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Taxonomie Des Bactéries Anaérobies : De La Reclassification À La Découverte De Nouveaux Pathogènes Corentine Alauzet

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Taxonomie Des Bactéries Anaérobies : De La Reclassification À La Découverte De Nouveaux Pathogènes Corentine Alauzet Taxonomie des bactéries anaérobies : De la reclassification à la découverte de nouveaux pathogènes Corentine Alauzet To cite this version: Corentine Alauzet. Taxonomie des bactéries anaérobies : De la reclassification à la découverte de nouveaux pathogènes. Biochimie, Biologie Moléculaire. Université Henri Poincaré - Nancy 1, 2009. Français. NNT : 2009NAN10123. tel-01748308 HAL Id: tel-01748308 https://hal.univ-lorraine.fr/tel-01748308 Submitted on 29 Mar 2018 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. AVERTISSEMENT Ce document est le fruit d'un long travail approuvé par le jury de soutenance et mis à disposition de l'ensemble de la communauté universitaire élargie. Il est soumis à la propriété intellectuelle de l'auteur. Ceci implique une obligation de citation et de référencement lors de l’utilisation de ce document. D'autre part, toute contrefaçon, plagiat, reproduction illicite encourt une poursuite pénale. Contact : [email protected] LIENS Code de la Propriété Intellectuelle. articles L 122. 4 Code de la Propriété Intellectuelle. articles L 335.2- L 335.10 http://www.cfcopies.com/V2/leg/leg_droi.php http://www.culture.gouv.fr/culture/infos-pratiques/droits/protection.htm UFR DE MEDECINE ECOLE DOCTORALE BIOLOGIE SANTE ET ENVIRONNEMENT THESE Présentée et soutenue publiquement pour l’obtention du titre de DOCTEUR DE L’UNIVERSITE HENRI POINCARE Mention : Génomique par Corentine ALAUZET Le 06 Novembre 2009 TAXONOMIE DES BACTERIES ANAEROBIES : DE LA RECLASSIFICATION A LA DECOUVERTE DE NOUVEAUX PATHOGENES MEMBRES DU JURY : Rapporteurs : Monsieur le Professeur Benoît JAULHAC Université Louis Pasteur, Strasbourg Monsieur le Professeur Jean-Louis PONS Université de Rouen Examinateurs : Madame le Professeur Estelle JUMAS-BILAK Université Montpellier I Monsieur le Professeur Pierre LEBLOND Nancy Université Monsieur le Professeur Alain LOZNIEWSKI Nancy Université, Directeur de thèse Madame le Docteur Francine MORY Nancy Université, Co-directeur de thèse EA 4369 – Relations Hôte-Environnement-Microorganismes Sommaire Sommaire LISTE DES TABLEAUX .............................................................................................................. 9 INTRODUCTION GENERALE .......................................................................................... 14 DONNEES BIBLIOGRAPHIQUES .................................................................................... 17 TAXONOMIE MIXTE ET CONSENSUELLE BACTERIENNE......................................................... 18 I. Historique de la classification des êtres vivants........................................................... 18 II. La phylogénie bactérienne........................................................................................... 22 1. De l’approche morphologique à l’approche moléculaire......................................... 22 2. ARN ribosomiques et horloges moléculaires........................................................... 25 a) Généralités sur l’ARNr 16S ................................................................................. 25 b) Nouvelle place des bactéries dans l’arbre du vivant............................................ 26 c) Radiation explosive des phyla.............................................................................. 27 3. Les marqueurs alternatifs à l’ARNr 16S pouvant être utilisés en phylogénie ......... 32 4. Approches phylogénétiques intégrées...................................................................... 35 a) Notion de séquences signatures ........................................................................... 35 b) Phylogénie de gène / phylogénie d’organisme .................................................... 36 5. L’évolution des bactéries est-elle une arborescence : prise en compte des transferts latéraux ......................................................................................................................... 38 III. L’unité taxonomique de base : la notion d’espèce bactérienne ................................. 40 IV. La taxonomie bactérienne .......................................................................................... 44 1. Intérêt d’une taxonomie bactérienne ........................................................................ 44 2. Caractères utilisés pour la classification des bactéries............................................. 45 a) Méthodes phénotypiques...................................................................................... 47 b) Méthodes génomiques et génétiques ................................................................... 52 3. Méthodes phylogénétiques appliquées à la taxonomie ou phylotaxonomie ............ 58 a) Les méthodes........................................................................................................ 58 b) La phylogénomique ............................................................................................. 67 4. Approche taxonomique mixte et consensuelle......................................................... 69 5. Les classifications actuelles ..................................................................................... 70 a) Le Bergey’s Manual of Systematic Bacteriology ................................................. 71 b) La List of Prokaryotic names with Standing in Nomenclature (LPSN)............... 72 c) Les règles de description et de publication des nouveaux organismes ................ 73 6. La nomenclature bactérienne ................................................................................... 74 LES FIRMICUTES : UN PHYLUM EN PLEIN REMANIEMENT ....................................................... 76 I. Généralités.................................................................................................................... 76 1. Historique et diversité des Firmicutes...................................................................... 76 2. Classification actuelle des Firmicutes...................................................................... 78 a) Révisions du phylum Firmicutes ......................................................................... 78 b) Exemples de remaniements taxonomiques au sein des Clostridia ...................... 79 II. Cas particulier des Clostridium spp............................................................................ 86 1. Les Clostridiaceae : une bien grande famille ! ........................................................ 86 2. Les outils taxonomiques utilisables avec les Clostridium spp. ................................ 89 3. Clostridium, structure de paroi et coloration de Gram............................................. 90 4. Clostridium et sporulation........................................................................................ 91 5. Clostridium et résistance aux glycopeptides ............................................................ 92 a) Les glycopeptides : mécanismes d’action et de résistance................................... 92 b) Sensibilité diminuée à la vancomycine chez certains Clostridium...................... 97 1 Sommaire 6. Clostridium hastiforme ou Tissierella praeacuta ? Une histoire pleine de rebondissements !......................................................................................................... 98 7. Clostridium orbiscindens : to be or not to be a Clostridium? .................................. 99 LE GENRE PREVOTELLA : UN GROUPE TAXONOMIQUE COHERENT ........................................ 102 I. Données générales ...................................................................................................... 102 1. Habitat .................................................................................................................... 102 2. Facteurs de virulence.............................................................................................. 102 3. Pouvoir pathogène chez l’homme.......................................................................... 103 II. Classification des Prevotella spp. ............................................................................. 105 III. Identification des bactéries du genre Prevotella...................................................... 109 1. Caractères morphologiques .................................................................................... 109 2. Caractères métaboliques......................................................................................... 109 3. Caractères génétiques............................................................................................. 112 a) Données génomiques ......................................................................................... 112 b) Données génotypiques ....................................................................................... 113 IV. Sensibilité aux antibiotiques au sein du genre Prevotella........................................ 115 1. Résistance aux antibiotiques des Prevotella spp.................................................... 115 2. Cas particulier du métronidazole...........................................................................
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