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Impact Du Régime Alimentaire Sur La Dynamique Structurale Et Fonctionnelle Du Microbiote Intestinal Humain Julien Tap

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Impact Du Régime Alimentaire Sur La Dynamique Structurale Et Fonctionnelle Du Microbiote Intestinal Humain Julien Tap Impact du régime alimentaire sur la dynamique structurale et fonctionnelle du microbiote intestinal humain Julien Tap To cite this version: Julien Tap. Impact du régime alimentaire sur la dynamique structurale et fonctionnelle du microbiote intestinal humain. Microbiologie et Parasitologie. Université Pierre et Marie Curie - Paris 6, 2009. Français. tel-02824828 HAL Id: tel-02824828 https://hal.inrae.fr/tel-02824828 Submitted on 6 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THESE DE DOCTORAT DE L’UNIVERSITE PIERRE ET MARIE CURIE Spécialité Physiologie et physiopathologie Présentée par M. Julien Tap Pour obtenir le grade de DOCTEUR de l’UNIVERSITÉ PIERRE ET MARIE CURIE Sujet de la thèse : Impact du régime alimentaire sur la dynamique structurale et fonctionnelle du microbiote intestinal humain soutenue le 16 décembre 2009 devant le jury composé de : M. Philippe LEBARON, Président du jury Mme Karine CLEMENT, Examinateur Mme Annick BERNALIER, Rapporteur Mme Gabrielle POTOCKI-VERONESE, Examinateur M. Jean FIORAMONTI, Rapporteur M. Eric PELLETIER, Examinateur Mme Marion LECLERC, Examinateur Université Pierre & Marie Curie - Paris 6 Tél. Secrétariat : 01 42 34 68 35 Bureau d’accueil, inscription des doctorants et base de Fax : 01 42 34 68 40 données Tél. pour les étudiants de A à EL : 01 42 34 69 54 Esc G, 2 ème étage Tél. pour les étudiants de EM à MON : 01 42 34 68 41 15 rue de l’école de médecine Tél. pour les étudiants de MOO à Z : 01 42 34 68 51 75270-PARIS CEDEX 06 E-mail : [email protected] « Tous pour un ! Un pour tous ! » Alexandre Dumas, Les Trois Mousquetaires (1844). 3 Cette thèse a été effectuée sous la direction de Marion Leclerc à l’INRA au sein de l’unité Ecologie et Physiologie du Système Digestif et financée par le projet ANR AlimIntest : INRA Unité Ecologie et de Physiologie du Système Digestif Centre de Recherche de Jouy Domaine de Vilvert 78352 Jouy-en-Josas cedex FRANCE 4 REMERCIEMENTS Ce travail de thèse n’a été possible que par l’intermédiaire de multiples collaborations et enrichi par différentes personnes, associant plusieurs compétences allant de la modélisation mathématique à la biologie moléculaire, en passant par la bioinformatique. Il ne fut possible que par l’apport, le soutient moral et scientifique de toutes ces personnes. Je tiens à remercier : Philippe Lebaron, Annick Bernalier et Jean Fioramonti d’avoir accepté de faire parti de mon jury de thèse et de me faire l’honneur de juger mon travail. Marion Leclerc, pour sa confiance absolue en mon travail et son soutien actif de tous les instants. Je souhaite à tous les doctorants de l’avoir comme encadrante. Joël Doré, pour sa confiance et son soutien dans toutes mes initiatives, mais aussi pour m’avoir rapidement mis sur le chemin du noyau phylogénétique dès mon arrivée à l’INRA. Stanislas Mondot, pour son énergie et notre travail en synergie en bioinformatique et en statistique, et j’espère que nous continuerons à travailler ensemble dans le futur. Jean-Pierre Furet, pour son apport technique et son soutien moral, mais aussi pour les multiples aventures que nous avons vécues notamment avec la métatranscriptomique. Ludovic Legrand et Christophe Caron, pour leur bonne humeur, leur réceptivité, leur capacité à dialoguer avec des biologistes et tout simplement pour RapidOTU. (Je n’oublie pas Clément Gauthey qui en a réalisé la première version). Eric Pelletier, Edgardo Ugarte et Denis Le Paslier, pour tous leurs coups de pouce, toujours au bon moment, leur intervention a toujours été cruciale pour faire avancer cette thèse. Florence Levenez, pour son soutien technique qui a été à la base de ce travail de thèse. Patricia Lepage et Karine Gloux, pour toutes nos conversations enrichissantes. Rafaël Muñoz Tamayo, pour son ouverture d’esprit et sa modélisation mathématique du côlon humain que j’ai pu utiliser dans ce travail de thèse. Gérard Corthier, pour son apport dans mon travail de thèse qui a été considérable aussi bien sur le plan technique que scientifique, notamment pour la mise en œuvre de la méta-transcriptomique. Tout le consortium du projet AlimIntest mais aussi toute l’Unité d’Ecologie et Physiologie du Système Digestif, qui m’ont fourni un cadre idéal pour mener à bien ce travail de thèse. Gabrielle Veronese et Lena Tasse, en particulier, pour notre collaboration notamment sur l’approche métagénomique fonctionnelle. Catherine Philippe et Sylvie Rabot, pour leur apport technique dans le dosage des acides gras à chaînes courtes. Eric Fontaine et Hubert Roth, pour leur rôle dans l’étude clinique AlimIntest. Toute l’équipe de Karine Clément, pour notre collaboration fructueuse et de m’avoir transmis beaucoup de connaissance sur les maladies métaboliques. Un remerciement particulier à Omar Lakhdari car cela fait maintenant huit ans que nous travaillons ensemble, et bien évidemment Karine Le Roux mais ça elle sait pourquoi…♥ 5 RESUME Nutritionnistes et gastroentérologues s’accordent pour admettre que le microbiote intestinal conditionne de nombreuses fonctions de l’hôte et joue un rôle important dans le bien-être digestif. Comprendre comment notre régime alimentaire modifie la structure et les fonctions du microbiote intestinal est essentiel afin de connaître en retour son impact sur notre santé. Le consortium d’espèces du microbiote intestinal de l’Homme adulte apparaît spécifique de l’individu. Ceci constitue un paradoxe dans la mesure où il existe une grande homogénéité fonctionnelle de l’écosystème intestinal quant à sa fonction physiologique de dégradation des fibres alimentaires. A partir d’un inventaire moléculaire basé sur le gène de l’ARNr 16S à partir de 17 volontaires sains ayant des régimes alimentaires variés, il apparaît en effet que la plupart des phylotypes sont spécifiques de l’individu. Néanmoins, 2% des phylotypes sont partagés par plus de 50% des individus représentant 35,5% des séquences obtenues. Ce petit nombre limité de phylotypes constituerait le noyau phylogénétique du microbiote intestinal et son rôle apparaît critique dans le bien-être digestif. Dans le cadre d’une étude clinique sur volontaires sains, impliquant deux régimes alimentaires contrôlés variant selon la teneur en fibres, une approche microbiomique a montré que la dynamique structurale et fonctionnelle du microbiote pouvait être modifiée en cinq jours. De plus, il a été montré que la structure du microbiote intestinal restait sous influence du régime alimentaire administré au moins 15 jours auparavant. Ces travaux ouvrent de nouvelles perspectives pour de futures investigations nutritionnelles et épidémiologiques. Mots clés : Microbiote, Fibres, Microbiomique, Noyau, Alimentation, Santé 6 ABSTRACT Nutritionists and gastroenterologists agree to admit that intestinal microbiota determines many host functions and plays an important role in the digestive well being. Understanding how our diet alters the structure and functions of intestinal microbiota is essential to know in turn its impact on our health. The species consortium of adult's intestinal microbiota appears specific to the individual. This seems a paradox since there are homogeneous physiological functions of the intestinal ecosystem such as dietary fiber degradation. From a molecular inventory, based on 16S rRNA genes from 17 healthy volunteers with different diets, it indeed appeared that most phylotypes were specific of the individual. However, 2% of the phylotypes were shared by more than 50% of individuals and represented 35.5% of the sequences obtained. This small and limited number of phylotypes constitutes an intestinal microbiota phylogenetic core and its role appears critical for digestive well-being. As part of a clinical study on healthy volunteers, involving two controlled diets varying according to fiber content, a microbiomics approach showed that the structural and functional dynamics of the microbiota could be modified within five days. Moreover, unexpectedly, the intestinal microbiota structure remained under the influence of the diet for at least 15 days after its administration. These results open new perspectives for future nutrition and epidemiology investigations. Keywords : Microbiota, Fiber, Microbiomics, Core, Food, Health Title : Diets impact on structural and functional dynamic of the human intestinal microbiota 7 TABLE DES MATIERES REMERCIEMENTS........................................................................................................................................5 RESUME ..........................................................................................................................................................6 ABSTRACT.......................................................................................................................................................7 TABLE DES MATIERES ................................................................................................................................9 LISTE DE PUBLICATIONS........................................................................................................................
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