Détermination de sondes oligonucléotidiques pour outils moléculaires à haut débit : application pour le développement d'une nouvelle approche de capture de gènes pour l'écologie microbienne

Abstract : Microorganisms play a crucial role in all biological processes related to their huge metabolic potentialities. They are involved in global changes such as global warming partially caused by the growing methane emissions in the atmosphere, but also by the release of pollutants such as Polycyclic Aromatic Hydrocarbons. Thus, microbial communities will contribute to reduce or increase the negative effects of human impacts on ecosystems. The regulation of global changes needs a better knowledge of the microbial communities involved in complex environments functioning. Nevertheless, a complete exploration of such environments requires the use of high-throughput tools, due to the extraordinary diversity of microorganisms within the ecosystems. The use of DNA microarrays requires a probe design step allowing the selection of highly sensitive, specific and explorative oligonucleotides. For this purpose, we have developed KASpOD, a new software, allowing the generation of efficient probes dedicated to environmental applications. Using high quality probe sets, an innovative in solution-based gene capture method combined with Next Generation Sequencing, was developed and applied for the exploration of the methanogen communities in lake Pavin, Results showed the relevance of this approach that allows a better evaluation of the methanogen diversity with an efficient detection of populations belonging to the rare biosphere. The other main advantage of this approach is the identification of large regions of genomic DNA, useful for the characterization of new genes or adaptive processes.
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Jérémie Denonfoux. Détermination de sondes oligonucléotidiques pour outils moléculaires à haut débit : application pour le développement d'une nouvelle approche de capture de gènes pour l'écologie microbienne. Sciences agricoles. Université Blaise Pascal - Clermont-Ferrand II, 2013. Français. ⟨NNT : 2013CLF22331⟩. ⟨tel-01077860⟩

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