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Le pathobiome, « un concept nouveau et partagé » en santé des plantes, de l’Homme et de l’animal

Dans l’entretien qu’elle nous a accordé, Muriel Vayssier-Taussat, directrice de recherche au département santé animale de l’Inra, présente le pathobiome. Elle explique ce nouveau concept conçu en 2013 par un groupe de chercheurs à l’Inra. Il est issu d’une réflexion commune entre spécialistes de la santé des animaux, des plantes, de l’Homme et de l’environnement.

Paroles d'expert. © Inra, Véronique Gavalda
Par Delphine Achour
Mis à jour le 23/03/2017
Publié le 14/03/2017

Muriel Vayssier-Taussat. © Muriel Vayssier-Taussat
© Muriel Vayssier-Taussat
Muriel Vayssier-Taussat dirige l’équipe « Vectotiq » de l’unité BIPAR* à Maisons-Alfort. Ses recherches portent sur les agents pathogènes transmis par les tiques chez l’Homme et l’animal.


En juin 2015 vous avez organisé avec des collègues le 1er congrès international sur le pathobiome. Un nouveau concept dans les sciences de la vie ?

Muriel Vayssier-Taussat : Un nouveau concept, mais aussi une réalité. C’est parti d’une réflexion avec d’autres chercheurs, menée en 2013 dans le cadre du méta-programme MEM** de l’INRA. Nous partions du constat que notre vision pour aborder les agents pathogènes était réduite à l’association : un seul agent pathogène, un hôte. Elle repose sur le postulat de Koch établi au 19e siècle avec la découverte des microbes : « un microbe, une maladie ». Autrement dit, depuis cette époque, l’agent pathogène était principalement étudié isolément, sans prise en compte de son environnement microbien, c’est à dire les autres micro-organismes avec lesquels il vit, en interaction.

Afin de mieux comprendre les maladies infectieuses, nous proposons d’étudier l’agent pathogène au sein de son écosystème microbien et les interactions qu’il y développe. C’est ce que nous avons appelé le pathobiome. Ce nouveau concept a fait l’objet en 2014 d’une publication co-signée par des chercheurs en santé des plantes, de l’Homme et de l’animal et des écologues.

Peut-on parler d’une révolution dans les sciences du vivant ?

MVT : Non, il s’agit plutôt d’une approche plus globale et plus proche de la réalité. Elle reste compliquée car elle nécessite de la multidisciplinarité.

Des outils spécifiques sont-ils nécessaires pour explorer les pathobiomes ?

MVT : Etudier le pathobiome c’est pouvoir décrire l’écosystème microbien dans lequel vit l’agent pathogène. C’est aussi mettre en  lumière les interactions qui y règnent et comprendre leur rôle vis-à-vis de l’agent pathogène. Vont-elles atténuer ses propriétés ou les amplifier ?

Jusqu’à présent les pathobiomes n’étaient pas explorés car les micro-organismes qui les composent ne sont pas toujours faciles à cultiver, voire impossibles pour certains. Il est possible maintenant de les identifier et de comprendre leur fonction  grâce aux techniques de séquençage à haut débit.

Le principe consiste à prélever un échantillon dans l’environnement que l’on souhaite étudier (fragment végétal, intestinal, broyat d’insectes ou d’acariens mais aussi échantillons du sol, …). L’ADN ou l’ARN sont ensuite extraits, suivant les analyses souhaitées, puis séquencés. Les données brutes sont ensuite analysées avec les outils de bio-informatique et de statistiques. Nous pouvons ainsi caractériser l’environnement microbien de l’agent pathogène et identifier certaines fonctions  qui y sont exprimées.

Cette nouvelle approche a-t-elle permis de progresser dans la compréhension des maladies transmises par les tiques ?

MVT : Elle y contribue. Par exemple, nos travaux ont permis de mettre en évidence l’étendue des micro-organismes présents dans les tiques. Ceux qui sont pathogènes, ceux qui ne le sont pas. Nous avons également ainsi mis en évidence que les tiques sont souvent multi-infectées. Il reste à identifier si ces co-infections se retrouvent chez les malades piqués par des tiques. Et quelles sont leurs implications sur les symptômes.

Nos recherches se focalisent maintenant sur le microbiome des tiques vis à vis des agents pathogènes qu’elles transmettent. Quel rôle a-t-il dans l’acquisition, le maintient puis la transmission des agents pathogènes par la tique ? Par ailleurs, nous étudions le rôle des infections multiples sur l’évolution des pathogènes. A terme, l’identification de composés capables d’empêcher le pathogène d’être actif dans la tique permettrait d’imaginer des moyens de lutte contre les maladies qu’elles transmettent.

Quel avenir pour l’étude des pathobiomes ?

MVT : Tout d’abord, la deuxième édition en mars 2018 du congrès international sur le pathobiome, à Ajaccio. La révolution de ces dernières années a été de prendre conscience que nous et nos animaux sommes aussi faits de micro-organismes (nous avons 10 fois plus de cellules bactériennes dans notre corps que de cellules humaines). Comprendre les interactions entre les agents pathogènes et les constituants microbiens dans les processus pathologiques apportera de nouvelles connaissances indispensables pour définir des approches innovantes et alternatives aux anti-infectieux classiques.


Propos recueillis par Delphine Achour

* Biologie Moléculaire et Immunologie Parasitaires - Unité mixte de recherche BIPAR, INRA/ANSES/ENVA

** Projet PATHO-ID, méta-programme MEM (Méta-omiques et Ecosystèmes Microbiens)

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Microbiologie et chaîne alimentaire
Centre(s) associé(s) :
Jouy-en-Josas

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Référence

Muriel Vayssier-Taussat, Emmanuel Albina, Christine Citti, Jean-Franҫois Cosson, Marie-Agnès Jacques, Marc-Henri Lebrun, Yves Le Loir, Mylène Ogliastro, Marie-Agnès Petit, Philippe Roumagnac and Thierry Candresse. Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics. Frontiers in Cellular and Infection Microbiology. March, 2014, Volume 4, Article 29.

@gr_pathobiome : le compte Twitter des activités "pathobiomes"

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