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Master Thesis

Recherche de polymorphismes chez Lactobacillus plantarum potentiellement associés à la promotion de la croissance de son hôte Drosophila melanogaster et création d'un pipeline Bioinformatique de détection de mutations bactériennes

Abstract : A vast majority of organisms maintains a complex interaction with bacterial community. In the case of the intestinal bacterial flora or microbiota, it has been shown that bacteria could optimize the digestion of host and limit its colonization by pathogens. In parallel, in the intestine, bacteria have a rich nutrient medium and are protected. The benefits of this interaction for the host have been demonstrated but the molecular mechanisms of the viewpoint of the host or the bacteria remain poorly understood. To study these mecanisms in bacterial, the model Drosophila melanogaster mono-associated with Lactobacillus plantarum strain is used by the team Leulier at the IGFL. The team demonstrated that Drosophila larvae associated with this bacterium have an accelerated maturation and superior size compared to germ-free larvae. From the perspective of the bacteria, the goal is to determine which genes are associated with this larval growth promotion. In this study the genomes of seven strains of L.plantarum, experimentally evolved in a drosophila niche were compared to detect mutations that are potentially involved in this promotion. Indeed, the potential to promote larval growth of these seven strains is higher than the one of the ancestral strain from which they arise and the mutations acquired by bacteria to adapt to their new environment might be responsible. The genomes of these seven strains were sequenced with Ion Torrent PGM and a bioinformatics pipeline was developed from Breseq software and dedicated R scripts to compare the seven strains to the genome of the ancestral strain and detect mutations. This provides a list of potentially present mutations. Seventeen mutations have been detected and the actual presence of six of them was validated by PCR. The eleven remaining mutations have yet to be tested. The independent effects of each of these mutations in the promotion of larval growth will then be tested with directed mutagenesis experiments. In this research of potential mutations and PCR validation, resulted the creation of a prediction tool of the real presence of a mutation that would have been detected by the bioinformatics pipeline created for this project. The pipeline and prediction tool are applicable to any bacterial genome comparison study.
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Master Thesis
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Pauline Joncour. Recherche de polymorphismes chez Lactobacillus plantarum potentiellement associés à la promotion de la croissance de son hôte Drosophila melanogaster et création d'un pipeline Bioinformatique de détection de mutations bactériennes . Sciences du Vivant [q-bio]. 2015. ⟨dumas-01255286⟩

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