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Microbio group
UMR STLO Unit
Research
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.

chef_equipe_microbio

 

Éric Guédon
eric.guedon@inrae.fr
Tel : 02 23 48 52 70

 

Objectives

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

Strategies

  • 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)

Expertise

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

 

Microbio team members
© STLO - N. Daniel
  • Technician & Assistant engineer: Fabienne Gonnet, Noël Grosset, Véronique Lebret, Jessica Musset, Sandrine Parayre, Sandrine Péron, Lucie Rault, Danièle Vassaux
  • Scientist: Nadejda Berkova, Florence Baron, Sylvie Bonnassie, Nathalie Daniel, Stéphanie Deutsch, Clara Douadi, Sergine Even,  Valérie Gagnaire, Michel Gautier, Éric Guédon, Gwénaël Jan, Sophie Jan, Yves Le Loir, Marie-Bernadette Maillard, Aurélie Nicolas, Nathalie Roland, Anne Thierry
  • Fixed term contract: Juan Ariute Oliveira, Céline Even, Marina Giblaine, Gabriela Munis Campos

 

PhD and post-doctoral students

  • MITEUL Adèle 2025 / Post-Doc / ANR Biofores
  • TREBOSSEN Ewen 2024 / Thèse / Supervision: Gagnaire V. / Jan G. - Production et utilisation des protéines de lupin : ré-émergence d'une légumineuse orpheline grâce aux associations d'espèces
  • ANDRADE Bruno 2023 / Post-doc / Supervision: Guédon É
  • FRANJUS Cyril 2023 / Thèse / Supervision: Guédon É / Nicolas A. Expression et localisation d’entérotoxines de Staphylococcus aureus nouvellement décrites lors d’une croissance en produit laitier
  • CHOUDHURY Adrija 2023 / Thèse / Supervision: Falentin H /Deutsch S - Antifungal action of Fermented Vegetable Juice
  • GUIMARAES LAGUNA Juliana 2023 / Post-doc / Supervision: GUÉDON Eric
  • PAPAIL Julia 2022 / Thèse / Supervision: GUÉDON Eric - Role of small RNAs transported by extracellular vesicles from Staphylococcus...

 

Projects

SATORIX (2025-29) The SaToRix project aims to assess the risks of staphylococcal food poisoning outbreaks associated with plant-based foods i) by finely characterizing Staphylococcal enterotoxins (SE) producing strains, particularly new SEs, using omics approaches, ii) by studying their behavior and their toxinogenic capacities in various types of plant matrices and iii) by developing extraction and identification procedures adapted to these matrices and able to identify the most commonly found new SE.

BIFORES (2024-29) : The BIFORES ANR project proposes to rethink the production routes of infant formula in order to make them more biomimetic, while meeting the safety and environmental challenges associated with these products. This multidisciplinary project, coordinated by STLO, involves UMR NUMECAN, SECALIM, MEDIS and the BBA Milk Valley consortium as partners.

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.

In this folder

For pictures of bacterial cells observed with a microscope

From cow's milk to soy juice, when yoghurt cultures have to adapt

Know more

Plant-based yoghurts are allies in the food transition because they represent a great opportunity to reduce the amount of animal protein in our diet in favour of plant protein. While the selection of cultures for the production of dairy yoghurts has benefited from many years of research, the selection of cultures for making plant-based yoghurts is still in its infancy. However, in this context of plant-based diets, the challenges are considerable: the quality of these plant-based yoghurts depends on the choice of starter cultures (masking off-notes, breaking down compounds that cause digestive discomfort, for example).

Several glass jars of “Yalup” yogurts

Spotlight on fermented milk-lupin mixes!

Know more

In an article published by The Conversation and on INRAE's institutional website, Valérie Gagnaire, Research Director (Microbio Team), talks about the results of Fanny Canon's PhD and the avenues this work has opened up for STLO in the design of yogurt substitutes based on milk and legumes.

Gut cells and propionibacteria

The cheese-born probiotic bacterium Propionibacterium freudenreichii strengthens the intestinal epithelial barrier

Know more

The increasing incidence of diseases involving inflammation and increased intestinal permeability makes the search for protective functional foods more crucial than ever. Propionibacterium freudenreichii is a beneficial bacterium isolated from cheese, used in dairy and probiotic applications. Some strains have proven anti-inflammatory effects in vitro and in vivo. This protective effect was further clarified in vivo where the integrity of the intestinal epithelial barrier was preserved, when subjected to inflammatory stress.

Carottes lactofermentées

Do you know fermented vegetables ?

Know more

Fermented vegetables, traditional in Asia and Eastern Europe, are booming in Western countries. They are made using a simple process consisting of incubating cut and salted raw vegetables, packed in jars in their juice or in brine, at room temperature. Fermented vegetable, apart sauerkraut, are mainly produced on a domestic and artisanal scale by spontaneous fermentation, which raises questions about their health safety.

mCherry cells

The wolf in the sheepfold: how S. aureus penetrates host cells...

Know more

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

Nyons Table Olives: a microbial diversity to be treasured !

Know more

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: 13 October 2025 | Publication date: 25 October 2022 | By: stlo