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Fabrice ROUX

Research Director CNRS (co-head of the team)

ECOGEN

RESEARCH SUBJECTS

Fabrice Roux obtained his Ph.D. degree in 2004 on the management of herbicide resistance using Arabidopsis thaliana as an experimental model (under the supervision of Xavier Reboud, laboratory of Biology and Management of Weeds, INRAE Dijon). After his Ph.D., he spent one year as a junior lecturer in the laboratory of Genetics and Evolution of Plant Populations (GEPP, University of Lille 1) and worked on the evolution of early-flowering in plants. He then spent a too short period (only one year) in the laboratory of Joy Bergelson (University of Chicago), where he became interested in identifying the genetic basis of quantitative resistance in the pathosystem A. thaliana-Pseudomonas viridiflava. Recruited as a CNRS researcher in 2006 at the GEPP (University of Lille 1), he developed his own research theme on ecological genomics of adaptation in A. thaliana. In 2012, he then co-led the research theme 'Global change: from ecological genomics to community ecology’. The research of Fabrice mainly focused on (i) the identification of the genetic basis of complex adaptive traits with the desire to replace A. thaliana in an ecologically realistic context, and (ii) the study of adaptation at different spatial and temporal scales. Since July 2013, Fabrice joined the LIPME after obtaining a junior starting grant from the Labex TULIP (Toulouse). His current projects focus on ecological genomics of organism – organism interactions. He is particularly interested in identifying the genetic basis underlying coevolution in plant-microbiota-pathobiota pathogen and plant-plant interacting systems. Since 2021, he co-leds the team with Fabienne Vailleau.

Fabrice Roux
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Fabienne VAILLEAU

Research Director INRAE (co-head of the team)

ECOGEN

RESEARCH SUBJECTS

Fabienne Vailleau obtained her Ph.D. degree in 2003 at the University of Toulouse, Ph.D. realized at the LIPM in Dominique Roby’s group, on the Arabidopsis thaliana/Xanthomonas campestris pv. campestris pathosystem. After her Ph.D. she was Assistant Professor at the INP-ENSAT, where she set up the Medicago truncatula/Ralstonia solanacearum pathosystem.  She was then recruited in Michel Petitprez’s group at the INP-ENSAT with a position of Associate Professor, where she continued her research on plant-bacteria interactions, giving lectures at the same time at INP-ENSAT in Plant Pathology and Weeds Science. From 2008 to 2015, she was the head of the 3rd year of specialization “Plant Agrobiosciences’. In 2008, Fabienne joined LIPM to perform her research in the group of Stéphane Genin and Christian Boucher. She worked on the post translational mechanisms required for the pathogenicity of the bacterium R. solanacearum. She obtained her Habilitation in 2016, and reoriented her projects on searching for plant proteins targeted and manipulated by R. solanacearum effectors, especially with approaches using association genetics. In 2020, she joined the team of Fabrice Roux to continue and integrate her work into a more global research theme in order to characterize and understand the molecular dialogue between the plant and its associated microbial cortege. In this context, she is currently developing a theme in the ECOGEN team on plant-microbiota-pathobiota interactions. Since 2021, she co-leds the team with Fabrice Roux.

Fabienne Vailleu
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Dominique Roby
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Dominique ROBY

Research Director CNRS

ECOGEN

RESEARCH SUBJECTS

Dominique ROBY, Research Director CNRS

Dominique did her PhD in the Laboratory of Plant Physiology in Toulouse; her work concerned the study of defense mechanisms triggered by fungal elicitors in plants and the signalling role of ethylene. She was then recruited in 1982 as a CNRS researcher to work on the regulation of chitinase genes in plants upon fungal infection. After 4 years, she moved to Rutgers University (USA) and then to the Department of Agricultural Products of E. DuPont de Nemours (USA) where she investigated the role and transcriptional regulation of chitinase genes during plant immune responses. Then she joined the LIPM in 1990 and started a group in collaboration with Yves Marco, working on plant-bacteria interactions, and more particularly on plant genes involved in the control of the Hypersensitive Response, a form of programmed cell death for which there was still very limited information. The main goals of her research are now to identify  key components of quantitative disease resistance (QDR) in Arabidopsis to an agronomically important pathogen: Xanthomonas campestris, and to understand the role of some QDR components on the plant microbiota. In parallel, she is exploring the genetic and molecular bases of competitive plant-plant interactions. These projects, first developed in tight collaboration with Fabrice Roux, are now run in the ECOGEN team. 

Dominique has been director of the LIPM from 2011 to 2015, coordinator of the LabEx TULIP from 2011 until 2019 (https://www.labex-tulip.fr/Le-LabEx) and is currently Deputy Head of INRA Division - Plant Health & Environment  (http://www.spe.inra.fr/) since 2013.

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Mathieu HANEMIAN

Researcher INRAE

ECOGEN

RESEARCH SUBJECTS

During my 1st postdoc in Olivier Loudet's team at INRA Versailles, I used quantitative genetics combined with high throughput phenotyping to identify the genetic and molecular bases of vegetative growth in A. thaliana. The use of natural variation in these experiments led me to work on the ecological reasons of plant adaptation and in evolutionary biology. I did a 2nd postdoc in Cris Kuhlemeier's team at the University of Bern, where I studied the influence of pollinators on speciation in the Petunia genus, combining quantitative genetics, functional genomics and molecular biology.

I joined the ECOGEN team as a researcher since October 2019, to work on the molecular mechanisms involved in natural variation of the response to other plant species in A. thaliana. This is a fascinating subject because despite the importance of the interactions between plants in shaping plant communities, we know very little about the mechanisms of adaptation and co-evolution between them. In addition, a better understanding of these interactions may be useful for the agroecological transition.

TRAINING

2006 - BSc Sciences, Technologies, Health major in Biology - University of Burgundy, France

2007 - MSc (1st year) Sciences & Plant Technologies - University of Burgundy, France

2008 - MSc (2nd year) Microbiology-Agrobiosciences - University Toulouse III, France

2012 - PhD in Plant-Microbe Interactions - University Toulouse III, France

RECENT FUNDING

2020-2023 – PhD project – Plant-Plant interactions : Functional analysis of a gene involved in the response to competition in A. thaliana. Co-funded INRAE Plant Health Department (47 k€) - Occitanie Région (55 k€). Co-Pis with Dominique Roby

2021-2022 – PIPPIN project. Pathways involved in Plant-Plant interactions. Département INRAE – SPE. 27k€. PI

2019 - Unibe initiator grant 2019 (#38990), 20kCHF, PI (declined)

EDUCATION

2021 – Practical « From QTL mappingto gene identification and more » over 2 days

2021/2022 – Tutelage in the Junior Lab (master international Functional Biology & Ecology)

COMMITTEE MEMBER

  • Member of the LIPME sustainable development committe (2020-)

  • Member of the LIPME lab council (2021-)

  • Member of the pedagogic council of the labex (2020-), with a particular focus on the Guided Tour and Junior Lab modules from the international TULIP master « Functional Biology and Ecology »

SCIENTIFIC PRODUCTION

Hanemian, M., Vasseur, F., Marchadier, E., Gilbault, E., Bresson, J., Gy, I., Violle, C., and Loudet, O. (2020). Natural variation at FLM splicing has pleiotropic effects modulating ecological strategies in Arabidopsis thaliana. Nature Communications 11: 4140.

Yarahmadov, T., Robinson, S., Hanemian, M., Pulver, V., and Kuhlemeier, C. (2020). Identification of transcription factors controlling floral morphology in wild Petunia species with contrasting pollination syndromes. The Plant Journal 104(2):289-301.

Marchadier, E., Hanemian, M., Tisné, S., Bach, L., Bazakos, C., Gilbault, E., Haddadi, P., Virlouvet, L., and Loudet, O. (2019). The complex genetic architecture of shoot growth natural variation in Arabidopsis thaliana. PLOS Genetics 15: e1007954.

Bazakos, C., Hanemian, M., Trontin, C., Jiménez-Gómez, J.M., and Loudet, O. (2017). New Strategies and Tools in Quantitative Genetics: How to Go from the Phenotype to the Genotype. Annual Review of Plant Biology 68: 435–455.

Hanemian, M. et al. (2016). Arabidopsis CLAVATA1 and CLAVATA2 receptors contribute to Ralstonia solanacearum pathogenicity through a miR169-dependent pathway. New Phytologist 211: 502–515.

Yadeta, K.A., Valkenburg, D.-J., Hanemian, M., Marco, Y., and Thomma, B.P.H.J. (2014). The Brassicaceae-Specific EWR1 Gene Provides Resistance to Vascular Wilt Pathogens. PLOS ONE 9: e88230.

Hanemian, M., Zhou, B., Deslandes, L., Marco, Y., and Trémousaygue, D. (2013). Hrp mutant bacteria as biocontrol agents. Plant Signal Behav 8: e25678.

Feng, D.X., Tasset, C., Hanemian, M., Barlet, X., Hu, J., Trémousaygue, D., Deslandes, L., and Marco, Y. (2012). Biological control of bacterial wilt in Arabidopsis thaliana involves abscissic acid signalling. New Phytologist 194: 1035–1045.

Yadeta, K.A., Hanemian, M., Smit, P., Hiemstra, J.A., Pereira, A., Marco, Y., and Thomma, B.P.H.J. (2011). The Arabidopsis thaliana DNA-Binding Protein AHL19 Mediates Verticillium Wilt Resistance. MPMI 24: 1582–1591.

CONNECTIONS

HOBBY

Gardening (where I most probably learn more about plants than during research work!)

Hiking

Mathieu Hanemian
Carine Chauveau
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Carine HUARD-CHAUVEAU

Engineer INRAE

ECOGEN

RESEARCH SUBJECTS

During her PhD in the Protein Biochemistry and Structure laboratory, INRAE Jouy-en Josas, Carine worked on the characterization of peptidoglycan hydrolases of Lactococcus lactis. She was then recruited in the Small Ruminant Pathology unit of Sophia-Antipolis laboratory of ANSES (French Agency for food, environmental, and occupational health and safety). She joined the LIPM in 2005. She developed projects to characterize genes controlling quantitative resistance of Arabidopsis to Xanthomonas campestris pv campestris. She used approaches including molecular biology, transcriptomic, system biology and functional genomic.

RECENT FUNDING

  • Projet QuID (Quantitative Immunity Dissection) financé par le département SPE INRAE - 2021-2023 (29k€). Coordinatrice: Carine Huard-Chauveau.

  • Projet TERO. Pépinière de projets contribuant à la stratégie RSE INRAE - Création d’une filière pour la gestion des déchets de culture sur le centre INRAE Occitanie-Toulouse. 2022-2023 (20 k€). Coordinateurs : Carine Huard-Chauveau & Mathieu Hanemian

COMMITTEE MEMBER

  • Référente Développement Durable pour le LIPME et animateur comité DD du LIPME (2020-   )

  • Membre de la « Commission avancement ITA » (2011-  ).

  • Membre élu du Conseil Scientifique du laboratoire LIPME (2016 - 2020)

  • Membre élu au Conseil De Laboratoire (2007 et 2015)

  • Membre nommé au CLHS (2005 - 2017)

  • Assistant Prévention INRA (2005 – 2017)

Baptiste Mayjonade
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Baptiste MAYJONADE

Engineer INRAE

ECOGEN

RESEARCH SUBJECTS

Baptiste obtained a Master degree at the University of Limoges in 2010. He spent two years in the laboratory of molecular biology of Limagrain Europe (Chappes). In the context of molecular breeding and marker-assisted selection, he developed molecular markers on crops. In 2012, he joined the LIPME to work on the genetics and genomics of response to biotic and abiotic stresses in sunflower. He was in charge of projects related to transcriptomics and genomics. He was also involved in the development of technologies in molecular biology. Since September 2015, he has a permanent position in the ECOGEN team. He is responsible for the genomic, ecological and phenotypic characterization of 168 populations of Arabidopsis thaliana located southwest of France, and their associated plant and microbial communities. To do this, it implements innovative methodologies, in particular based on the most recent high-throughput sequencing technologies.

Chrystel Gibelin
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Chrystel GIBELIN-VIALA

Engineer Assistant INRAE

ECOGEN

RESEARCH SUBJECTS

Chrystel Gibelin-Viala was recruited at INRA Poitou-Charentes in 2000. She worked in the molecular biology laboratory of URP3F, unit which study the functioning of the forage crop on grassland. She joined the LIPME in 2009 in the group of Clare Gough and Julie Culimore, where she studied the arbuscular mycorrhizal symbiosis using potential mutants of mycorrhization. She also developed genetic approaches to dissect the host range control in the rhizobium-legume symbiosis. Since January 2020, she joined the team of Fabrice Roux, ECOGEN (Ecological genomics of adaptation in plant communities). Her main missions are focused on the plant-microbiota-pathobiota interactions, one of the ECOGEN team themes of research. One of her main objectives is to contribute to characterize and understand the molecular dialog between Arabidopsis thaliana and its microbial cortege. Chrystel has skills in molecular biology (DNA extraction, PCR, genotyping), microscopy, plant biology (plant supply, plant experimentation, phenotyping), microbiology.

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Béatrice GABINAUD

Technician INRAE

ECOGEN

RESEARCH SUBJECTS

Béatrice joined INRAE ​​in 1993 at Nantes veterinary school, after a master's degree in organism and population biology and a master in parasitology. Her assignments focused on model animal surgery (Duchene muscular dystrophy), primary satellite cell cultures, histology and microscopy (image analysis). Following a mobility in 1999 at GenPhySE (genetics, physiology and breeding systems), she worked for 7 years on meat quality, and then 14 years on the characterization of the microbiota of farm animal digestive ecosystems by preparing samples for sequencing (DNA extraction, PCR, qPCR, microbiology).

Then she wanted to work with plants and joined the ECOGEN team in September 2020 (part-time 50%) to monitor plants grown in the field or in the greenhouse, and to perform the molecular characterization of interspecific plant-plant interactions (Arabidopsis thaliana with 4 associated species).

During her other half of the part-time, she works on the Plant Production and Experimentation platform of the LIPME.

Béatrice Gabinaud
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Rémi DUFLOS

PhD student

ECOGEN

RESEARCH SUBJECTS

Rémi Duflos obtained two master degrees in 2021, the first one at INP-ENSAT University (Toulouse, France) in AgroBiosciences and the second one at Paul Sabatier University (Toulouse, France) in Plant Biology. He performed his Master internship in the ECOGEN team, under the supervision of Fabienne Vailleau and Fabrice Roux. The goal of this project was the establishment of a genomic map of local adaptation in Arabidopsis thaliana to its most abundant bacterial species in the leaf compartment in south-west of France. His PhD   project follows this internship with (i) the functional validation of candidates genes underlying QTLs identified in A. thaliana during his Master internship, and (ii) the identification, in Pseudomonas koreensis, of genes that mediate the genetic and molecular dialog with A. thaliana.

Rémi Duflos
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Roxane Lion

Engineer Assistant, CNRS

ECOGEN

RESEARCH SUBJECTS

After obtaining a Professional License in Molecular Biology at the IUT of Mont-de-Marsan, Roxane was recruited on a fixed-term contract at INRA in Bordeaux within the Fruit Biology and Pathology unit. She worked in the Virology team on the ANR Potymove project where she studied the genes involved in resistance to the TuMV virus as well as its movement in the Arabidopsis thaliana model. Since November 2021, she has joined the ECOGEN team to work on the ERC Pathocom project.

Roxane Lion
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Paloma DURÁN

Post-doc CNRS

ECOGEN

RESEARCH SUBJECTS

Paloma comes from Spain and studied Biology at the University of Salamanca. For her PhD, she moved to the MPIPZ in Cologne, Germany, and worked in the groups of Paul Schulze-Lefert and Stéphane Hacquard. There, she studied the multikingdom microbial communities associated with roots of natural Arabidopsis thaliana populations across Europe and the impact of microbial interactions on plant health. She was then then granted a Postdoctoral Fellowship with CEPLAS and moved to the group of Ruben Garrido Oter, also at the MPIPZ. There, she studied the microbiota composition and interactions at the phycosphere of the model microalgae Chlamydomonas reinhardtii, and investigated the microbial composition overlap with land plants. She is now part of the ECOGEN lab, where she will study the pathobiota of A. thaliana natural populations, investigating the host and microbial genetic factors, as well as environmental cues, that underlie these interactions.

Relevant publications

  • Durán, P., Flores-Uribe, J., Wippel, K., Zhang, P., Guan, R., Melkonian, B., Melkonian, M. & Garrido-Oter, R. (2022). Nat Commun 13, 406

  • Thiergart, T., Durán, P., Ellis, T. et al. (2020) Root microbiota assembly and adaptive differentiation among European Arabidopsis populations. Nat. Ecol. Evol. 4, 122–131.

  • Durán, P., Thiergart, T., Garrido-Oter, R., Agler, M., Kemen, E., Schulze-Lefert, P., & Hacquard, S. (2018). Microbial interkingdom interactions in roots promote Arabidopsis survival. Cell, 175(4), 973-983.

  • Hassani, M. A., Durán, P., & Hacquard, S. (2018). Microbial interactions within the plant holobiont. Microbiome, 6(1), 58.

Coralie FUERTES
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Sonia SILVA

Engineer, CNRS

ECOGEN

RESEARCH SUBJECTS

Sonia obtained a Master's degree in Biotechnology, Molecular Biology and Microbiology at the Toulouse’s University. Then, she worked during two years for TWB (Toulouse White Biotechnology) in the High Throughput Strain Engineering platform where she worked on bacterial, yeast and micro-algae genetic engineering. Since March 2022, she joined the ECOGEN team to work on the ERC Pathocom project.

 

Personal link

https://www.linkedin.com/in/sonia-silva-ba9796171/

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Coralie FUERTES

Technician, CNRS

ECOGEN

RESEARCH SUBJECTS

Coralie obtained a bachelor degree in genome and biotechnology for plant breeding from the University of Toulouse in September 2023. As part of this degree, she did an internship with the ECOGEN and ENOD teams on plant-plant interactions between Arabidopsis thaliana and Medicago truncatula. She was supervised by Matthias Benoit and Mathieu Hanemian. In December 2023, she was hired in the ECOGEN team to work on the ERC PATHOCOM project as a research technician. She will participate in setting up bacterial collections that will be used to test for interactions within the bacterial pathobiota of Arabidopsis thaliana, but also between the pathobiota and the microbiota of Arabidopsis thaliana.

Paloma Duran
Sonia Silva
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Tifaine FOLLETTI

Engineer INRAE

ECOGEN - RLE

RESEARCH SUBJECTS

Tifaine graduated with a Master’s degree in Tropical Plants Biotechnology in Montpellier University in 2021. During her studies she took a year’s break (between Master 1 and Master 2) during which she worked as engineer assistant in SPI team at LIPME with Mireille Chabaud. She worked on research of resistance against a parasitic plant: the broomrape on sunflower. After obtaining her Master’s degree she took a short-term contract as biotechnology engineer at SYNGENTA where she worked on the improvement of a mitochondrial DNA extraction protocol on barley. Since april 2022 she joined the LIPME between two teams, ECOGEN and RLE, to work on the PATHOSYM ANR project.

Tifaine FOLLETTI
Léonie FALGOUS
Otto Bohm
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Léonie FALGOUS

Engineer student

ECOGEN

RESEARCH SUBJECTS

I'm currently in my 5th year at the Purpan engineering school in Toulouse. My first internship was at LIDEA, where I worked on a marker-assisted breeding program in rapeseed. At the beginning of 2024, I joined the ECOGEN team for my final year internship. I will be studying the natural genetic variation of plant competition.

Corentin CHALAS

PhD student

ECOGEN

RESEARCH SUBJECTS

I'm currently a PhD student in the ECOGEN team at LIPME, after graduating with a Master's degree in Plant Biology, “Plant-Microbe Interaction for Plant Health” in 2024, and a Bachelor's degree in Life Sciences, “Biodiversity Sciences” in 2022, from the Université Claude Bernard Lyon 1.

My thesis topic is “Eco-functional genomics of interspecific diversity of the beneficial microbiota of Arabidopsis thaliana”, under the supervision of Fabienne VAILLEAU and Carine CHAUVEAU. The aim of my thesis is to identify and functionally validate bacterial genes conferring beneficial effects on A. thaliana, by studying interspecific natural variation in a collection of over 1000 bacterial strains from the South-West of France. One of the main objectives of my thesis is to identify new bacterial genetic and molecular mechanisms involved in natural variation between wild bacterial species on plant biostimulation.

I had the opportunity to do my Master 1 and 2 internships in this team, under the supervision of Rémi DUFLOS, Fabienne VAILLEAU and Fabrice ROUX. 

- In 2023 during my Master 1 internship (2 months) on beneficial plant-bacteria interactions, I studied the response of five natural accessions of A. thaliana to single inoculations or co-inoculations of pairs of 4 OTUs (Operational Taxonomic Units) of commensal bacteria of the phyllosphere.

- In 2024 during my Master 2 internship (6 months) on the identification and functional validation of Pseudomonas siliginis genes involved in the promotion of A. thaliana growth, by studying the natural intraspecific genetic variation of 74 strains of P. siliginis and starting the generation of bacterial mutants.

Otto BOHM

Master 2 student

ECOGEN

RESEARCH SUBJECTS

I completed a Bachelor’s degree in Biodiversity (BOPE) at Paul Sabatier University, specializing in plant physiology. I am now pursuing a Master’s degree in TULIP "Functional Biology and Ecology" at the same institution. During my first year of the Master's program, I worked on a project focused on tripartite interactions between plants, arbuscular mycorrhizal fungi (AMF), and rhizosphere bacteria. For my second-year internship, I joined the ECOGEN team to study plant-plant interactions under abiotic conditions (such as drought) and biotic factors (commensal bacterial inoculation). My research involves Arabidopsis thaliana, with four different accessions examined, in both solitary and competitive contexts with natural competitors Poa annua and Sonchus oleraceus.

Corentin CHALAS
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Former members

Visiting scientists

Hanna Susi (University of Helsinki) 2022

Quanjing Zheng 2023 (PhD student from the University of Copenhagen)

 

Post-docs

Claudia Bartoli (2014-2016)

Ullrich Dubiella (2015-2018)

Tatiana Vernié (2017-2018)

Florent Delplace (2020-2021)

Alexandre Perrat (2022-2024) 

 

PhD students

Romain Villoutreix (2010-2013)

Etienne Baron (2011-2014)

Lea Frachon (2014-2017)

Cyril Libourel (2015-2019)

Nathalie Aoun (2016-2019)

Lorenzo Favale (2017)

Jaishree Subrahmaniam (2017-2020)

Florent Delplace (2017-2020)

Nargess Razavi (2017-2021)

Choghag DEMIRJIAN (2019 - 2022)

Daniela Ramirez-Sanchez (2019-2022)

Marie Invernizzi (2020-2024) 

 

Technical staff

Rémi Zamar (2018 - 2022)

Oriane Besset (2022 - 2023)

Students

Cyril Libourel - Master 2 (2015)

Eve Coutant - Master 1 (2015)

Arnaud Chevalier-Mairet - Master 1 (2016)

Wijmer Taeken - Master 1 (2016)

Thomas Dussarat - Master 1 (2017)

Arnaud Chevalier-Mairet - Master 2 (2018)

Laurie Thailades - Master 1 (2019)

Marie Invernizzi - Master 2 (2019)

Louis Uhlmann - Vocational degree (2020)

Alexandre Boubegtitène - Master 2 (2021)

Paul Baumet - Master 1 (2021)

Manon Pradel - Master 1 (2021) + Master 2 (2022)

Corentin Chalas - Master 1 (2023)

Irene Leccia - Stage de césure (2023)

Leo Zbierski - BTS 1ère et 2ème année (2023)

Elena Dangla - Master 2  (2023)

Anais Botello - Master 2 (2023)

Clara Lapasse - Licence professionnelle (2024)

Audrey Vidal - L3 (2024)

​Pauline Faure - BUT 2ème année (2024)

Edwin Wagner - Master 1 (2024)

Lila Rigolot - Master 1 (2024)

Matteo Antoine - Master 1 (2024)

Léonie Falgous - Master 2  (2024)

Corentin Chalas - Master 2  (2024)

Anciens membres
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