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24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

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Cheese Microbial Ecosystems

Understanding and dynamics of cheese microbial ecosystems

Understanding and controlling cheese microbial ecosystems represents a major scientific, economic and safety challenge. These ecosystems can in fact be considered as an important part of our cultural heritage and constitute a unique resource for the food industry. The cheese microbial community is quite complex, ranging from tens to hundreds of different micro-organisms. It is composed of diverse bacteria, yeast and fungi, all culturable, whose density can be > 100 billion cells per gram of cheese and whose development is closely related to the ripening process. Micro-organisms largely contribute to cheese organoleptic properties and safety. For example, different types of metabolic cooperation between different strains that lead to important technological properties of cheese such as flavour compound production have been identified. However, most of the action mechanisms responsible for cheese quality are not yet fully understood. Therefore, the cheese microbial ecosystem provides a unique opportunity to study (i) consortia composed of both eucaryotes and procaryotes, and (ii) microbial interactions in a natural environment. In addition, the physico-chemical composition of food products and abiotic conditions governed by transformation process are rarely taken into account in studies aimed at controlling microbial developments and the resulting functionalities. We are convinced that only an integrative and global view of microbial ecosystems will make it possible to understand the complex mechanisms behind the diversity of cheese products.

Our activities in a few keywords

  • Acquisition of knowledge concerning microbial diversity and dynamics;
  • Expression studies focusing on functions of interest in ripening bacteria and yeasts;
  • Understanding the adaptation of micro-organisms to the cheese environment.
Our research objective: to manage cheese microbial ecosystems and their functionalities, to more effectively control the ripening process, and to develop molecular biomarkers of biological functions.

The cheese ecosystem as a model

  • Low complexity (< 10 species)
  • Culturable Micro-organisms/genomes available
  • Quantifiable functionalities (e.g., flavour compounds (CSVs), colour, barrier effect, deacidification, proteolysis, lipolysis)
  • Strategic industrial (e.g., fermented products) and safety (e.g., immunomodularity effect) challenges.

Our research questions

  • What is the phylogenetic diversity of microbial fluxes from incoming ingredients to the final products?
  • What are the genetic determinants involved in the adaptation of micro-organisms to their environment?
  • What is the impact of abiotic factors (salt reduction, biogenic amine) on the structure, the activity of micro-organisms and the global productivity of the ecosystem?
  • How do cheese micro-organisms behave in the digestive tract and what are the possible interactions with the host?
Étude intégrée écosystème fromager

Ongoing projects

ANR (National Research Agency)

ExEco (2010 –2014) : A joint meta-transcriptomic and biochemical approach of the cheese ecosystem: for an improved monitoring of the EXpression of a complex food ECOsystem.
Coordinator: Pascal Bonnarme

INRA (National Institute for Agricultural Research)

AIC EcoBiot (2013 – 2014) : Impact of the composition of the milk matrix on the behaviour of micro-organisms from dairy products during digestion and on the structuration of the intestinal microbiota?
Coordinator: Daniel Picque

MEM EcoStab (2013 - 2015) : Stability and functional redundancy of a microbial ecosystem.
Coordinator: Jean-Marie Beckerich

MEM FORTRESS (2015 - 2016) : Impact of microbial diversity on the barrier effect against an exogenous species.
Coordinator : Eric Dugat-Bony

MEM MICROFIT (2016 - 2018) : Unraveling the genetic determinants of fitness of a food microorganism in its natural ecosystem by a Tn-seq approach (massive sequencing of transposon insertion libraries).
Coordinator : Catherine Madzak

MEM VIROME ACCESS (2016 - 2018) : Accessing to virus genomes out of metagenomics data: improving statistical and bio-informatics analytic tools to better assess the contribution of phages on microbial ecosystems.
Coordinator : Stéphane Chaillou

Industrial contracts

CNIEL Collective data Genome (2011 - 2013) : Genomic catalog of 150 bacteria isolated from cheese.
Coordinator: Pierre Renault

Nestlé NESTEC (2011 - 2014) : Biogeneration of sulfur-containing aroma compounds from fermented vegetable.
Coordinator: Pascal Bonnarme

Syndifrais EcoDige (2012 – 2015) : Does cheese microflora survive during the digestion process and can micro-organisms have immuno-modulatory effect on the host?
Coordinator: Pascal Bonnarme

FranceAgriMer REDSEL (2014 - 2016) : Reduction / substitution of salt in cheese : impact on the development of the technological microbiota and on the growth of potential spoilage microorganisms.
Coordinator : Sébastien Fraud

PhD projects

More information about ongoing PhD projects at EcoMic as well as PhD theses recently defended at GMPA is available at the corresponding web pages.


Members can be contacted:

  • by phone: +33 (0)1 30 81 + extension (click on the member name)
  • par e-mail: firstname.lastname[at]

Permanent staff


Marie-Noëlle Bellon-Fontaine (Professor, AgroParisTech)

Thibault Caron (PhD Student)

Pascal Bonnarme (Research Director, INRA)

Valentine Chartrel (PhD Student)

Alice Danel (Research Technician, INRA)

Célia Carbonne (Study Ingeneer)

Eric Dugat-Bony (Researcher, INRA)

Cynthia El-Youssef (PhD Student)

Gilles Gerlot (Research Technician, INRA)

Thomas Paillet (PhD Student)

Morgan Guilbaud (Research Ingeneer, AgroParisTech)

Carolane Auguet (Assistant Ingeneer)

Sandra Helinck (Assistant Professor, AgroParisTech)

Jean-Marie Herry (Study Ingeneer, INRA)

Françoise Irlinger (Research Ingeneer, INRA)

Sophie Landaud (Professor, AgroParisTech, Team leader)

Catherine Madzak (Researcher, INRA)

Christophe Monnet (Researcher, INRA, Team leader)

Anne-Sophie Sarthou (Research Technician, INRA)

Anne-Claire Peron (Research Technician, AgroParisTech)

Margareth Renault (Assistant Ingeneer, INRA)

Dominique Swennen (Researcher, INRA)

Stéphane Thomas (Research Technician, INRA)

Publications 2008-2020