Graduate Thesis Or Dissertation
 

Using the Microbial Tree of Life to Describe Mammalian Health and Disease

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https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/dn39x845x

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  • The past decade of research has potentiated a revolution in our understanding of mammalian health and evolution by revealing that the gut microbiome plays a central role in mammalian physiology. Our ability to unlock this potential hinges upon the identification of specific groups of gut microbes that elicit effects on mammalian physiology. While notable discoveries in this regard have been made in recent years, our ability to advance this research objective remains in part limited by the analytical tools that scientists have access to. This dissertation seeks to expand this toolkit in impactful ways by introducing ecophylogenetic methods into the analysis of microbiome data. Briefly, these methods integrate microbial phylogenetic information into the analysis of host-microbe relationships, and in so doing can increase our resolution into which specific evolutionary groupings of microbes – whether they be sub-species or ancestral monophyletic clades of taxa – that share evolutionary traits that link to a mammalian phenotype of interest. Additionally, this approach enables the discovery of monophyletic core taxa, which are those evolutionary groups of microbes that are effectively conserved across a defined group of hosts, such as those that are healthy relative to a given disease, implicating the potential importance of the evolutionary group of microbes in health homeostatic mechanisms. In addition to introducing the first analytical workflow for the ecophylogenetic analysis of microbial communities, this dissertation demonstrates the impact of this approach in our understanding of mammalian macroevolution as well as population genetics, and illustrates how it can advance our ability to resolve related microbial groups associated with health and disease using feline upper respiratory tract infections as an example. This dissertation also discusses the recent development of a second software workflow that conducts ecophylogenetic analyses of microbial communities at scale, which was used to clarify the link between the composition of the human gut microbiome and Crohn’s disease through an extensive meta-analysis. Collectively, the work presented here provides a novel opportunity to discover related groups of microorganisms which associate with host health status, as well as a novel lens to view chronic disease processes against a backdrop of evolutionary history.
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  • Oregon State University Institutional Funds
  • United States Geological Survey
  • Morris Animal Foundation
  • California Department of Fish and Wildlife
  • Carlson College of Veterinary Medicine
  • National Park Service
  • National Science Foundation (Grant 1557192)
  • California Chapter of the Wild Sheep Foundation
  • National Institutes of Health Loan Repayment Program
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  • Intellectual Property (patent, etc.)
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  • 2021-09-19 to 2023-10-19

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