Created 12/06/2020 Updated 28/07/2020

The Le Roux team at the Department of Integrative Biology of Marine Models, Marine station of Sorbonne University (Roscoff, France), is recruiting a engineer fellow to study key ecological and evolutionary processes underlying phage-bacteria dynamics in nature, with potential applications for phage therapy in aquaculture. An oyster bacterial pathogen, Vibrio crassostreae and its infecting phages will be used as model system to investigate the molecular bases and evolution of phage infections in oyster farms.

The Le Roux team seeks to understand the evolution of microbial populations in the wild and their adaptation to the environment. To this aim they develop an integrated approach (from ecology to the gene, from mathematical modeling to genetic) to understand the evolution and adaptation of bacterial pathogens (the Vibrionaceae) threatening animal species (e.g. the oyster Crassostreae gigas) that are a major importance for both environmental and socio-economic reasons. Given the abundance of phages, their potential impact on bacterial selection and potential applications for phage therapy in aquaculture, the team initiates a new research project to understand the co-evolutionary processes underlying interactions between bacteria and phages.

References

1- Bruto M, Labreuche Y, James A, Piel D, Chenivesse S, Petton B, Polz MF, Le Roux F. Ancestral gene acquisition as the key to virulence potential in environmental Vibrio populations. ISME J. 2018 Dec;12(12):2954-2966.

2- Labreuche Y, Chenivesse S, Jeudy A, Le Panse S, Boulo V, Ansquer D, Pagès S, Givaudan A, Czjzek M, Le Roux F. Nigritoxin is a bacterial toxin for crustaceans and insects. Nat Commun. 2017 Nov 1;8(1):1248.

3- Bruto M, James A, Petton B, Labreuche Y, Chenivesse S, Alunno-Bruscia M, Polz MF, Le Roux F. Vibrio crassostreae, a benign oyster colonizer turned into a pathogen after plasmid acquisition. ISME J. 2017 Apr;11(4):1043-1052.

4- Lemire A, Goudenège D, Versigny T, Petton B, Calteau A, Labreuche Y, Le Roux F. Populations, not clones, are the unit of vibrio pathogenesis in naturally infected oysters. ISME J. 2015 Jul;9(7):1523-31.

Appointment and benefit.

IFREMER permanent position (CDI). The engineer fellow will begin the 1st January 2021.

Job description.

We are looking for an enthusiastic and motivated computer analyst with good background in microbiology (if possible phage and bacteria). The main goal of this engineer fellowship is to identify, using bioinformatics, the molecular mechanisms involved in vibrio-phage interaction. This will be done through characterization of the different gene families within phage and bacterial genomes as well as gene classification according to their distribution, function and origin. This work will aim at investigating the evolution of specific genes to decipher putative relationships with the species/strain/cluster biology, and at characterizing mobile genetic elements implicated in resistance. Virome metagenomic will explore phages dynamic at both temporal (sampling once each day during V. crassostreae blooms) and spatial level (oyster versus seawater).

He/she will work in close collaboration with other members of the lab (who will provide experimental data). This fellow comprises short stays in the laboratory of our collaborator Eduardo Rocha (Institut Pasteur, Paris), to improve the quality and complementation of our work. Successful candidate must have high degree of independence and real abilities to work in synergy with other people from the team (students and scientist). In addition to our collaborative network, complementarity and cohesion are a fundamental element of the strength of our team.

Required profile.

The successful candidate will preferably have:

· a PhD in microbiology, genomics or bioinformatics,

· a good knowledge of microbiology, ecology and evolution,

· strong expertise in genome bioinformatics, especially in the analysis of DNA and protein sequence data,

· a good knowledge of statistical analysis and management of biological (incl. multivariate) data,

· a good knowledge of at least one programming language (preferably R or Python),

· a high degree of enthusiasm for the advertised project,

· a fondness for support of and interaction with other group members,

Eligibility criteria.

To apply for the position, candidates must hold an internationally-recognized engineer and/or PhD degree in computing analysis. A good written and spoken English is a requirement for the position. Application should include: i) a Curriculum Vitae; ii) the description of your past achievements (max. 1 page); iii) At least two letters of references

Selection process.

A first selection will be based on CV, past achievements and references letter. A second selection will be based on interviews.