequencing and bioinformatics services for microbiome analysis.


Matching starter phenotype to functionality for low salt Cheddar cheese production based on viability, permeability, autolysis and enzyme release characteristics in model systems.

Martin G. Wilkinson, M.Sc. Ph.D, Associate Professor, Department of Biological Sciences, University of Limerick, Ireland.
Martin Wilkinson is currently Associate Professor in Food Microbiology at the University of Limerick (UL) and lectures on the B.Sc in Food Science and Health degree programme at UL. Prof Wilkinson has 35 years of research experience in the dairy sector has published extensively. His research interests are in cheese and dairy technology, cheese starter microbiology, development and safety aspects of reformulated low salt/low foods and since joining UL he has also developed a particular specialisation in the use of flow cytometry and cell sorting for the study of cheese starter culture permeabilization, autolysis and intracellular enzyme release during cheese ripening. He recently undertook a sabbatical with Prof Gisèle LaPointe at the University of Guelph and jointly published a review and research article related to cheese starter microbiology.


Bacteriophages on the cheese surface: what diversity and what ecological role?

Eric DUGAT-BONY, Ph. D., Paris-Saclay Food and Bioproduct Engineering Research Unit (SayFood), INRAE, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, 78850 Thiverval-Grignon, France
Research scientist at INRAE in the Paris-Saclay Food and Bioproduct Engineering Research Unit (SayFood), Eric Dugat-Bony is a microbial ecologist working on the structure and functioning of microbial ecosystems. During his PhD at Blaise Pascal University with Dr Corinne Petit (2008-2011, Clermont-Ferrand, France), he developed functional DNA microarrays and related bioinformatic solutions in order to monitor microbial populations involved in the bioremediation of contaminated groundwater. Then, he moved to the University of Lethbridge (2012-2013, Alberta, Canada) for a postdoctoral position with Pr Brent Selinger to study the relationship between disbyosis of the cattle intestinal microbiota and the shedding of Escherichia coli O157:H7 with metagenomic tools. Since his recruitment at INRAE in 2013, he developed research projects to understand the effect of biotic (e.g. diversity level, microbial interactions, bacteriophages) and abiotic (e.g. NaCl content, temperature, oxygen level) factors inducing perturbations of the stability and functioning of the microbial ecosystem involved in food fermentation. His favorite model ecosystem is the cheese surface. Eric is also Associate Professor at Université Laval (Québec), where he spent one year (2018-2019) as a visiting scientist for studying cheese fungi with Pr Steve Labrie.