The French National Research Institute for Agriculture, Food, and Environment (INRAE)
is seeking to fill the position of a Postdoc to work on the project titled Pathogenic bacteria and antimicrobial resistance in a mountain-river-lake continuum: assessment with untargeted metagenomics in the framework of the One Health concept
Work environment, missions and activities
Framework:
The One-health concept is based on the principle that protecting human health depends on animal and environment health protection. Rivers and lakes are impacted by human activities, which induce microbiological contaminations. Consequently, microbial communities inhabiting such ecosystems can act as reservoirs and vectors for fecal bacteria, pathogens, or carriers of antibiotic resistance genes (ARG). These communities can impact human health if waters are used. Monitoring this risk is important, especially in the region of Lake Geneva where hundreds of thousands of people are using these water ecosystems (bathing, drinking, fishing, etc.).
Several recent projects enabled to get untargeted metagenomic data from natural fresh waters in key areas of the French region of Lake Geneva. The objective will be to use these data to assess the pathogen contamination and the presence of ARG along a mountain -> river -> lake continuum, where urban and agricultural activities discharge waters in the ecosystems.
Work context:
This recruitment will enable the fulfillment of a temporary mission of a research engineer (post-doc) mobilizing knowledge in molecular biology and environmental microbiology. The person will work with scientists of the UMR Carrtel INRAE (F.Rimet, N. Tromas, E. Lyautet and 3 other post-doc and an engineer) on very similar topic (freshwater microbiology, metagenomics, biomonitoring, functional ecology).
Mission:
Several shotgun Illumina NovaSeq runs (at least 3 runs) have already been sequenced and bioinformatic analyses have been already carried out (various pipelines were used SqueezeMeta, MetaNGS, etc.). From these analyses, the recruited postdoc (or engineer) will have to detect and semi-quantify pathogenic bacteria and ARG. She/He will have to link these findings to environmental factors (wastewater treatment plants, agriculture) and risks for populations (drinking water, bathing etc.).
Our team already has a good experience in molecular ecology (metabarcoding, untargeted metagenomic of algae and bacteria), and if the person recruited is well organized, she/he should have time to develop other, more fundamental topics. She/He will be in connection with several projects (Co-assemble, Biolashot, BioDive).
Offer reference
- Contract: Postdoctoral position
- Duration: 12 months
- Beginning: 01/06/2026 ~ 1/09/2026
- Remuneration: between 2300 and 2900 € (gross salary) depending on experience
- Work place: Lake Geneva shore, UMR Carrtel, Thonon les Bains, France
Training and skills
Recommended education:
- PhD (preferred) in microbial ecology
- Eventually engineer (master degree) with a good experience
Required skills:
- untargeted metagenomics applied to environmental/complex samples
- good skills in bash, python, R,
- good knowledge in bioinformatics and biostatistics
- ability for communication: writing papers, oral presentations
Desired skills:
- Leadership and critical thinking skills
- Ability to work in a team
How to apply
Send a cover letter and a CV including your publications list and contacts of your supervisors by email to frederic.rimet@inrae.fr
Or via:
Post mail: UMR Carrtel INRAE, 75 bis avenue de Corzent, 74200 Thonon les Bains, France https://carrtel.lyon-grenoble.hub.inrae.fr/unit
Application deadline
1st July 2026