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Last update: May 2021

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Environmental Microbiology and Health Risk


  • Human pathogens colonize biotic and abiotic environments and may circulate among environmental, animal and human reservoirs. 
  • Adaptation to variable environmental conditions is a key mecanism in the life cycle of pathogens.

Humans live in interaction/contact with multiple microbial communities. Indeed, skin and mucous membranes are colonized with commensal micro-organisms. Meanwhile, agricultural practices (recycling of livestock manure, organic amendments, urban sewage sludge ...) may contribute to the spread of human pathogens in environmental and/or animal reservoirs. Consequently soil, water, plants and animals can be a source of food contamination.

Environmental reservoirs for human pathogens may increase the risk for the emergence of transmissible diseases and the spread of antibiotic resistance strains and /or genes. The resulting health risk might be increased by climate change, population growth, lack of access to safe drinking water and lack of sanitation.

Pathogens developped complex mechanisms to adapt to various physico-chemical conditions microbial or biological microenvironments such as those encountered in plant, human or animal hosts as well as in soil, water : understanding the mechanisms by which micro-organisms may adapt to various environmental conditions may help understanding the circulation of pathogen micro-organisms from human/animals to the environment and vice versa.

Research TOPICS

The team "Health Risk and Environmental Microbiology" (MERS) addresses issues concerning i) the prevalence of human pathogens (including pathogens resistant to antibiotics) in environmental/animal reservoirs and their characterization, ii) the mecanisms of adaptation of these pathogens to various environments.

Research topic 1

  • Prevalence of human pathogens (and antibiotic resistant bacteria or genes) in environmental reservoirs, impact of organic waste recycling in agriculture, microbial source tracking. Consequences on water ressource quality (spreading or leaching from soils to surface or underground water)

Research topic 2

  • Investigating adaptation of human pathogens within complex environments : microbial communities and hosts. Mechanisms that underlie adaptation of saprophytic and/or pathogenic microorganisms are investigated within a range of environments including soils, plants and the Gastro Intestinal tract.


The MERS team groups together specialists and researchers in clinical and veterinary microbiology, environmental microbiology, cellular and molecular microbiology, microbial physiology, genetics, and biochemistry.


Betelli Laetitia MCF

Depret Géraldine, IE, INRA

Dequaire-Rochelet Murielle, MCF, université de Bourgogne

Gal Laurent, MCF, Université de Bourgogne

Garmyn Dominique, MCF, Université de Bourgogne

Hartmann Alain, DR, INRA

Lemaitre Jean-Paul, MCF, université de Bourgogne

Piveteau Pascal, MCF, université de Bourgogne

Revellin Cécile, IR, INRA

Solanas Sébastien, ATP, INRA

Vienney Fabienne, MCF