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Microbiote Intestinal Chez Le Porc, Facteurs De Variation Et Relations Avecles Performances Des Animaux Mathilde Le Sciellour Hazon

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Microbiote Intestinal Chez Le Porc, Facteurs De Variation Et Relations Avecles Performances Des Animaux Mathilde Le Sciellour Hazon Microbiote intestinal chez le porc, facteurs de variation et relations avecles performances des animaux Mathilde Le Sciellour Hazon To cite this version: Mathilde Le Sciellour Hazon. Microbiote intestinal chez le porc, facteurs de variation et relations avecles performances des animaux. Biologie animale. Agrocampus Ouest, 2019. Français. NNT : 2019NSARB323. tel-02966534 HAL Id: tel-02966534 https://tel.archives-ouvertes.fr/tel-02966534 Submitted on 14 Oct 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 AGROCAMPUS OUEST COMUE UNIVERSITE BRETAGNE LOIRE ECOLE DOCTORALE N° 600 Ecole doctorale Ecologie, Géosciences, Agronomie et Alimentation Spécialité : Biologie et physiologie animales Par Mathilde LE SCIELLOUR HAZON « Microbiote intestinal chez le porc, facteurs de variation et relations avec les performances des animaux » Thèse présentée et soutenue à Rennes, le 29 octobre 2019 Unité de recherche : Agrocampus Ouest, INRA UMR 1348 Physiologie, Environnement et Génétique pour l’Animal et les Systèmes d’Elevage (PEGASE) Thèse N° : B-323 – 2019-15 Rapporteurs avant soutenance : Sandrine GRASTEAU Directrice de recherche, INRA Val de Loire, UMR 0083 BOA Philippe FRAVALO Professeur, Université de Montréal, Faculté de médecine vétérinaire Composition du Jury : Présidente : Lucile MONTAGNE Professeure, Agrocampus Ouest, INRA UMR 1348 PEGASE Examinateurs : Patricia LEPAGE Chargée de recherche, INRA Jouy-en-Josas, UMR 1319 MICALIS Mahendra MARIADASSOU Chargé de recherche, INRA Jouy-en-Josas, UR 1404 MaIAGE Mathieu CASTEX Directeur R&D, Société Lallemand Animal Nutrition Dir. de thèse : David RENAUDEAU Directeur de recherche, INRA St Gilles, UMR 1348 PEGASE Co-dir. de thèse : Olivier ZEMB Chargé de recherche, INRA Toulouse, UMR 1388 GenPhySE Thèse de doctorat Agrocampus Ouest Comue Université Bretagne Loire Ecole Doctorale n°600 : Ecole doctorale Ecologie, Géosciences, Agronomie et Alimentation Spécialité : Biologie et physiologie animales Par Mathilde LE SCIELLOUR HAZON Microbiote intestinal chez le porc, facteurs de variation et relations avec les performances des animaux Thèse présentée et soutenue à Rennes le 29 octobre 2019. Unité de recherche : Agrocampus Ouest, INRA UMR 1348 Physiologie, Environnement et Génétique pour l’Animal et les Systèmes d’Elevage (PEGASE) Thèse N° : B-323 – 2019-15 Composition du Jury : Présidente : Lucile MONTAGNE Agrocampus Ouest, INRA UMR 1348 Rapporteur : Sandrine GRASTEAU INRA Val de Loire, UMR 0083 Philippe FRAVALO Université de Montréal, Faculté de médecine vétérinaire Examinateurs : Patricia LEPAGE INRA Jouy-en-Josas, UMR 1319 Mahendra MARIADASSOU INRA Jouy-en-Josas, UR 1404 Mathieu CASTEX Directeur R&D, Société Lallemand Animal Nutrition Dir. de thèse : David RENAUDEAU INRA St Gilles, UMR 1348 Co-dir. de thèse : Olivier ZEMB INRA Toulouse, UMR 1388 1 Résumé Microbiote intestinal chez le porc, facteurs de variation et relations avec les performances des animaux L’amélioration de l’efficacité alimentaire (EA) est un enjeu important pour la filière porcine. L’EA est un phénotype complexe faisant intervenir un grand nombre de fonctions chez le porc. Au travers son rôle dans le métabolisme de son hôte et le maintien de sa santé, le microbiote intestinal est susceptible d’impacter les performances de l’hôte et en particulier son EA. Ce travail de thèse vise à étudier les modifications de composition du microbiote intestinal du porc soumis à différents facteurs environnementaux et à évaluer les relations entre cette composition microbienne et les performances de l’hôte. Pour cela, les données de trois études réalisées sur des porcs en croissance-finition (entre 60 et 1 200 porcs par étude) soumis à des perturbations de natures différentes (aliment riche en fibres, aliment contaminé par des mycotoxines (DON) ou exposition à un stress thermique chronique ou aigu) ont été utilisées. L’analyse du microbiote a été réalisée sur la base de prélèvements de fèces obtenus avant et après les perturbations. Parallèlement, des phénotypes en lien avec l’EA de l’hôte ont été mesurés afin d’évaluer et quantifier les relations entre les performances du porc et son microbiote intestinal. L’analyse bio-informatique et statistique approfondie des données microbiennes a montré que les perturbations environnementales impactent la composition du microbiote fécal mais que cet effet n’est généralement que transitoire. Selon la nature du challenge (régime alimentaire standard vs. riche en fibre, exposition à un stress thermique chronique ou aigu, et aliment contaminé par DON), l’impact sur la composition du microbiote intestinal diffère. Les données d’abondances relatives des OTU permettent de discriminer les groupes de porcs suivant des facteurs de variation qualitatifs mais ne permettent pas d’établir des modèles de prédiction quantitatifs entre les performances et les profils bactériens. Des phénomènes de redondance fonctionnelle pourraient expliquer la faible capacité prédictive de ces modèles. Une approche écosystémique basée sur la notion d’entérotype a été utilisée pour caractériser le microbiote. Ces travaux montrent que les entérotypes peuvent être instables au cours du temps chez le porc mais peuvent être associés à des phénotypes, notamment en lien avec la robustesse. Ces résultats ouvrent des perspectives quant à l’utilisation fonctionnelle des données microbiennes pour l’étude des performances de l’hôte. Mots-clés : microbiote, porc, efficacité alimentaire, fibres, stress thermique, mycotoxines 2 Abtract Intestinal microbiota in pigs, variation factors and relationships with animals’ performance Improving feed efficiency (FE) is a major preoccupation for pig production. The FE is a complex trait dealing with lots of functions in pig. The intestinal microbiota is known to play a key role in host metabolism and health with subsequent impact on its performance. The PhD program aimed at studying the modifications of the intestinal microbiota composition on pigs exposed to several environmental perturbations and to evaluate the relationships between digestive microbiota composition and the host performance. Data from three experimental studies conducted on growing-finishing pigs (60 to 1.200 depending on the study) which were exposed to different perturbations [high fiber diet, diet contaminated by mycotoxin (DON), or exposed to acute or chronic heat stress] have been used. The microbiota analysis was based on fecal samples collected before and after the perturbations. Phenotypes directly or indirectly related to FE were measured to evaluate and to quantify the relationships between the host performance and its microbiota. A detailed bioinformatic and statistical analysis of the microbial data demonstrated that the environmental perturbations affect the fecal microbiota composition but these effects were generally transient. Depending on the nature of the challenge (standard or high fiber diet, exposition to a chronic or acute heat stress, or DON-contaminated diet), the impact on fecal microbiota composition seemed to differ. In this PhD program, the relative abundance of the OTU does not allow to implement quantitative prediction models of pig performance. Functional redundancy found in the microbiota related information could explain the low predictive capacity of these models. An ecosystemic approach based on the enterotypes was used to characterize the microbiota. This work shows that enterotypes are unstable across ages in pigs but that they can be related to phenotypes, in particular those in relation with robustness. These results offer some promising perspectives on the functional use of microbiota data to study the host performance. Keywords: microbiota, pig, feed efficiency, fiber, heat stress, mycotoxins 3 Remerciements Je souhaite tout d’abord remercier mes encadrants, David Renaudeau et Olivier Zemb, pour m’avoir fait confiance en m’engageant pour réaliser cette thèse ainsi que pour tout ce qu’ils m’ont apporté durant ces trois années intenses. Grâce à cela, j’ai eu l’opportunité de me former sur un sujet passionnant, très complet et plein d’avenir. Merci aux membres de mon comité de thèse, Etienne Labussière, Hélène Gilbert, Sébastien Dejean, Jordi Estellé-Fabrellas et Mathieu Castex, pour leurs conseils, leur aide, leur disponibilité et tous les échanges constructifs que nous avons pu avoir tout au long de la thèse. Je remercie les membres de mon jury de thèse, Lucile Montagne, Sandrine Grasteau, Philippe Fravalo, Patricia Lepage et Mahendra Mariadassou, qui ont accepté d’évaluer mon travail. Je souhaite aussi remercier les financeurs de ma thèse: le département PHASE de l’INRA et la région Bretagne, ainsi que le projet européen Feed-a-Gene et le projet ANR PigHeat. Je remercie aussi Etienne Labussière, Jean-Luc Gourdine, Hélène Gilbert et Juliette Riquet pour m’avoir permis d’utiliser les données de certains de leurs essais dans le cadre de ma thèse. Je remercie l’UMR PEGASE qui m’a accueillie durant ces trois ans sur le site de l’INRA de St Gilles, ainsi que l’UMR GenPhySE à Castanet-Tolosan
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