DNA Microchips: Detecting Microbes in Oral Cavity Fluids

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DESCRIPTION (provided by applicant): The human oral cavity harbors complex microbial assemblages, which are associated with the manifestation or prevention of local and systemic disease. In addition, the oral cavity is one of the main ports of entry for potentially life-threatening agents released in the course of a bioterroristic attack. Conventional culture-based approaches for monitoring microbes in the oral cavity are not feasible since they are time-consuming and capture only a minor fraction of the oral microbiota. This project uses nucleic acid-based hybridization assays as an alternative to culture-based approaches. Specifically, target-specific and generic high-density DNA microchips will be used for the fast and reliable detection of microbial biomarkers in oral fluids. Two general formats of DNA microarrays will be used: (I) the OralChip, consisting of hierarchical sets of pro-and eukaryal ribosomal RNA-targeted oligonucleotide probes, and (II) the generic HexamerChip, containing all possible (4096) DNA hexamers. To further increase its diagnostic power, the OralChip will be expanded to include probes that detect the expression of genes involved in microbial community structure and virulence. Innovative statistical and mathematical tools will be applied for the integrated data analysis of both formats (i.e. artificial neural networks combined with conventional statistical approaches such as cluster analyses). This novel approach is expected to (i) provide population- and community-specific signature patterns of microbiota associated with oral microbial communities, ii) yield fast and unambiguous detection of biothreat-agents, (iii) determine the limitations (sensitivity, resolution) of the formats, and iv) reveal structural and functional attributes of the oral microbiota at high spatial and temporal resolution, specifically those associated with manifestation and prevention of local and systemic disease.