Applying Anaerobic Microbial Cultivation, Molecular Techniques, and In-Silico Taxonomy to the Mammalian Microbiome

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dc.contributor.advisorLawson, Paul
dc.contributor.authorMiller, Samuel
dc.contributor.committeeMemberSankaranarayanan, Krithivasan
dc.contributor.committeeMemberKarr, Elizabeth
dc.contributor.committeeMemberBourne, Christina
dc.contributor.committeeMemberSiler, Cameron
dc.date.accessioned2024-07-17T13:57:29Z
dc.date.available2024-07-17T13:57:29Z
dc.date.issued2024-08-01
dc.date.manuscript2024
dc.description.abstractThe mammalian gastrointestinal tract is an ecosystem home to a considerable number of bacteria, archaea, microeukaryotes, viruses, and their genomic components, collectively termed the "microbiome." This microbiome consists of many organisms that are "yet-to-be-cultured' representing a huge amount of uncharacterized bacterial biodiversity. In addition, the phylogeny of many groups of bacteria prevalent in the mammalian microbiome ecology is heterogeneous, with many taxa misclassified and needing revision. Furthermore, most studies of the non-human mammalian microbiome focus primarily on metagenomic inventories. However, cultivation-based studies should be undertaken to better characterize the broader gut microbial diversity within the class Mammalia. First, I restricted the historically heterogeneous Eubacterium genus to its type species, Eubacterium limosum, and its closest relatives. Additionally, two previously misclassified taxa, Eubacterium aggregans, and Eubacterium barkerii, were assigned to a novel genus, Paraeubacterium gen. nov., more accurately representing their phylogenetic placement. Using culture-dependent and independent approaches, I also explored the gut microbiomes of two understudied mammals, alpacas and bats. Further, two novel alpaca gut-associated anaerobes, Clostridium tanneri sp. nov. and Bacteroides vicugnae sp. nov., were isolated and characterized from the feces of two domesticated alpacas. Lastly, one novel genus, Aleya cavernae gen. nov., sp. nov., and one novel species, Lacrimispora spelaei sp. nov., were isolated and characterized from the bat gut microbiome. These studies represent a polyphasic approach using cultivation, chemotaxonomic, phenotypic, genomic, and in-silico methods, providing valuable insights into mammalian microbiomes, including the first step in the taxonomic revision of the genus Eubacterium and the description of novel taxa.en_US
dc.identifier.urihttps://hdl.handle.net/11244/340482
dc.languageen_USen_US
dc.subjectAnaerobic Microbiologyen_US
dc.subjectTaxonomyen_US
dc.subjectNovel Bacteriaen_US
dc.thesis.degreePh.D.en_US
dc.titleApplying Anaerobic Microbial Cultivation, Molecular Techniques, and In-Silico Taxonomy to the Mammalian Microbiomeen_US
ou.groupDodge Family College of Arts and Sciences::School of Biological Sciencesen_US
shareok.nativefileaccessrestricteden_US
shareok.orcid0000-0002-6165-2892en_US

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