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Address: 3-615D BSB
Phone: (319) 335-7938
Mentor: John R. Kirby, PhD
Undergraduate Institution: University of Wisconsin, Madison
Studying our microbial flora began with the advent of constantly evolving sequencing techniques. The human microbiome project began in the gut to discover not only how microorganisms affect the gut physiology, but also how the total combined gut flora acts as a whole to affect the human host and possible pathogens. The vast numbers of microbial communities that are found within a human host remain unstudied, thus microbial influences on human development, physiology and immunity remain largely unknown. Initial human microbiome studies focus on the identification of bacterial phylogeny based on the 16s rRNA sequencing. Within the 16s rRNA gene, unique hypervariable regions are PCR amplified and subsequently sequenced. This transition to a high throughput sequencing technique has opened a new door for microbial identification techniques. Current 16s surveys of the environment and microbiomes suggest that a small fraction of microbes have been discovered. Only 38% of the bacteria identified in the human intestine had been previously seen, and a total of 80% of the identified bacteria by pyrosequencing techniques were considered to be uncultivable. Through the use of high-through put sequencing, millions of sequences are produced. Bioinformatic tools such as QIIME (Quantitative Insights Into Microbial Ecology) are used to decode these complex datasets. Each dataset can consist of thousands of sequences from one organism, which are clustered into individual operational taxonomic units (OTUs). Specific OTUs will vary from patient to patient. However, there are a core set of OTUs in a specific environment and treatment / disease state.
My dissertation project focuses on characterizing various microbiomes of the upper respiratory system including the sinus, middle ear, tonsils, and nasal passages. I hypothesize that there is a core microbiome in the healthy state of all individuals. As a chronic infection takes place the microbiome shifts. I hope to characterize the microbiome of these various environments and provide insight to the ecological dynamics of the bacterial interactions as they shift to a chronic disease state.
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