Réévaluation de la biodiversité du microbiote méthanogène intestinal humain et influence de l'âge sur sa constitution

The intestinal microbiota constitutes a rich and varied enzymatic activities tank. Its expression is an integral part of the organism's physiology and has an influence on its health. The methanogenic Archaea, whose detection by classic cultural methods is difficult, are so far represented only by two hydrogenotrophic Methanobacteriales in this microbiota : Methanobrevibacter smithii and Methanosphaera stadtmanae. The purpose of this thesis was to bring a molecular vision of the diversity of the methanogenic Archaea of the microbiota and to look for the influence of age on this community. The research has been led by the analysis of the mcrA cistron, a specific molecular marker of methanogenesis, and of the 16S rRNA gene. It has revealed that the archaeal diversity colonizing this ecosystem is increased by new phylotypes which cannot be attached to any of the 5 previously described methanogenic orders, and may correspond to other methanogens affiliated to Thermoplasmatales or cohabiting with unknown Thermoplasmatales. Their frequency appears to be associated with their host's age, according to a study carried out on 63 individuals of different age-groups : 23 newborns (3 weeks to 10 months), 20 adults (from 25 to 45 years) and 20 elderly (from 70 to 90 years). A relation with the host's ageing is therefore possible. Finally, the potentiality of a 6th order of methanogenic Archaea distantly related to a group of Archaea which anaerobicaly oxidized methane, the ANME 1, and its surprising association recovered with unknown Archaea affiliated with Thermoplasmatales, raises the question on the phylogenetic origin of these various microorganisms and underlines our current relative ignorance of one ofthe three domain of life.Le microbiote intestinal constitue un réservoir d'activités enzymatiques riche et varié dont l'expression fait partie intégrante de la physiologie de l'organisme et influe sur sa santé. La mise en évidence par méthodes culturales classiques des Archaea méthanogènes est difficile et n'a permis à ce jour que la mise en évidence de 2 Methanobacteriales hydrogénotrophes au sein de ce microbiote : Methanobrevibacter smithii et Methanosphaera stadtmanae. Les travaux de cette thèse ont eu pour but d'apporter une vision moléculaire nouvelle de la diversité des Archaea méthanogènes du microbiote et de rechercher l'influence de l'âge sur ces communautés. Ces travaux ont été menés par analyse d'une partie du cistron mcrA, marqueur moléculaire spécifique de la méthanogenèse, et du gène codant pour l'ARNr 16S. Ces études ont révélé une plus grande diversité des Archea colonisant cet écosystème et ont mis en évidence de nouveaux phylotypes ne pouvant être rattachés à aucun des 5 ordres méthanogènes précédemment décrits. Ils correspondent probablement à d'autres espèces méthanogènes affiliées aux Thermoplasmatales ou cohabitent avec des membres encore inconnus des Thermoplasmatales. Une étude réalisée sur 63 individus répartis en nouveau-nés, adultes et seniors a montré que la fréquence de ces nouveaux phylotypes augmente avec le vieillissement. Ces résultats interrogent à la fois sur l'origine de ces divers organismes et leur présence au sein du mcrobiote intestinal du sujet âgé et soulignent notre relative méconnaissance d'un des trois domaines du vivant

Tools for stools: the challenge of assessing human intestinal microbiota using molecular diagnostics

International audienceThe human GI tract is inhabited by an incredibly complex and abundant microbiota, whose composition is dependent on a variety of factors. The gut microbiota has an influence in the morphological, immunological and nutritional functions of the digestive tract and may be involved in many diseases. This article proposes the rationale behind conducting in vitro diagnostics (IVDs) of the human microbiota, as well as outlining the conceptual and technical difficulties involved in IVD testing. The molecular methods that can be used according to whether the IVD tools are employed to study one individual constituent species or to determine the microbiota as a whole will also be described. In the latter case, these technologies include high-throughput sequencing for metagenomics and DNA microarrays, which can now be efficiently used to study gut ecology and are believed to represent the future of standardized diagnostics

A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene

International audienc

Bacterial diversity associated with saline efflorescences damaging the walls of a French decorated prehistoric cave registered as a World Cultural Heritage Site

International audienc

Characterization of the archaeal and fungal diversity associated with gypsum efflorescences on the walls of the decorated Sorcerer’s prehistoric cave

International audienc

Genome Sequence of "Candidatus Methanomassiliicoccus intestinalis" Issoire-Mx1, a Third Thermoplasmatales-Related Methanogenic Archaeon from Human Feces

International audience"Candidatus Methanomassiliicoccus intestinalis" Issoire-Mx1 is a methanogenic archaeon found in the human gut and is a representative of the novel order of methanogens related to Thermoplasmatales. Its complete genome sequence is presented here