At the Micalis Institute, our mission is to conduct groundbreaking research in food microbiology and health. We aim to unravel the complex relationships between food, foodborne bacteria, and gut microbiota, exploring their links to human health and diseases from food-borne pathogens. Our research spans from molecular microbiology to synthetic ecology, focusing on the interactions between commensal and pathogenic microorganisms with host cells. Through translational research, we apply this knowledge to tackle societal challenges in food safety, human and animal health, and biotechnology, advancing scientific discoveries into practical applications.
The Bacterial Adaptation and Pathogenesis pillar (BAP) comprises 10 Micalis teams that collectively contribute to advancing our understanding of microbial behavior in the areas of food safety, host-pathogen interactions, and microbial adaptation mechanisms. Research within the BAP spans a broad spectrum of critical areas, addressing factors such as microbial establishment, intercellular communication, persistence, and the intricate dynamics of phage interactions. The teams study microorganisms with specific properties relevant to food production, particularly those that pose risks after ingestion.
The research portfolio covers a wide range of topics, including pathophysiology, antibiotic resistance, biofilm emergent properties, and the epigenetic consequences of bacterial infections. Investigations are multifaceted, exploring the impact of cell walls on microbial interactions and the transition of bacteria from commensalism to pathogenesis. This holistic approach, incorporating cutting-edge molecular and genomic insights, allows these teams to address scientific challenges such as therapeutic innovation, microbiota dysbiosis, infectious risks, and the potential applications of bacteriophages in health and industry. Collectively, the work of the BAP teams sheds light on critical aspects of microbiology with the goal of improving infection prevention and therapeutic strategies to improve human and animal health in an evolving microbial landscape.
Head: Romain Briandet
Molecular mechanisms, genome, metabolism, adaptation, virulence, host response, immunity, epigenetics, pathobiomes, bacteriophages, cell wall, cell membrane, antibiotics and alternatives, quorum sensing, food matrix, biofilms.
The « Food and Digestive Ecosystems (FDA) » pillar of MICALIS is composed of 8 Micalis teams (Amipem, ChemSyBio, FME, FInE, Probihôte, MIHA, PhylHom, NutriPhage) that are collectively exploring the microbial food and intestinal ecosystems and the functional interactions between food, microbiota and host. These teams consider food and human gut complex microbial ecosystems as fundamental elements for preservation of food quality and human health. Their main objectives are to understand mechanisms that govern maintenance of homeostasis of food-microbiota-host interactions and conditions that disrupt this equilibrium and thereby potentially contribute to the onset or chronicity of various immune, metabolic or degenerative pathologies currently rising in modern and emerging economies. The work of the FDA pole is directed
The understanding of the potential role of the gut microbiota in serious, frequent and/or incurable chronic pathologies of unknown etiology will help to develop tools for diagnosis and prognosis as well as preventive nutrition and innovative therapeutic applications based on the principle that a modification of microbiota parameters could contribute to maintain or restore a healthy global context.
Head: Philippe Langella
Microbiota, commensal microorganisms, probiotic microorganisms, metagenome, prebiotics, synbiotics, postbiotics, metabolome, inflammation, diet, nutrition, normobiosis, dysbiosis, microbes-host cross-talk, nutrional and therapeutic innovations, cohorts, mode of action
The “Systems and Synthetic Microbiology” (SSM) pillar comprises 5 Micalis teams that collectively contribute to decrypt and exploit bacterial and yeast functions by holistic, interdisciplinary approaches. Our ambitions are
The research portfolio covers a wide range of topics spanning from applied to fundamental research, such as building and controlling synthetic microbial communities for bioproduction, bioproduction from renewable sources by synthetic biology approaches, building of workflows to automate design and engineering in synthetic biology, biodetection and biocomputing in cellular and cell-free systems, engineering of genetic toolboxes and of genome engineering tools, real-time single cell investigation of mutations occurrences and its evolutionary consequences, phage infection, mode of action and resistance to antibiotics, bacterial cytoskeleton and cell morphogenesis. The teams of the MSS pole study model organisms (notably Bacillus subtilis and Escherichia coli) as well as microorganisms with specific properties relevant to bioproduction. Collectively, the work of the MSS teams contributes to tackle great challenges in the areas of health, food and environment by rationally exploiting the formidable biosynthetic and transformation capacities of bacteria and yeast.
Head: Rut Carballido-López
Systems Biology, Synthetic Biology, molecular mechanisms, metabolic engineering, cell factories, bacterial cell biology, mathematical modeling, biosensors, yeast lipid metabolism, morphogenesis, mutagenesis, antibiotics, phages, evolution, microfluidics, fluorescence microscopy.
These axes integrate the efforts of multiple teams across the thematic pillars and are pivotal in fostering innovative research directions.
Fighting Antimicrobial Resistance: Molecular and Ecological Mechanisms to Drive Innovation
Food, Fermented Food and Microbiota: Steering Functions for Health
