Microbio group

Microbiology of Milk and Egg Sectors group

Microbio team is interested in bacteria of the food chain: i) bacteria used to produce fermented foods from milk, plants or legumes, ii) some pathogenic and spoilage bacteria of the milk and egg industries. In these bacteria, we study the important properties that impact the quality and safety of food, and the beneficial effects on human health.


Éric Guédon
Tel : 02 23 48 52 70



Our objective is to understand the properties of bacteria, the interactions and the functioning of bacterial communities in the dairy and egg industries, from the production of raw materials to the food at the consumer's via the processing.  We thus wish to :

  • Contribute to the development of healthy, safe and good food
  • Develop foods with health benefits for target populations
  • Diversify protein sources in fermented foods
  • Reduce losses and waste through fermentation
  • Develop probiotic approaches to prevent mastitis in milk producing animals


  • Multi-scales approaches: from gene to food, through RNA and protein; from bacteria in monoculture to bacterial communities
  • Multi-systems approaches: from model systems (in culture medium) to real systems (fermented feed, udder, egg products, ...)
  • Multi-disciplinary approaches : bacterial- (and meta) genomics, transcriptomics and proteomics, targeted metabolomics (peptides, sugars, amino acids, organic acids, volatile organic compounds), bioinformatics (molecular modelling, reconstruction of synthethis pathways), food fermentation, metabolism in relation to bacterial physiology, cell biology for the study of bacterial properties (models in relation to inflammation, intestinal permeability and persistent infection)


The team Microbio has different objects of study:

  • Propionic bacteria and lactic acid bacteria, key players in food fermentation
  • Staphylococcus aureus, and other pathogenic and spoilage bacteria in egg products

The research topics include:

  • Mechanisms of adaptation, resistance and defense of bacteria
  • Production by fermentation of functional ingredients and molecules of technological, nutritional and health interest (flavors, antimicrobial compounds, vitamins, ...)
  • Diversification of foods by fermentation of mixed milk/vegetables
  • Mechanisms of the antimicrobial activity of egg white
  • Bacteria-bacteria, bacteria-host, bacteria-food matrix interactions and intercellular communication
  • Development of probiotics in human and animal health
  • Production of extracellular vesicles

The team

Picture of the Microbio Team in 2023
  • Technician & Assistant engineer: Fabienne Gonnet, Noël Grosset, Véronique Lebret, Marie-Bernadette Maillard, Jessica Musset, Sandrine Parayre, Sandrine Péron, Lucie Rault, Danièle Vassaux
  • Scientist: Nadejda Berkova, Sylvie Bonnassie, Nathalie Daniel, Stéphanie Deutsch, Sergine Even, Hélène Falentin, Valérie Gagnaire, Michel Gautier, Éric Guédon, Marielle Harel-Oger, Gwénaël Jan, Sophie Jan, Yves Le Loir, Aurélie Nicolas, Nathalie Roland, Anne Thierry
  • CDD/pHD/post-doct: Sarah Blanchet, Rodrigue Brossaud, Adrija Choudhury, Céline Even, Cyril Franjus, Marina Giblaine, Coralie Goetz, Koffigan Kponouglo, Juliana Laguna, Charles Le Bras, Julie Legros, Julia Papail, Marine Penland, Charles Silande




LOCALNUTLEG (2021-24): LOCALNUTLEG aims to boost the use of local Mediterranean nuts and legumes through the development of innovative, high value-added food products, making the Mediterranean diet more attractive.

PROLIFIC (2020-25) : PROLIFIC (PROduits Laitiers et Ingrédients Fermentés Innovants pour des populations Cibles) aims to assess the health benefits of fermented dairy products for young children and senior citizens. PROLIFIC is supported by a consortium of Bba Milk Valley industrialists and research teams from Brittany and the Loire Valley.

FAIRCHAIN (2020-24): Innovative technological, organisational and social solutions for FAIRer dairy and fruit and vegetable value CHAINs. The project tests or develops technological, organizational and social innovations to increase the production of nutritious food at an affordable price. Within this framework, STLO is working on the development of a fermented drink based on cheese whey.

ANR EQLIPSE (2019-23): Enhancing the Quality and the Level of Internal Protections of Shell Eggs. EQLIPSE is set against a backdrop of longer rearing periods for laying hens. It aims to study the consequences of this lengthening on egg quality and natural defenses, and to identify levers for controlling internal egg alterations induced by hen age and egg storage conditions.

FUI PROBIOVEG: ProbioVeg aims to develop new plant-based fermented foods within a framework of sustainable exploitation of the techno-functional and probiotic properties of ferments.

In this folder

mCherry cells
Staphylococcus aureus, an opportunistic pathogen, causes a wide range of illnesses, from benign skin infections to potentially fatal food poisoning. It is also one of the main bacteria responsible for nosocomial infections in France. Initially thought to be extracellular, S. aureus has recently been detected inside various cell types of infected hosts. Identifying the biological processes involved in the cellular response to S. aureus is necessary to understand the mechanisms of chronic infection, and to develop methods of combating it.
Nyons Table Olives
Artisanal fermented foods constitute a significant part of the Mediterranean diet and represent a cultural heritage that needs to be preserved and protected. Nyons table black olives are produced in south-eastern France, and benefit from a PDO Label. They are produced according to a traditional process by a slow spontaneous fermentation in brine, i.e., without any starter adjunction. The manufacture and unique sensorial properties of these olives thus only relies on autochthonous complex microbiota, which we have deciphered.

Modification date: 22 February 2024 | Publication date: 25 October 2022 | By: stlo