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Micalis (Food microbiology for health)

UMR 1319 AgroParisTech, INRAE, Université Paris-Saclay

General scientific background

The Micalis unit aims to perform innovative research in the field of food and gut microbiology for health. The activity of the UMR focuses on the role of microorganisms in food processing, food digestion by humans and their effects on health as well as on the development of microorganisms as cell factories for production molecules of interest. The unit makes use of bacterial genetics, molecular biology, cell biology, metagenomics, high-resolution microscopy and systems and synthetic biology approaches.

Fields of research

The work of the 21 research teams of the unit addresses three major themes with complementary scientific objectives :
Alimentary and intestinal microbial ecosystems : functional food/microbiota/host interactions
♦ Characterization of microbial ecosystems by analysis of their metagenomes and studies of their functional ecology
♦ Understanding how and why the diversity of microbial populations is established and maintained within food and digestive ecosystems
♦ Studies of the mechanisms of dialog between the intestinal microbiota and human cells and organs
♦ Proposal of levers for maintaining the equilibrium of the microbiota and beneficial interactions with the host or the food matrix
Ecosystems studied : human, intestinal and buccal microbiotas, cheese and meat ecosystems, alimentary fermentation starters, etc.

Bacterial adaptation and pathogenesis : mechanisms of bacterial adaptation to the environment, emergence and pathogenesis of opportunistic bacteria of dietary origin
♦ Characterization of the molecular mechanisms by which bacteria adapt to changes in their environment
♦ Studies of the conditions and molecular mechanisms of emergence for so-called “opportunistic” pathogenic bacteria
♦ Development of tools for identifying and defining preventive and control strategies for pathogenic microorganisms
♦ Studies of the responses of useful, food-altering and pathogenic microorganisms to the constraints of food manufacture and storage
Microorganisms studied : lactic acid bacteria, streptococci, enterococci, staphylococci, clostridiae, Bacillus cereus, bacteriophages,etc.

Systems and synthetic biology : from a global approach to biological processes to biotechnological applications
♦ Studies of microorganisms or biological processes as integrated systems
♦ Characterization of biological processes at the scale of single microbial cells, and their variability at the level of the cell population
♦ Modeling to predict and control their behavior
♦ Design and construction of biosynthetic pathways of interest and of ad hoc bacterial platforms for biotechnological applications in food chemistry, white chemistry or health
Microorganisms studied : Bacillus subtilis, commensal organisms and opportunistic pathogens from the Firmicutes, Escherichia coli, oil-producing yeasts, etc.

For more information
Check out the open access publications of Micalis on HAL-AgroParisTech :

Contact details
jj-micalis-accueil chez inrae.fr
+ 33 (0)1 34 65 27 51

16 rue Claude Bernard
F-75231 Paris Cedex 05
Tel: 33 (0) 1 44 08 18 43
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