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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, CRCN 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, CRCN 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, IEHC 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.


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".


Nargess Razavi, PhD Student, University of Toulouse, doctoral school SEVAB 2017-2020


I obtained my master’s degree at ENSAT University, in Agro bioscience in 2017. I did my Master project in Stephane Genin’s group under the supervision of Fabienne Vailleau to study hpaP mutant of Ralstonia solanacearum against the natural diversity of Arabidopsis thaliana. I started my PhD at LIPM in November 2017 on the following topic: “Deciphering Arabidopsis thaliana responses to bacterial virulence factors of Ralstonia solanacearum through the study of natural diversity of the two partners”, under the supervision of Fabienne Vailleau and Richard Berthomé.


Léa Casagrande, CDD IE, 2017-2021


I obtained a Master of Molecular Biology and Microbiology at the University of Pau in 2017 after having completed my internship in Stéphane Genin’s group under the supervision of Alice Guidot. During this internship, I studied the importance of methyltransferases in the virulence of Ralstonia solanacearum. Since December 2017, I’m involved in the ANR project « EPI-PATH » which aims to investigate the role of epigenetic modifications in Ralstonia solanacearum in host adaptation.


David Landry, PhD Student, University of Toulouse, doctoral school SEVAB 2018-2021

David Landry

In 2016, I obtained my Master specialized in Plant Biology at University of Poitiers. I did my internship at EBI lab – team SEVE in Poitiers, where I studied the implication of sugar transport in tripartit interaction between: Arabidopsis thalianaPseudomonas fluorescens WSC417r – Botrytis cinerea. Then, I was recruited as engineer at LIPM. I studied decoy domain integrated within R protein in order to demonstrate their interaction with core effectors from Ralstonia solanaceaum. In 2018, I was selected by SEVAB in the PhD contest and I started the PhD under the supervision of Nemo PEETERS and Laurent DESLANDES. The aim of this project is to decipher R protein that recognize the RipAA effector delivered by Ralstonia solanacearum in model plant species Nicotiana benthamiana.


Léo Gerlin, PhD Student, University of Toulouse, doctoral school SEVAB 2018-2021

Leo Gerlin

I obtained a master’s degree in biological engineering at INSA Toulouse in 2018, after a master project in Stéphane Genin’s team. This project aimed to reconstruct and analyze the metabolic network of the bacterium Xylella fastidiosa, and was under the supervision of Caroline Baroukh and Ludovic Cottret. Since October 2018, I started a PhD in the team, funded by a ministerial grant. Under the supervision of Stéphane Genin and Caroline Baroukh, I will develop a metabolic model of the interaction between Ralstonia solanacearum and tomato.


Antoine Escourrou, CDD IE, 2018-2020

Antoine Escourrou

After a license degree in organisms, populations and ecosystems biology (BOPE), obtained in 2013 from Université Paul Sabatier (Toulouse 3), Antoine has rapidly developed an interest for natural compounds biosynthesis, and for the methods aiming at these substances’ characterization. After an internship graduation performed at the French National Institute for Agronomical Research (INRA) in Bordeaux where he had to establish the metabolomic profiles of different strains of a phytopathogenic fungus, co-supervised by MycSA (Mycology and food safety, UR 12647) and Bordeaux metabolomic platform, it is then equipped with a Master’s degree Phytoressources from Université Claude Bernard (Lyon 1) that he was first hired as an engineer on LABERCA’s analytical chemistry platform (The laboratory of food residues and contaminants studies, UMR INRA 1329) in Nantes for two years. He then worked on the biodegradation of health products as an engineer/ researcher for Pierre Fabre Dermo-Cosmétique in the LBBM team (Microbial biodiversity and biotechnologies laboratory, USR 3579, Banyuls-sut-Mer), before being hired as an MSc engineer in Stéphane Génin’s team at LIPM under the supervision of Caroline Baroukh.