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Portail > Offres > Offre UMR5244-DIAMER-003 - Post doc H/F en écologie microbienne Montpellier (34)

Post doc H/F in microbial ecology

This offer is available in the following languages:
Français - Anglais

Date Limite Candidature : vendredi 6 août 2021

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General information

Reference : UMR5244-DIAMER-003
Date of publication : Friday, July 16, 2021
Type of Contract : FTC Scientist
Contract Period : 24 months
Expected date of employment : 1 October 2021
Proportion of work : Full time
Remuneration : between 2675 and 2728 € gross/month
Desired level of education : PhD
Experience required : 1 to 4 years


Aquaculture has been identified as a gateway for antimicrobial resistance (AMR) spread worldwide. Still, little is known on AMR in the oyster aquaculture environment. The economically important oyster species Crassostrea gigas is cultured in coastal areas that are often contaminated by AMR determinants (antibiotics, resistance genes, and resistant bacteria) and other pollutants known to co-select for AMR. Moreover, antibiotics are used in hatcheries. AMR therefore threatens the safety of coastal marine systems, the sustainability of shellfish farming and human health. Preliminary data obtained at the IHPE lab have shown that antibiotic-resistance genes (ARG) are present in the genomes of oyster-associated vibrios (Rubio T et al, PNAS, 2019 ; Lagorce A et al., non publié) and are expressed by the oyster-associated microbiota (metatranscriptomic data) (Lucasson A et al., BioRxiv, 2020). A first inventory has evidenced a broad diversity of ARG circulating in Vibrio isolated from coastal environments used for oyster culture (unpublished). The post-doctorate is part of the European SPARE-SEA project aimed at characterizing the environmental spread and persistence of antibiotic resistances in aquatic systems use for oyster farming. The objective of the postdoctoral researcher will be (i) to estimate ARG occurrence and expression in microbiota of oysters sampled along anthropization gradients using metatranscriptomics analysis and (ii) to identify potential human/environmental drivers of ARG selection in coastal marine environments through statistical analysis. The study will be conducted in four European regions used for oyster farming.


The postdoctoral researcher will be in charge of metatranscriptomics data production and analysis. She/He will be involved in RNA extraction and library preparation with the support of a technician in molecular biology, and will develop bioinformatics pipeline for NGS data analysis (quality control and filtering, assembly, annotation with a special focus on ARG, and between sample comparisons). She/He will also be involved in bacterial genome analysis for ARG inventory. Depending on ARG identified, she/he will develop targeted approaches for field sample screening using digital PCR, and perform statistical analysis to identify drivers of ARG selection.


The candidate will hold a PhD in microbial ecology with strong skills in biostatistics, bioinformatics and NGS data analysis. Experience in RNAseq and metatranscriptomics would be appreciated. Knowledge in antibiotic resistance mechanisms will be a plus. The candidate will be involved in a multidisciplinary consortium and should thus have excellent English skills as well as oral and written communication capacities. She/he will be able to work in a multidisciplinary team.

Work Context

The candidate will be involved in a European project involving numerous collaborators throughout Europe. She/He will join the Interactions Hosts Pathogens Environments laboratory at the Montpellier site.

Constraints and risks

The research unit is split into two sites (Montpellier and Perpignan) and the candidate will interact regularly with colleagues in Perpignan. She/He will report project progression in consortium meetings.

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