Scientist of Ifremer

Principal investigator

Directrice de recherche (C3 Ifremer)
Principal investigator of the Genomic of Vibrio (GV) team

Frédérique Le Roux has used a human herpes virus model system to address critical questions regarding the switch from latency to lytic cycle and the oncogenic properties of viral regulators (PhD and first post-doctoral fellowships, 1991–98). Having acquired substantial background and experience in molecular virology, she initially focused on applied research questions (IFREMER 1998–2004). Her work highlighted the complex eco-evolutionary dynamics of environmental pathogens and the urgent need of pathosystems to explore disease emergence and virulence mechanisms. She then focused her research on bacterial pathogens, the vibrios (2004–now). To develop the genetic toolbox for the diverse systems she had to work on, she joined the group of Didier Mazel at the Pasteur Institute (2004-08), the lab of Matt Waldor at Harvard Medical School (2008-10), and more recently Melanie Blokesch, at the EPFL for a mini-sabbatical. Since 2007, she leads, in collaboration with the CEA, a project analyzing hundreds of vibrio genomes. Since 2011, she is the principal investigator of the Genomic of Vibrio team at the marine station of Roscoff. She has brought together all the teams in France working on non-human pathogenic vibrios, increasing the impact of publications and grant success for the whole community. She also created a European network focused on Vibrio pathogen emergence in natural populations (Le Roux 2015).
She published 63 articles an obtained very competitive funding resources from the French National Research Agency (4 grants as PI in ten years) and the European Research Council (ERC Advanced Grant). She is actively involved in participative science, aiming to promote microbiology across social, age, gender and cultural barriers.



2012 -              Scientific director at the “Institut français de Recherche pour l’Exploitation de la mer” (IFREMER), France.

2010 -              Group Leader at the “Station biologique, Sorbonne Université”, Roscoff, France.

2008 - 2010   Guest researcher with Prof Matthew Waldor, Harvard Medical School, Boston, USA.

10/2004         Habilitation to direct research (Highest Diploma of the French University), Sorbonne University (SU), Paris, France.

2004 - 2008   Guest researcher with Prof Didier Mazel, Pasteur Institute, Paris, France.

2000 -              Permanent position as researcher at IFREMER, France

1998 - 2000   Postdoctoral research fellow (EU) with Dr Manolo Gouy, Claude Bernard University, Lyon and IFREMER, France. Research project: “Molecular epidemiology of Marteilia, a parasite for Ostrea edulis”.

1996 - 1998   Postdoctoral research fellow (Agence de la recherche sur le cancer, ARC) with Dr Irene Joab, Institut Gustave Roussy, Villejuif, France, including 2 months at Lineberger Cancer Institute, Chapel Hill, North Carolina, USA, with Dr Shannon Kenney. Research project: “Characterization of a variant of an Epstein Barr Virus transcriptional factor identified in rhinopharynx carcinoma”.

11/1995          Ph.D. degree (Molecular Biology), Claude Bernard University, Lyon, France. Title: “Latency and reactivation of the Epstein Barr virus: transcriptional regulation of EB1, a key regulator of the lytic cycle”.

1991 – 1995   PhD student fellow (Ministère de la recherche and ARC) with Dr Alain Sergeant and L. Corbo, Ecole Normale Supérieure, Lyon, France.

09/1991          Master degree (Molecular biology), Université de Rennes, France.

1986 - 1991    Study of cellular and molecular biology, Université Grenoble Alpes, Grenoble, France.



2020 - 2025    ERC Advanced grant (DYNAMIC), 2,500,000 EURO, PI: F. Le Roux.

The goal of this project is to shed light on key ecological and evolutionary processes underlying phage-bacteria dynamics in the marine environment. 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 nature. Based on a field approach, we will determine whether phages influence V. crassostreae dynamics in the wild by reducing bacterial density via predation and if co-evolution applies in this natural system. Combining comparative and functional genomics we will identify genes involved in the phage host range, host resistance, and phage counter resistance. Exploring phage-vibrio interactions in culture, we will analyze whether fitness costs can constrain evolution of resistance in vivo and identify vibrio virulence genes that are negatively selected by phages.

2020 - 2024    ANR project grant (RESISTE), 442,704 EURO, PI: F. Le Roux.

The aim of this project is to understand the evolution of antimicrobials resistance in environmental vibrios. This will allow to i) understand the diversity, mechanisms and evolution of antibiotic resistance in vibrio and determine if the oyster acts as a hotspot of HGT; ii) determine the trade-offs of antimicrobial and phage resistance with virulence and identify combinations of phages acting synergistically to control vibrio pathogens.

2016 - 2020    ANR project grant (REVENGE), 502,531 EURO, PI: F. Le Roux.

The aim of this project was to investigate the evolution of vibrio virulence in relation to the oyster as a host and phages as predators. This allowed to determine whether i) pathogenic genotypes of Vibrio emerge in areas experiencing mass mortalities; ii) Vibrio and oysters co-evolve; iii) Vibrio-phage infection networks are more highly connected in co-occurring phages and hosts

2014 - 2018     ANR project grant (OPOPOP), 362,698 EURO, PI: F. Le Roux.

The aim of this project was to investigate the partitioning of vibrios into ecologically distinct populations at fine environmental and genotypic resolution scales. This allowed us to determine (i) from what types of microhabitats oyster pathogens emerge, (ii) how populations shift during disease events, and (iii) what genomic features correlate to differential microhabitat association (including pathogenesis)

2012 - 2016     ANR project grant (VIBRIOGEN), 539,922 EURO, PI: F. Le Roux.

The aim of this project was to investigate virulence as an emerging property of strains or population in vibrios infecting marine invertebrates. Virulence was viewed not only as the result of acquiring new genetic resources through genomic plasticity but also, and foremost, through the interactions between vibrios, be it at the level of the interaction between replicons or between strains within the population

2011 - 2012     Starting grant Bretagne (VIBRIGEN), 50,000 euros, PI: F. Le Roux.

Start-up funding to install my new team of the Marine Station of Roscoff.



2017 - ​Microbiology, Master 2, Sorbonne University-Pasteur Institute (2 hours/year)

2015 - ​Microbiology, Master 1, Sorbonne University (2 hours/year)

2015 - Environmental Genomics, Master 2, Sorbonne University - National Museum of Natural History (2 half days of lectures and practical work/year)

2015 - Genomes and Genetics, Master 2, SU – Pasteur Institute (2 hours/year)

1998 - 2004 ​She created and taught Continuing education in molecular biology at IFREMER.



Pr Eduardo Rocha, Pasteur Institute, Paris, France

Pr Didier Mazel and Dr Céline Loot, Pasteur Institute, Paris, France

Dr David Bikard, Pasteur Institute, Paris, France

Dr Claudine Medigue, CEA, Ivry, France

Dr Sylvain Gandon, CNRS, Montpellier, France

Dr François Blanquart, CNRS, Collège de France, Paris, France

Dr Delphine Destoumieux, CNRS, Montpellier, France

Dr Alain Givaudan, INRA Montpellier, France

Dr Ika Paul Pont, CNRS Brest, France

Dr Tom Defoirdt, CMET, Ghent University, Belgium

Dr Mathias Wegner, AWI, Sylt, Germany

Pr Martin Polz, MIT, USA (now University of Vienna, Austria)

Pr Matt Waldor, Harvard Medical School, Boston, USA

Pr Jesse Shapiro, Montreal, Canada

Pr Melanie Blokesch, EPFL, Lausanne, Switzerland


Past PhD students

Damien Piel, Adèle James, Johan Binesse, Yann Reynaud, Mélanie Gay





1 -  Hussain FA, Dubert J, Elsherbini J, VanInsberghe MD, ArevaloP, KauffmanK, Kotska Rodino-Janeiro, Gavin H, Gomez A, LopatinaA, Le Roux F*, Polz MF*. Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages. Science 374, 484-492. doi: 10.1126/science.abb1083 (2021). (*co-correspondence)

2 -  Piel D, Bruto M, James A, Labreuche Y, Lambert C, Janicot A, Chenivesse S, Petton B, Wegner KM, Stoudmann C, Blokesch M, Le Roux F. Selection of Vibrio crassostreae relies on a plasmid expressing a type 6 secretion system cytotoxic for host immune cells. Environ Microbiol. 2019 Aug 7. doi: 10.1111/1462-2920

3 -  Rubio T, Oyanedel-Trigo D, Labreuche Y, Toulza E, Luo X, Bruto M, Chaparro C, Torres Bejar M, de Lorgeril J, Haffner P, Vidal-Dupiol J, Lagorce A, Petton B, Mitta G, Jacq A, Le Roux F*, Charrière G* and Destoumieux-Garzón D1*. Species-specific mechanisms of cytotoxicity towards immune cells determine the successful outcome of Vibrio infections. Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):14238-14247.(*co-correspondence)

4 -  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.

5 -  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.

6 -  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.

7 -  Le Roux F, Wegner KM, Polz MF. Oysters and Vibrios as a Model for Disease Dynamics in Wild Animals. Trends Microbiol. 2016 Jul;24(7):568-80. (review)

8 -  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.

9 -  Goudenège D, Travers MA, Lemire A, Petton B, Haffner P, Labreuche Y, Tourbiez D, Mangenot S, Calteau A, Mazel D, Nicolas JL, Jacq A, Le Roux F. A single regulatory gene is sufficient to alter Vibrio aestuarianus pathogenicity in oysters. Environ Microbiol. 2015 Nov;17(11):4189-99.

10 - Goudenège D, Labreuche Y, Krin E, Ansquer D, Mangenot S, Calteau A, Médigue C, Mazel D, Polz MF, Le Roux F. Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits. ISME J. 2013 Oct;7(10):1985-96.



Regular meetings with shrimp and oyster farmers

Oral presentations in public schools (from 5 to 9th grades), see for example

Several interventions at « the Café des Sciences »

Conference at Oceanopolis September 2020

Creation of a class on Microbes with children in Laos

Creation of a booklet to discover the world of microbes with Zoe Chaplain (, see this BOOKLET (en) or this BOOKLET (fr)

Participation to a child-centric microbiology education framework, see this PDF