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Paléomicrobiologie Des Coprolithes

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Paléomicrobiologie Des Coprolithes Aix-Marseille Université Faculté de Médecine École Doctorale des Sciences De la Vie et de la Santé (EDSVS) THÈSE DE DOCTORAT/PhD Présentée par Sandra APPELT Née le 05 Décembre 1985 à Neuruppin, Allemagne Pour obtenir le grade de docteur de L’UNIVERSITÉ AIX-MARSEILLE SPÉCIALITÉ : Pathologie Humaine, Maladie Infectieuse Paléomicrobiologie des coprolithes Présentée et publiquement soutenue devant La Faculté de Médecine de Marseille Le 09 Décembre 2013 COMPOSITION DU JURY M le Professeur Jean-Louis Mege Président de Jury Mme le Professeur Christine Keyser Rapporteur M le Professeur Antoine Andremont Rapporteur M le Professeur Michel Drancourt Directeur de Thèse Unité de Recherche sur les Maladies Infectieuses Tropicales et Emergentes (URMITE) UM 63 CNRS 7278 IRD 198 INSERM 1095 PREAMBULE 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 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. i ii SOMMAIRE Préambule i Sommaire ii Acronymes iv RÉSUMÉ ........................................................................................................ 1 ABSTRACT ................................................................................................... 3 INTRODUCTION ET OBJECTIFS ............................................................ 5 CHAPITRE I.................................................................................................. 9 REVUE DE LITTERATURE : Des coprolithes humains comme source pour la paléomicrobiologie.......................................................................... 9 Des coprolithes humains comme source pour la paléomicrobiologie ......... 9 Avant-propos ............................................................................................. 11 MINI REVIEW ......................................................................................... 13 Annexe I ............................................................................................. 41 CHAPITRE II .............................................................................................. 57 ARTICLE : Analyse polyphasique de la flore microbienne associée à un coprolithe du Moyen Âge, découvert en Belgique .................................... 57 ................................................................................................................... 57 Avant-propos ............................................................................................. 59 JOURNAL ARTICLE ............................................................................... 61 Annexe II ............................................................................................ 97 ii 6 CHAPITRE III .......................................................................................... 129 ARTICLE : Des virus dans un coprolithe du 14ième siècle ..................... 129 Des virus dans un coprolithe du 14ième siècle .......................................... 129 Avant-propos ........................................................................................... 131 JOURNAL ARTICLE ............................................................................. 133 Annexe III ........................................................................................ 167 CHAPITRE IV ........................................................................................... 195 ARTICLE : Culture d’Acanthamoebae et d’un endosymbionte associés à un coprolithe de Moyen Âge ........................................................................ 195 ................................................................................................................. 195 Avant-propos ........................................................................................... 197 JOURNAL ARTICLE ............................................................................. 199 Annexe IV ...................................................................................... 2301 CONCLUSIONS ET PERSPECTIVES................................................... 249 REFERENCES .......................................................................................... 255 REMERCIEMENTS ................................................................................. 261 iii ii ACRONYMES aDNA ancient Deoxyribonucleic acid AD Anno Domini Amplicon product of artificial amplification BLAST Basic Local Alignment Tool bp base pair BP before present Contig Contiguous sequence dsDNA double stranded DNA NCBI National Center for Biotechnology Information ORF Open Reading Frame PCR Polymerase Chain Reaction Read A sequenced DNA fragment RNA Ribonucleic acid rRNA Ribosomal Ribonucleic Acid Shotgun sequencing Sequencing of random fragments ssDNA single stranded DNA Virome Viral metagenome WGS Whole Genome Shotgun sequencing iv 0 RÉSUMÉ Les coprolithes sont le produit de la dessiccation et de la minéralisation de matières fécales. En faisant le parallèle avec les selles modernes, les coprolithes peuvent être des échantillons appropriés à l’étude des habitudes alimentaires, de la flore intestinale et des maladies, des animaux et des hommes ayant vécu il y a plusieurs siècles. Leur analyse a d’abord reposé sur des observations macro et microscopiques, puis sur les détections d’ADN ou de molécules non-nucléotidiques en respectant les standards paléomicrobiologiques et en appliquant des méthodes couramment utilisées pour le diagnostic routine. Dans le travail de thèse ici présenté, un coprolithe datant des 14- 15ième siècles et provenant de Namur en Belgique, a été étudié. Ce coprolithe a été retrouvé dans un tonneau, utilisé à l’époque comme latrine. Dans un premier temps, nous avons caractérisé l’ensemble de la communauté microbienne associée au coprolithe et identifié certains pathogènes. Pour cela, des observations microscopiques, la culture et la métagénomique ont été combinées. La confirmation des résultats importants a reposé sur des PCR ad hoc. Les résultats ont montré qu’une partie du microbiote est similaire à l’environnement. De plus, des bactéries typiques de la flore intestinale, des parasites intestinaux et des pathogènes systémiques ont été trouvés. Pour en apprendre davantage, un second projet a visé à la purification de particules virales à partir du coprolithe de Namur et leur analyse par microscopie électronique et métagénomique virale. Des particules virales sphériques, ainsi que des bactériophages, ont ainsi été observés. Les virus associés au coprolithe correspondent à des virus d’eucaryotes, de procaryotes et d’archaea. La communauté virale était dominée par des bactériophages détectés dans le sol et les selles modernes. Bien que la composition phylogénétique diffère de celle des selles modernes, les fonctions métaboliques de ces communautés virales semblent être plus conservées. Parmi les fonctions métaboliques détectées, une correspond à des résistances aux antibiotiques. Dans un troisième projet, des cultures et des identifications moléculaires ont été réalisées sur des kystes d’amibes précédemment observés dans le coprolithe de Namur. Les amibes ainsi isolées appartiennent au genre Acanthamoeba et pourraient avoir été conservées sous forme de kystes pendant des siècles dans le coprolithe de Namur. De plus, les co-cultures d’amibes permis l’isolement et l’identification d’une nouvelle bactérie bi-flagellée résistante aux amibes, proche des Rickettsiales. S’agissant de la première étude globale portant sur un coprolithe retrouvé en Europe, notre travail contribue à la connaissance de la flore du Moyen-âge sur ce continent. De plus, notre approche démontre que l’application, sur des coprolithes, de méthodes utilisées habituellement pour le diagnostic de routine, permet de détecter des pathogènes dans des échantillons anciens. Mots-clés : paléomicrobiologie, coprolithes, flore intestinale, infections anciennes, virus, amibes 1 2 ABSTRACT Coprolites result from the desiccation or mineralization of feces material. Accordingly, by drawing parallels to modern stools, coprolites can be suitable specimen to study diet habits, gut microbiota and diseases of animals and humans that have lived centuries ago. Their investigations relied first mainly on macroscopic and microscopic observations, then on nucleotidic and non-nucleotidic biomolecules detection through the application of paleomicrobiological standards and routine diagnostic methods. During this thesis work, a 14-15th century coprolite specimen from Namur, Belgium was analyzed. The Namur coprolite was found in a barrel – used at this period as pits or latrines. At the initiation of this thesis work, it was
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