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Laboratory of Plant-Microbe Interactions - LIPM

Laboratory of Plant-Microbe Interactions

Members - Ralstonia pathogenesis and adaptation to the plant environment

Dr Stephane Genin, HDR, DR1 CNRS

Stéphane GENIN

After studying Genetics in Lyon, I received a Ph.D. from the Paris XI-Orsay University in 1993. I spent two years (1993-1995) as a Post-doctoral Fellow at the Department of Genetics at the University of Munich investigating Ustilago maydis filamentous growth, under the direction of Prof. Regine Kahmann. I joined LIPM in the INRA Toulouse Center in 1989 where I worked with Christian Boucher on several aspects of Ralstonia solanacearum pathogenicity. In 1995 I was recruited as a scientist at CNRS and I am leading the R. solanacearum research group since 2005.


Dr Nemo Peeters, HDR, DR2 INRA

Nemo Peeters

After studing Biology at the university of Montpellier, I obtained a PhD in january 2000, in plant cell and physiology from the University of Paris XI, Orsay under the supervision of Dr Ian Small at INRA Versailles. I then spend 2 1/2 years at Cornell university, Ithaca NY, studying chloroplast RNA editing in the lab of Professor Maureen Hanson. in 2002,  joined the group of Stephane Genin to use plant cell biology approaches to study Ralstonia solanacearum type III effectors (T3Es). Since then I have worked on the identification and the characterisation of the multiple T3E from Ralstonia solanacearum. I obtained my HDR in 2007 and have been a Directeur de Recherche at INRA since decembre 2015.

 My authored publications via ORCID



Dr Fabienne vailleau, HDR, Associate Professor ENSAT


Fabienne did her PhD thesis at the University of Toulouse, at the LIPM in the Dominique Roby’s group, on the Arabidopsis thaliana/Xanthomonas campestris pv. campestris pathosystem. She demonstrated that AtMYB30 was a positive regulator of the Hypersensitive Cell Death and highlighted the importance of a lipid pathway (very-long-chain fatty acid biosynthesis) in plant resistance. Then she moved at the INP-ENSAT as a postdoc, where she set up the Medicago truncatula/Ralstonia solanacearum pathosystem. She then was recruited in the Michel Petitprez’s group at the INP-ENSAT with a position of Associate Professor, where she continued to work on plant-bacteria interactions, at the same time teaching at the ENSAT in Plant Pathology and Weeds Science. Since 2008 she is the Director of the Plant Biosciences Department at INP-ENSAT, and the head of the 3rd year of specialization “Plant Agrobiosciences’ (DAA ABSV, ENSAT). In 2008, Fabienne joined the group of Stéphane Genin and Christian Boucher to focus her research of the post translational mechanisms required for the pathogenicity of the bacterium Ralstonia solanacearum.


Dr Alice Guidot, CR1 INRA


After studying biology at the University Lyon 1, I did a PhD in the Laboratory of Microbial Ecology in Lyon where I studied population genetics of the ectomycorrhizal fungus Hebeloma cylindrosporum. In 2001-2003, I did a first post-doc on fungal population genetics in the Mycology and forest pathology laboratory at the University of Uppsala in Sweden. In 2004-2007, I did a second post-doc in the CIRAD in Reunion Island where I studied the role of horizontal gene transfers in evolution of the plant pathogenic bacterium Ralstonia solanacearum. In 2008, I joined the group of Stephane Genin to develop an experimental evolution project with R. solanacearum. The principal aim of this project was to identify the molecular bases of adaptation to plants. Genomic analysis of the experimentally evolved clones showing adaptive traits on plants allowed me to identify one essential regulatory gene impacting bacterial fitness in plants. I am now supervising two phD students, Anthony Perrier, working on the functional characterization of this gene and Rekha Gopalan Nair, working on the importance of epigenetic alterations in bacterial genomes for adaptation to hosts.


Dr Caroline Baroukh, CR2 INRA

Caroline Baroukh

In 2010, I obtained a diploma from Ecole Centrale de Lyon as well as a MSc from Imperial College of London. Afterwards, I did my PhD at the Laboratory of Environmental Biotechnology at INRA Narbonne. During my PhD, I developed a new metabolic modeling approach to model and understand microalgae metabolism submitted to several trophic growths. Then, I did a postdoctorate at the laboratory Physiology and Biotechnology of Algae (IFREMER), where I reconstructed a core metabolic network of Tisochrysis lutea as well as performed experiments to verify the models’ predictions from my PhD. I also did a postdoctorate in the team of Pr. Chachuat in the chemical engineering department of Imperial College of London. There, I developed new metabolic modeling approaches using mathematical optimization. In 2016, I joined the APAR group to develop and apply systems biology approaches aiming at studying in details the link between metabolism and virulence, as well as initiating the modeling of the infectious dynamics of plant pathogens.

On a non-professional level, one of my favorite hobby is to hold a blog on cooking and pastry


Xavier Barlet, IE1 CNRS


I obtained a Master degree in plant biotechnology at the University of Paris 7 in 1997. I then worked for two years in H. Keller’s lab on plant oomycetes interactions at INRA Antibes before my recruitment in 2001 by the CNRS for working on a human microarray platform at Villejuif. I joined the LIPM in 2005 where I worked on plant susceptibility to Ralstonia solanacearum. I participated to different microarray programs and to the characterization of different plant mutants leading to tolerance to Rs. I joined the group of Stephane Genin in July 2014. I am also in charge of the BSL-2 facility for working on Rs at LIPM.


Patrick Barberis, Technician INRA


Patrick joined the group at the very begining of the work on Ralstonia solanacearum. He has been following the changes from classical genetics to the sequencing of the genome. He has been a key person in managing the Ralstonia solanacearum mutant database and the bioassays on tomato.


Fabien Lonjon, PhD Student, University of Toulouse, doctoral school SEVAB 2014-2017


I obtained a Master’s degree in Microbiology at the University Paul Sabatier of Toulouse in 2013. I joined the group in January 2013 first for my Master Internship and then as lab engineer. I worked on proteins that control type III effectors secretion using post-translational mechanisms. I began a PhD financed by the MESR (French Ministry of Higher Education and Research) in october 2014, under the supervision of Nemo Peeters and Fabienne Vailleau to continue this work.


Anthony Perrier, PhD Student, INRA-Région Occitanie, doctoral school SEVAB 2015-2018


Après l’obtention du Master 2 Recherche Microbiologie de l’université Paul Sabatier – Toulouse III, j’ai rejoint le groupe début octobre 2015, dans le cadre d’une thèse INRA/Région, sous la direction d’Alice Guidot.  Je vais m’intéresser au gène efpR mis en évidence dans l’équipe, par évolution expérimentale, afin de déterminer son rôle dans la transmission de R. solanacearum.


Alice Morel, PhD Student, University of Toulouse, doctoral school SEVAB 2015-2018


J'ai reçu mon diplôme d'ingénieur agronome de l'ENSAT (École Nationale Supérieure en Agronomie de Toulouse) spécialisation agrobiosciences végétales en septembre 2015. Dans le cadre de ce diplôme j'ai eu la possibilité de faire mon stage de fin d'étude dans l'équipe de Stéphane Genin sous l'encadrement de Nemo Peeters. J'ai travaillé sur la caractérisation fonctionnelle des effecteurs de type III RipH1, 2, 3 de Ralstonia solanacearum sur la tomate. J'ai ensuite obtenu un financement du MESR (Ministère de l'enseignement supérieur et de la Recherche) pour continuer ces travaux en thèse depuis octobre 2015.


Rekha Gopalan-Nair, PhD Student, TULIP, doctoral school SEVAB 2017-2020

Rekha Gopalan Nair

I did my Master's in Molecular Biology at the University of Skӧvde, Sweden (2016). I joined LIPM in Feb 2017 as a PhD candidate under the supervision of Stéphane Genin and Alice Guidot. The project emphasizes on the role of epigenetic modifications in a plant pathogen during host adaption and the work is funded by "The TULIP LabEx".