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Methanobrevibacter Smithii AIX-MARSEILLE UNIVERSITE FACULTE DE MEDECINE DE MARSEILLE ECOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTE THESE DE DOCTORAT Présentée par Sory Ibrahima TRAORE En vue de l'obtention du grade de D2&725$7G¶$,;-MARSEILLE UNIVERSITÉ Spécialité Pathologie Humaine Etude de microbiote digestif Africain par culturomics et nouvelle technique d'isolement et de culture de Methanobrevibacter smithii Soutenue le 2 Novembre 2018 COMPOSITION DU JURY Mme le Professeur Florence Fenollar Président du jury Mr le Professeur Mahamadou Ali Théra Rapporteur Mr le Professeur Max Maurin Rapporteur Mr le Professeur Didier Raoult Directeur de thèse MEPHI, Aix Marseille Université, IRD, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille Prof – Didier Raoult 2018 1 Avant-propos Le format de présentation de cette thèse correspond à une recommandation de la spécialité Maladies Infectieuses et Microbiologie du Master des Sciences de la Vie et de OD6DQWpTXL GpSHQGGHO¶(FROH'RFWRUDOHGHV6FLHQFHVGHOD9LHGH0DUVHLOOH/H FDQGLGDWest amené à respecter des règles qui lui sont imposées et qui comportent un format de WKqVHXWLOLVpGDQVOH1RUGGHO¶(XURSH Ht qui permet un meilleur rangement que les thèses traditionnelles. Par ailleurs, la partie introduction et bibliographie est remplacée par une revue publiée dans un journal scientifique afin de permettre une évaluation extérieure de la qualité de la revue HW GH SHUPHWWUH j O¶pWXGLDQW GH FRPPHQFHU OH SOXV W{W SRVVLEOH XQH bibliographie exhaustive sur le domaine de cette thèse. Par ailleurs, la thèse est présentée VXU DUWLFOH SXEOLp DFFHSWp RX VRXPLV DVVRFLp G¶XQ EUHI FRPPHQWDLUH GRQQDQW OH VHQVgénéral 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 EpQpILFLHURQWG¶XQHGLIIXVLRQLQWHUQDWLRQDOH Prof. Didier Raoult 3 Dédicaces Je dédie ce travail à : ¾ Mon père Lassana TRAORE qui nous a quitté le 21 décembre 2017. Face à toi je suis empli d’un sentiment d’humilité. Seul compte ton enthousiasme à vouloir propulser tes enfants. Dors en paix cher papa ! ¾ Professeur Ogobara K Doumbo qui nous a quitté le 9 juin 2018. Ce que je ressens pour vous est indicible. Vous avez laissé des empreintes à ma vie qui font que dans un souffle je vous appellerai toujours papa. Dors en paix Grand Professeur ! ¾ Ma mère, pour tout l’amour que j’ai pour toi, pour tous les sacrifices que tu as réalisés. Longue vie avec une parfaite sante ! ¾ Mes frères et sœurs, pour le regard que nous portons ensemble au delà de nos souffrances et de nos différends. Que nos différences ne nous séparent jamais ! ¾ Ma femme, pour sa patience et l’entente qu’elle cultive dans notre couple. 5 Remerciements Je tiens tout d’abord à remercier le Professeur Didier RAOULT qui, au delà de m’avoir donné l’opportunité de faire cette thèse, m’a assisté tout au long de ce travail, m’a relevé les nombreuses fois où j’ai trébuché. Ce travail est le résultat de votre patience et de votre souci constant d’accompagner vos étudiants dans les bons comme les pires moments de leur formation. Vous avez forcé mon admiration pour vous à travers votre équité et votre amour pour science. C’est un grand honneur pour moi d’avoir évolué à vos côtés. Je remercie le Professeur Florence FENOLLAR pour avoir accepté de présider ce jury de thèse. Je remercie sincèrement le Professeur Max MAURIN et le Professeur Mahamadou Ali THERA pour avoir accepté d’être les rapporteurs de ce travail. Je remercie le Professeur Jean Christophe LAGIER pour son co-encadrement. 7 Ce travail a été possible grâce à la participation et au soutien de toute l’équipe culturomics. Je remercie ainsi mes séniors : Docteur Saber Khelaifia, Docteur Gregory Dubourg et Docteur Matthieu Million pour leurs conseils scientifiques et leur soutien durant toute cette thèse. Mes remerciements vont également à l’endroit de mes collègues de travail: Amadou Togo, Melhem Bilen, Maxim Descartes, Ami Diakité, Fatima Zaara, Pamela Afouda, Thao Pam, Guillaume Durand, Aurélie Morand, Morgane Maihe, Davidé Ricaboni, Sophie Amrane, El hadji Seck, Elodie Guillot, Issa Isaac, Ngom, Camille Vales, Maryam Tidjiani Alou, Khoudia Diop, Awa Diop, Sokhna Ndongo, Elodie Neau, Sabrina Naud, Amael Fadlane . Merci à tous pour votre bonne collaboration. Je remercie aussi le Professeur Pierre-Edouard Fournier pour sa gentillesse et sa sympathie. 9 Je remercie mes amis maliens de Marseille pour le soutien et l’entraide que nous cultivons : Adama Diarra, Aly Kodjo, Issa Diarra, Cheick Khounta, Aminata Camara, Cheick Guindo, Bamoussa Fofana, Abdoulaye Guindo, Elisabeth Sogodogo, Ami Diakité, Mme Khounta, Amadou Togo. Je remercie tout le personnel de l’IHU Méditerranée infection et l’URMITE, en particulier Valérie Filosa, qui m’a accueilli et soutenu durant mes premiers jours à Marseille. Francine Verin, Fatma Zaourar, Annick, Veronick Roux. Merci aux ingénieurs de spectrométrie de mass Christophe, Carine, Philippe, Nicolas et Luc pour leur aide ainsi que Frédéric Cadoret et Claudia Andrieu. Merci à la fondation Méditerranée infection, à son directeur le Pr. Didier RAOULT et à sa gestionnaire Micheline Pitaccolo pour le rôle d’une mère qu’elle nous remplit. 11 Sommaire Résumé««««««««««««««««««««««««««««««« p.15 Abstract«««««««««««««««««««««««««««««««.p. 19 Introduction«««««««««««««««««««««««««««««S23 Chapitre 1 : Etude bibliographique du microbiote digestif humain africain....««.p.31 1.1.Etude du microbiote digestif humain Africain Chapitre 2 : Etude du microbiote Africain par culturomics.........................«««S53 2.1. Beduinella massiliensis, gen. nov., sp. nov. a new genus representing a new family in the phylum Firmicutes, and proposal of Beduinellaceae fam. nov. 2.2. Noncontiguous finished genome sequence and description of Bacillus andreraoultii strain SIT1T sp. nov. Chapitre 3 : Isolement et culture de Methanobrevibacter smithii par co-culture avec des bactéries SURGXFWULFHVG¶K\GURJqQH ««««««««««««««««««p.75 3.1. Isolation and culture of Methanobrevibacter smithii by co-culturing with hydrogen producing bacteria Conclusion««««««««««««««««««««««.«««««««....S95 Liste des références..................................................................................................... p.99 Annexe««««««««««««««««««««««...«««««««« S105 13 Résumé 15 Résumé /¶pWXGH GX PLFURELRWH GLJHVWLI D FRQQX XQ UHJDLQ G¶LQWpUrW au début des années 2000, DYHF O¶DYqQHPHQW GHV WHFKQLTXHV PROpFXODLUHV HQ SDUWLFXOLHU OD métagénomique. La culturomics (culture microbienne à haut débit avec identification des colonies par MALDI-TOF) a démontré sa complémentarité depuis 2010 en réduisant une partie des biais des méthodes moléculaires. Dans la première partie de mon travail de thèse, M¶DLUpDOLVpXQHUHYXHGHODOLWWpUDWXUHVXU OHVSULQFLSDOHVWHFKQLTXHVG¶pWXGHGXPLFURELRWHGLJHVWLIHWG¶DXWUHSDUWVXUO¶DQDO\VHGX PLFURELRWH GHV VXMHWV G¶RULJLQH $IULFDLQH Les principales études de métagénomique réalisées sur des prélèvemenWV G¶RULJLQH $IULFDLQH ont révélé une augmentation de la biodiversité, avec en particulier une augmentation des Spirochaetes et des Prevotella FKH]OHVVXMHWVG¶RULJLQH$IULFDLQHSDUUDSSRUWDX[VXMHWVRFFLGHQWDX[/HVpWXGHVSRUWDQW sur la malnutrition onW GpPRQWUp XQH UpGXFWLRQ GH O¶HQVHPEOH GHV EDFWpULHV HW HQ particulier des bactéries anaérobies et des archaea méthanogènes. Sur les 1162 bactéries LVROpHVSDUpWXGHGHFXOWXURPLFVRQWpWpLVROpHVVHXOHPHQWGHSUpOqYHPHQWVG¶RULJLQH DXWUH TXH G¶$IULTXH RQW pWp LVROpHV HQ FRPPXQ HW EDFWpULHV Q¶RQW pWp LVROpHV TX¶jSDUWLUGHSUpOqYHPHQWVG¶RULJLQH$IULFDLQHGRQWQRXYHOOHVHVSqFHV 'DQVXQHVHFRQGHSDUWLHM¶DLH[SRVpPDSDUWLFLSDWLRQDXWUDYDLOGHFXOWXURPLFV qui a consisté HQ O¶LVROHPHQW HW OH WHVW de 102 750 colonies bactériennes par MALDI- TOF, et qui ont donné lieu à O¶LGHQWLILFDWLRQ GH HVSqFHV EDFWpULHQQHV GLIIpUHQWHV incluant 40 nouvelles espèces, 17 nouveaux genres et 2 nouvelles familles. -¶DLHIIHFWXp la description complète par taxonogenomics (incluant le spectre MALDI-TOF et le 17 VpTXHQoDJHGXJpQRPH HWRXO¶DQQRQFHGHODFXOWXUH QHZVSHFLHVDQQRXQFHPHQW GHFHV nouvelles espèces. (QILQ GDQV XQH WURLVLqPH SDUWLH MH GpFULUDL OD GpFRXYHUWH HW OD PLVH DX SRLQW G¶Xne QRXYHOOHWHFKQLTXHG¶LVROHPHQWGHVDUFKDHDPpWKDQRJqQHVHWTXLDSHUPLVO¶LVROHPHQWGH Methanobrevibacter smithii, archaea méthanogène appartenant au phylum Euryarchaeota. Les archaea méthanogènes sont de plus en plus rencontrés dans la population humaine avec une prévalence de 97,4% pour Methanobrevibacter smithii et associés à des SDWKRORJLHV FRPPH O¶DEFqV GX FHUYHDX OHV SDURGRQWLWHV HWF« /D FXOWXUH GH FHV PLFURRUJDQLVPHV H[WUrPHPHQW VHQVLEOHV j O¶R[\JqQH HVW IDVWLGLHXVH HW QpFHVVLWDLW XQH source exWpULHXUHG¶K\GURJqQH Dans ce travail de thèse, sous enceinte anaérobie, nous avons cultivé avec succès M. smithii j SDUWLU G¶XQ PLOLHX GH FXOWXUH OLTXLGH LQRFXOp G¶pFKDQWLOORQGHVHOOHFROOHFWpHFKH]XQGRQQHXUVDLQW/¶LVROHPHQWHQFXOWXUHSXUH a été un succès sur milieu gélosé en réalisant une coculture avec Bacteroides thetaiotaomicron. Nous avons aussi testé avec succès la coculture de M. smithii DYHF G¶DXWUHV EDFWpULHV SURGXFWULFHV G¶K\GURJqQH FRQQXHV /HV WHVWV GH FKURPDWRJUDSKLH HQ SKDVH JD]HXVH PRQWUDLHQW TXH FHV VRXFKHV SURGXLVDLHQW GH O¶K\GURJqQH HQ TXDQWLWpV GLIIpUHQWHV /HV colonies isolées sur gélose étaient bien viables et observables et la production de méthane était mesurée par spectrométrie de masse. Mots-clés : Microbiote humain, microbiote africain, microbial culturomics, Archaea méthanogènes, Methanobrevibacter smithii. 18 Abstract 19 Abstract The study of the digestive microbiota was
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