http://www.sb-roscoff.fr/en/team-genomic-vibrio/open-positions
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Master 2 Microbiologie en alternance

Activités principales

Placé(e) sous l’autorité d’un chercheur Ifremer (Yannick Labreuche), au sein de l’unité Physiologie Fonctionnelle des Organismes Marins (IFREMER - PFOM) et dans le contexte du Laboratoire de Biologie Intégrée des Modèles Marins (LBI2M, Station Biologique de Roscoff), il/elle développera des approches de mutagénèse des vibrios pour caractériser le rôle de gènes bactériens candidats dans la virulence chez l’huître.  Il/elle aura pour principales activités :

  • d’effectuer les expériences de biologie moléculaire liées aux projets de l’équipe GV
  • d’établir des mutants à façon sur les bactéries du genre Vibrio en utilisant les protocoles disponibles au laboratoire GV
  • de mettre au point de nouvelles techniques de mutagénèse si nécessaire pour de nouvelles espèces/souches

 

Compétences mises en œuvre / à acquérir

  • Compétences techniques / métiers
  • Compétences en biologie moléculaire et microbiologie
  • clonage chez E. coli, transformation, conjugaison ; mutagénèse chez les vibrios
  • Compétences scientifiques : génomique fonctionnelle et microbiologie
  • Anglais (lu et parlé)

 

  • Qualités personnelles
  • Aptitude à travailler en équipe, facultés d’adaptation
  • Curiosité intellectuelle pour aborder les nouvelles technologies
  • Autonomie, ténacité
  • Sens de l’organisation et du partage des tâches collectives
  • Qualité de communication

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Master 2 (January-June 2021) Project#1

Oysters live in close association with abundant and diverse microorganisms. Phages are abundant in the oyster microbiota and their predation of bacterial populations suggests they may impact bacterial pathogenicity. This also raises the possibility of using them in therapeutic applications. Our preliminary data revealed that Vibrio crassostreae, an oyster pathogen, presents a highly dynamic pattern of infection in diseased oysters. Co-occurring virulent phages are genetically diverse and specific for certain combinations of vibrio clades with families of phages. In laboratory conditions, a vibrio strain infected by a phage rapidly evolved resistance in culture media but not in hemolymph, suggesting a fitness cost of escaping predation. These preliminary data lead us to the hypothesis that predation by virulent phages affects V. crassostreae infection dynamics for two reasons: it reduces pathogen density and it selects for less virulent phage-resistant clones of vibrios.

This project aims to explore the dynamics of infection (i.e. adsorption rate, latency time, burst size and growth rate of phage; growth of the host) of specific phage-vibrio combinations in culture media.

It will also explore whether turbid plaques obtained for some combination of phage-vibrio results from a pseudolysogeny, abortive infection, a partial resistance of the host or other unknown mechanism.

An ERC-funded PhD position (3 years), starting in September 2021 will then aim at exploring the molecular mechanisms and evolution of infection of phages infecting V. crassostreae.

The Le Roux team (Department of Integrative Biology of Marine Models, Marine station of Sorbonne University, Roscoff, France) 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.

Eligibility criteria. To apply for the position, candidates must hold a Master 1 in molecular biology, microbiology. Very 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. 1/2 page); iii) references.

Selection process. A first selection will be based on CV, past achievements and references letter. A second selection will be based on an interview with F. Le Roux.

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Master 2 (January-June 2021) Project#2

The One Health concept recognizes that human health is connected to the health of animals and plants, as well as the quality of their environment. It is thus crucial to break down interdisciplinary barriers separating human and veterinary medicine from ecological, evolutionary, and environmental sciences. In this context, exploring the origins, spread and evolution of antibiotic resistance genes (ARG) in the environment is critical to understand and control the processes leading to the emergence and dissemination of antibiotic resistance in pathogens.

Vibrionaceae are marine bacteria that are ecologically diverse members of planktonic- and animal-associated microbial communities. It encompasses the well-studied human pathogen, Vibrio cholerae, as well as some very important albeit less thoroughly characterized animal pathogens. For example, V. crassostreae, is a Vibrio species particularly abundant in oysters affected by the Pacific Oyster Mortality Syndrome. Although members of this species are genetically diverse, most of them can cause disease. Our preliminary data suggest that resistance to multiple antibiotics is common in Vibrio crassostreae, strains isolated from the environment. In many cases the resistance phenotype could not be linked with the presence of these known ARG. Our hypothesis is that environmental vibrios are reservoirs of ARGs, because these genes tend to be genetically linked with those involved in survival against toxic molecules present in the environment. For example, oysters naturally bio-accumulate heavy metals and selection for genes allowing bacteria to cope with them favor the acquisition of antibiotic resistance.

This project aim to discover novel mechanisms responsible for resistance to antibiotics and heavy metals by functional genomic.

An PhD position (ANR submitted in May 2020, fellow submitted at Ifremer 2021 or ED515), starting in September 2021 will then aim at exploring understand the diversity, mechanisms and evolution of resistance to antimicrobials in vibrio and to determine if the oyster acts as a hotspot of HGT (collaboration Eduardo Rocha, Pasteur Institute).

The Le Roux team (Department of Integrative Biology of Marine Models, Marine station of Sorbonne University, Roscoff, France) 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.

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.

Eligibility criteria. To apply for the position, candidates must hold a Master 1 in molecular biology, microbiology. Very 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. 1/2 page); iii) references.

Selection process. A first selection will be based on CV, past achievements and references letter. A second selection will be based on an interview with F. Le Roux.

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ERC-Funded Biocomputist

The Le Roux team at the Department of Integrative Biology of Marine Models, Marine station of Sorbonne University (Roscoff, France), is recruiting postdoctoral 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. The engineer fellow will begin the 1st January 2021 for a maximum of five years, and be funded by the ERC-2020-DYNAMIC (Ifremer as employer).

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 an interview with F. Le Roux and collaborators.

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ERC-Funded Post-doctoral position in Microbial ecology and evolution

The Le Roux team at the Department of Integrative Biology of Marine Models, Marine station of Sorbonne University (Roscoff, France), is recruiting postdoctoral 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. The postdoctoral fellow will begin the 1st April 2021 for a maximum of three years, and be funded by the ERC-2020-DYNAMIC.

Job description. We are looking for an enthusiastic and motivated scientist in environmental microbiology with excellent skill in statistics and good background in ecology and evolution. The post doc will be in charged of a specific aim of the DYNAMIC project, which is to understand the co-evolutionary processes underlying interactions between bacteria and phages in nature. The successful candidate will be in charge of i) time-series of consecutive sampling of a French Atlantic coastal zone site (July-August 2021; July 22, 23); ii) isolation and storage of phage and vibrio isolates, cross infection assays; iii) time shift and local adaptation analysis; iv) metagenomic analyses of phages dynamic.

He/she will work in close collaboration with other members of the lab (field, experimental and in silico work). Statistic analysis involves short stays in the laboratory of our collaborator Sylvain Gandon (CEFE, CNRS Montpellier).

Successful candidate must have high degree of independence and real abilities to work in synergy with other people from the team (technician, biocomputist, students). In addition to our collaborative network, complementarity and cohesion are a fundamental element of the strength of our team.

Eligibility criteria. To apply for the position, candidates must hold an internationally-recognized PhD degree in Microbiology. Excellent 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 an interview with F. Le Roux and collaborators.

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ERC-Funded technician

The Le Roux team at the Department of Integrative Biology of Marine Models, Marine station of Sorbonne University (Roscoff, France), is recruiting postdoctoral 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. The technician fellow will begin the 1st Januray 2021 for a maximum of five years, and be funded by the ERC-2020-DYNAMIC.

Job description. We are looking for an enthusiastic and motivated technician (IUT, “Licence professionelle”) with excellent background in molecular microbiology. He/she will be in charge of vibrio and phage isolation, storage, high titer stock and cross infection with numerous vibrio strains. He/she must have very good expertise in molecular technique such as qPCR and cloning, at least in E. coli. As the work involved high throughput screenings, establishment and storage of collection of hundreds of strains (bacterial and phage), he/she must be extremely well organized, rigorous and conscientious in particular concerning the on tractability and documentation of the experiments (note book). He/she will be in charged of some lab duties, such as the maintenance of some apparatus and consumables ordering.

Eligibility criteria. To apply for the position, candidates must hold an diploma of technician in molecular microbiology or biotechnology (IUT, Licence pro). 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 an interview with F. Le Roux and collaborators.