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UBC Theses and Dissertations

Metagenomic analyses of two female genital tract diseases : bacterial vaginosis and ovarian cancer Montoya, Vincent Keith


Metagenomics is a rapidly evolving field that has facilitated the expansion of microbiology into new areas of human and environmental health. Metagenomic studies have expanded the phylogenetic tree of life by increasing taxonomic resolution in individual phyla as well as adding entirely new branches of life. This revolution in microbiology has been made possible by the introduction of second-generation high-throughput sequencing, the associated methods for preparing DNA sequencing libraries, as well as new bioinformatic algorithms for analyzing these new types of data. Because of the novelty of these methods, very few have been systematically tested for their sensitivities and specificities outside of the initial development process. As the interpretation of metagenomic studies utilizing these tools depends greatly upon their efficiencies in both detection and classification, it is essential to best determine the performance of each tool. In this study, a variety of novel techniques were utilized and tested in their abilities to characterize the microbial populations in two regions of the female genital tract: ovarian cancer tissue and the vaginal microbiome. Although a diverse microbial population was initially observed in the transcriptome sequence data for ovarian cancer using next generation sequencing, we were unable to recover these microbial sequences through PCR and Sanger sequencing approaches. Optimized methods were applied to healthy vaginal microbiome samples and tested for their ability to differentiate them from a polymicrobial disease of the vagina, bacterial vaginosis. In addition to a high correlation between a microbial scoring system for bacterial vaginosis, this novel metagenomic pipeline also revealed microorganisms not yet associated with the vaginal microbiome such as specific Bifidobacteria spp., various bacteriophage, and Debaryomyces. Collectively, both of these studies provide unique insights into each disease as well as illustrate both the limitations and potential of the rapidly growing field of metagenomics.

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