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Research topics

The AFIM team is dedicated to food microbiology, the quality of fermented foods and microbiota/host interactions.


Thanks to the multidisciplinary association of scientists, the organisation of research is based on a dynamic and collegial structure around 4 main topics:

  • Microorganisms and environment
  • Microorganisms/microorganisms
  • Microorganisms and fermented products
  • Microorganisms/hosts

    Research questions


    Understanding the adaptation processes of microorganisms:molecular modifications and interaction phenomena.





    Adaptive response of microorganisms to their environment

    1. Circulation of microorganisms in a given ecosystem.

    2. Effects of inputs used on food raw materials or their processing on the development of targeted or non-targeted microorganisms

    3. Molecular, genetic and physiological mechanisms put in place to produce an adaptive response to their environment or a specific stress.

    Complex interactions between micro-organisms and micro-organisms

    1. Antagonism via the production of antimicrobial molecules.

    2. Competition for nutrients.

    3. Production of membrane vesicles.

    4. Influence of interactions on the gene expression profile of microorganisms.

    Microbial fermentation or transformation: quality control

    1. Controlling fermentation and developing new sourdoughs to ensure the organoleptic and sanitary quality of the product.

    2. New technological routes for low chemical input production

    3. Sustainability and value creation

    Microorganism/host interactions in complex ecosystems

    1. Mechanisms associated with the interaction of the microbiota with digestive epithelial cells.

    2. Impact of microbial resistance on microbiota-host relationships.

    3. Probiotic micro-organisms and the development of innovative formulations for their administration.

    4. Modulation of the oral microbiota and its impact on taste perception.

    5. The relationship between food and microbiota.


    Micro-organisms are constantly adapting to their environment by developing strategies for adapting to different perceived modifications (biotic or abiotic stresses) that bring different mechanisms into play. The scientific question is therefore to understand the mechanisms that enable the circulation of micro-organisms between environments and therefore the colonisation of different ecosystems (soil, water, food matrices, human body, ...). The knowledge acquired will make it possible to find ways of promoting or limiting the development of certain micro-organisms in a given environment, while ensuring the food and/or health quality of the environment studied.


    Whatever the type of environment, micro-organisms live as part of microbial communities, with varying degrees of diversity, in which they interact continuously. Interactions between micro-organisms are based on multiple mechanisms and are mediated by molecules of different chemical natures (proteins, nucleic acids, polysaccharides, lipids, ...).

    Understanding these complex interactions at the molecular level is essential for mastering industrial processes based on the use of micro-organisms (winemaking, cheese production, development of new fermented beverages, formulation of probiotics, ...).

    The development of a fermented product is the result of interactions between micro-organisms, a raw material and a technological route. This research into the development of fermented products with targeted properties will be fuelled by the acquisition of more fundamental knowledge about how the microbiome functions, in particular the production of functionalities in a defined context of matrix and transformation process.


    Understanding the mechanisms of micro-organism-host interactions in these complex ecosystems is crucial to human health, so this theme is being developed around two models: the oral microbiota and the digestive microbiota.    The first objective is to explore the importance of the digestive microbiota in human health.

    The second objective is to understand the interactions between micro-organisms and hosts within the oral microbiota (bacteria, yeasts, fungi).