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    Kristen Anne Earle.
    The community of commensal bacteria, viruses and eukaryotic microorganisms within our gastrointestinal tract, the gut microbiota, is a fundamental part of our biology. Foundational work has demonstrated that these organisms are required for proper development of the immune, circulatory and central nervous systems; and changes in the membership of this community are associated with pathologies such as obesity, colorectal cancer, type 2 diabetes and inflammatory bowel diseases. Though much research has focused on community composition assessed by pyrosequencing, emerging evidence suggests that many of these disease states are also associated with changes in bacterial localization within the intestines. However, standardized imaging and quantitation methods have not been established yet in the field. The work in this dissertation develops and validates such methods, and applies them to determine the effects of a low fiber diet on spatial organization of the gut microbiota. Chapter 1 contains a literature review of existing tools to study the microbiota, with a focus on the advantages and limitations of different imaging strategies. Chapter 2 includes the histological, imaging, and computational methods developed to develop a high-resolution imaging and quantification pipeline, using gnotobiotic and humanized mice on a polysaccharide-deficient diet as a test case. Chapter 3 further develops the work from Chapter 2, with a focus on host response to a low fiber diet. Chapter 4 contains perspectives and future directions for the applications of imaging to the gut microbiota field.
    Digital Access   2015