Microbial Ecology Research Unit

LEM research unit is supported by: (i) University Claude Bernard Lyon 1 which is a French university with a strong focus on education and research. Some of the key scientific domains include Earth and Environmental Sciences addressing issues such as sustainable development, (ii) CNRS - Ecology and Environment which is a national organization promoting research in ecology, environmental sciences, and biodiversity; (iii) INRAE which is promoting research activities in agricultural and environmental sciences, and (iv) VetAgro Sup which is a French institution involved in  education and research dedicated to veterinary medicine (vet school) and agricultural sciences.

Research interests & main objectives

• Integration of societal (urbanization, behavior) and environmental dimensions in understanding the factors leading to opportunistic infections and epidemic outbreaks
• Field investigations with acquisitions of data defining urban and agricultural settings harboring and spreading human bacterial opportunistic pathogens (BOP)
• Identification of key variables such as pollutants explaining the success of BOP in certain biotopes and clinical cases
• Implementation of DNA meta-barcoding, metagenomics, qPCR assays, and other DNA-based approaches to infer the ecology of BOP and their abilities at thriving in agricultural and urban settings

Principal investigator

Benoit Cournoyer – Senior scientist (Director of Research) in microbial ecology

Staff involved in Pharm-ERA

• Wessam GALIA: VetAgro Sup staff (lecturer), One Health issues involving BOP - impact of agricultural practices on the spread of BOP, and on animal/human exposures to BOP
• Emmanuelle Berger – Danty, INRAE Staff, BOP infectious processes and environmental health risk assessment

Equipment and processes

The BPOE research team has biological security labs of levels 2 and 3 allowing manipulation of infections agents and microbiologically contaminated environmental matrices. BPOE has all equipments to perform physiological analyses (bacteria and human cell lines), make microscopic examinations, molecular ecology analyses (DNA and RNA extractions, qPCR assays), and bacterial genetic manipulations. BPOE has official authorizations to conduct field investigations (over the Lyon conurbation) through the Lyon observatory of urban waters (OTHU, https://www.graie.org/othu/index.htm)