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2018AIXM0705.Pdf AVANT-PROPOS Le format de présentation de cette thèse correspond à une recommandation de la spécialité Maladies Infectieuses et Microbiologie, à l’intérieur du Master des Sciences de la Vie et de la Santé qui dépend de l’Ecole Doctorale des Sciences de la Vie de Marseille. Le candidat est amené à respecter des règles qui lui sont imposées et qui comportent un format de thèse utilisé dans le Nord de l’Europe et qui permet un meilleur rangement que les thèses traditionnelles. Par ailleurs, la partie introduction et bibliographie est remplacée par une revue envoyée dans un journal afin de permettre une évaluation extérieure de la qualité de la revue et de permettre à l’étudiant de commencer le plus tôt possible une bibliographie exhaustive sur le domaine de cette thèse. Par ailleurs, la thèse est présentée sur article publié, accepté ou soumis associé d’un bref commentaire donnant le sens général du travail. Cette forme de présentation a paru plus en adéquation avec les exigences de la compétition internationale et permet de se concentrer sur des travaux qui bénéficieront d’une diffusion internationale. Professeur Didier Raoult REMERCIEMENTS Au Professeur Didier Raoult, qui a accepté de diriger mon Master 2 d’abord, puis ma thèse de Science, pour m’avoir guidé tout au long de mon internat et ma spécialisation en microbiologie clinique, pour son indispensable soutien durant mon « après internat » malgré les difficultés administratives, Au Professeur Florence Fenollar, pour avoir acceptée de présider le jury de cette thèse, pour m’avoir conseillé, orienté et suivi durant mon internat de biologie, Aux Professeurs Jean-Philippe Lavigne et Gilbert Greub, pour m’avoir fait l’honneur de bien vouloir être rapporteurs de ma thèse et ainsi d’accepter de juger mon travail, Au Professeur Michel Drancourt, pour son soutien sans faille, pour son énergie et son enthousiasme communicatif, pour son accessibilité de tous les jours, et sa franchise, Au Professeur Jean-Christophe Lagier, pour sa disponibilité, ses précieux conseils et sa gentillesse, au Professeur Pierre Edouard Fournier pour votre gentillesse et votre accessibilité, au Professeur Matthieu Million, pour son aide régulière notamment sur les stat’, À toute l’équipe du CNR des Arbovirus qui m’a chaleureusement accueilli, Christophe, Isabelle, Gilda, Mathilde, Bernard, Patrick, Pierre, Thomas, Laurent, Manon, À Gregory Dubourg, le « grand frère », sa disponibilité sans faille, son soutien, c’était un plaisir de travailler avec toi et d’apprendre de toi, souvent première victime de mes blagues improbables, haut les cœurs ! À Sophie Baron, brillante pilier du laboratoire, j’espère que tu me pardonneras de t’avoir abandonné ; merci d’avoir toujours été là, même dans les vicissitudes de la vie professionnelle ! À mes collègues de culturomics, les « anciens » (Niokhor « président », Perrine sans qui la culturomics ne serait pas ce qu’elle est, Seck, Togo, Sory, Khoudia, Sokhna, Marion, Elodie, Pamela, Sara, Descartes, Isaac, Camille, Maryam, Gaël, Marcel, Saber, Bruno, Melhem), mais aussi les djeuns (Souad, Edmond, Rémi, Emilie, Sabrina). À Amaël parce que Freddy c’était le meilleur et le gras c’est la vie. À Fred, le chef d’orchestre de tout ce petit monde. Aux autres personnes que j’ai eu la chance de croiser durant mon cursus recherche, Lucie Bardet, Florent, Mordav, Erwan, Feriel, Elodie, Nawal, Ghiles, Hortense, Manolis, Maureen, Michel, Richard, À mes anciens co-internes, PBD, Aurélie la docteure des tout-petits, Sophie Amrane, Manu, PBD, Cléa ma copilote à jamais des Rickettsies, Edouard hodor, Antonin, Raquel, Shirley, Anne Ca, P-A, Armel, Baidy, Emma, Fanny, Florent, James, Emilie, Lindsey, Robin, À Julien Fromonot, heureusement que tu es là pour m’aider à décrypter le langage 15189 ! À la team biomol, Donia, Julie, Steph’, Emilie, Annick, Laurence, Sophie Edouard, Elsa, À la team internat, Léa, Estelle, Baptiste, Jean Sé, Chloé, Damien, Jordan, Maude, Florence, Boby, Aux anciens de Caen Sud, Ugo, Perlemoine, Paul, Sacha, Gros, Arnaud, Marc, Marie, Romain. À Alban et Axel pour notre trio rigolard de la P1, À Nico, depuis la 4eme, À Alex pour les avions ! Et pour finir, un grand merci à ma compagne Clémence, merci pour ton soutien et ton amour, pour le temps passé à relire ces pages (et d’autres aussi), merci d’être entrée dans ma vie et de l’embellir, À toute ma famille, Papa, qui m’a donné goût à la médecine et à qui je dédie cette thèse, Maman, qui a toujours cru en moi, mais aussi Amélie et Charles ainsi que leurs conjoints Marc et Satomi, merci pour votre soutien et merci de me rappeler que la famille, c’est le plus important, À mes neveux, Quentin, Pierre, Héloïse, Adrien et Virgile À Anne et Eric, pour leur soutien, à Nathan et Nils, Et à tous ceux que j’ai maladroitement oublié de citer… SOMMAIRE Résumé 1 Abstract 3 Introduction 5 Partie I : Le microbiote digestif comme source de nouveaux antibiotiques 8 Publication n°1: Antibiotic discovery: history, methods and perspectives (review) 11 Publication n°2: Antagonisms from gut microbiota against human-pathogens 62 Partie II : Culturomics et incompatibilités de culture 113 Publication n°3: Culture of previously uncultured members of the human gut microbiota by culturomics 116 Publication n°4: Dynamic variations of anaerobes during non-specific liquid enrichment of human fresh stool sample 152 Conclusion et perspectives 189 Annexes 192 Annexe 1 : Description de nouvelles espèces bactériennes par taxono-genomique 194 Publication n°5: Blautia massiliensis sp. nov., isolated from a fresh human fecal sample and emended description of the genus Blautia 196 Publication n°6: “Intestinimonas massiliensis” sp. nov, a new bacterium isolated from human gut 210 Publication n°7: Noncontiguous finished genome sequence and description of Intestinimonas massiliensis sp. nov strain GD2T, the second Intestinimonas species cultured from the human gut. 212 Publication n°8: Drancourtella massiliensis gen. nov., sp. nov. isolated from fresh healthy human faecal sample from South France 223 Publication n°9: ‘Bittarella massiliensis’ gen. nov., sp. nov. isolated by culturomics from the gut of a healthy 28-year-old man 232 Publication n°10: Description of Clostridium phoceensis sp. nov., a new species within the genus Clostridium 234 Publication n°11: Description of ‘Gorbachella massiliensis’ gen. nov., sp. nov., ‘Fenollaria timonensis’ sp. nov., ‘Intestinimonas timonensis’ sp. nov. and ‘Collinsella ihuae’ sp. nov. isolated from healthy fresh stools with culturomics 242 Publication n°12: Fournierella massiliensis gen. nov., sp. nov., a new human associated member of the family Ruminococcaceae 245 Annexe 2: autres publications 252 Publication n°13: A new highly sensitive and specific real-time PCR assay targeting the malate dehydrogenase gene of 3 Kingella kingae and application to 201 pediatric clinical specimens 253 Publication n°14: Acute Septic Arthritis of the Knee Caused by Kingella kingae in a 5-Year-Old Cameroonian Boy 274 Publication n°15: A modified multilocus sequence typing protocol to genotype Kingella kingae from oropharyngeal swabs without bacterial isolation 281 Publication n°16: Molecular tests that target the RTX locus do not distinguish between Kingella kingae and the recently described K. negevensis species 286 Publication n°17: Emergence of Clostridium difficile tcdC variant 078 in Marseille, France 296 Références 300 RESUMÉ L’étude du microbiote digestif est actuellement un enjeu important de recherche en microbiologie. Des altérations du microbiote digestif ont été corrélées à divers états pathologiques, comme l’obésité, les maladies inflammatoires chroniques de l’intestin ou encore des pathologies neuropsychiatriques (anxiété, dépression). Les relations entre l’hôte et le microbiote digestif sont extrêmement complexes et font intervenir des procaryotes, des virus, des champignons et des parasites. La description du microbiote intestinal apparaît donc comme la première étape dans la compréhension de la relation hôte – microbiote. Parmi les principales approches, la culturomics a permis une explosion du nombre de bactéries isolées dans le tube digestif, passant de 690 à 1705 en moins de dix ans. La première partie de cette thèse porte sur la recherche au sein du microbiote digestif de nouvelles molécules antibactériennes. La recherche et le développement de nouvelles molécules antibiotiques sont une des pistes clés dans la lutte contre la résistance aux antibiotiques, sujet majeur de santé publique actuellement. En effet, les trois quarts des antibiotiques actuels sont des produits naturels, ou dérivés de produits naturels, sécrétés par des bactéries ou des champignons de l’environnement et découvert entre 1940 et 1960 par des tests d’antagonisme de culture. Tout comme l’environnement, le microbiote digestif représente également un environnement complexe où les bactéries vivent en compétition. Dans cette compétition, la synthèse de molécules antibiotiques est un outil pour la survie. Nous avons recherché des antagonismes de culture parmi les bactéries commensales du tube digestif humain. Nous nous sommes focalisés sur des antagonismes contre les six bactéries pathogènes les plus isolées en microbiologie clinique. Nous avons trouvé une inhibition de croissance de S. aureus par P. avidum, une inhibition de E. cloacae par B. fragilis, E. dispar, L. delbruckii, P. acidipropionici, S. equinus, S. gallolyticus, et enfin une inhibition de E. aerogenes par B. vulgatus et E. dispar. De plus, des clusters de gène codant des métabolites 1 secondaires ont été trouvées dans le génome de toutes ces bactéries. Ce travail préliminaire confirme que le microbiote digestif est une source potentielle de nouveau antibactériens. En dépit de l’explosion du nombre d’espèces bactériennes isolées dans le microbiote digestif humain grâce à la culturomics, certaines espèces fastidieuses demeurent peu ou non isolées. Nous avons effectué une analyse métagénomique et culturomics d’une selle fraichement émise avant et après incubation dans un flacon d’hémoculture anaérobie enrichie avec 5% de rumen et 5% de sang de mouton. Ce travail montre que la dynamique de croissance des bactéries anaérobies est très hétérogène.
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