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Document Type

Open Access Dissertation

Degree Name

Doctor of Philosophy (PhD)

Degree Program

Microbiology

Year Degree Awarded

2016

Month Degree Awarded

September

First Advisor

Jeffrey L. Blanchard

Second Advisor

Kristen M. DeAngelis

Third Advisor

Susan B. Leschine

Fourth Advisor

Li-Jun Ma

Subject Categories

Biodiversity | Bioinformatics | Environmental Microbiology and Microbial Ecology | Evolution | Genomics | Microbial Physiology | Organismal Biological Physiology | Other Ecology and Evolutionary Biology | Other Microbiology | Systems Biology

Abstract

Many of the taxa in the family Lachnospiraceae are currently misclassified as Clostridium spp. Here attempt to rectify many of these issues, beginning with an in-depth genomic and physiologic analysis of Clostridium methoxybenzovorans, culminating in the assertion that is a heterotype of Clostridium indolis, followed by reclassification of the broader group in which this organism resides. We propose two novel genera, Lacriformis and Enterocloster, to reclassify this clade, this includes reclassification of Clostridium sphenoides, Clostridium indolis, Clostridium saccharolyticum, Clostridium celerecrescens, Clostridium xylanolyticum, Clostridium algidixylanolyticum, Clostridium aerotolerans, Clostridium amygdalinum, and Desulfotomaculum guttoideum as Lacriformis sphenoides, comb. nov., Lacriformis indolis, comb. nov., Lacriformis saccharolyticum, comb. nov., Lacriformis celerecrescens, comb. nov., Lacriformis xylanolyticum, comb. nov., Lacriformis algidixylanolyticum, comb. nov., Lacriformis aerotolerans, comb. nov., Lacriformis amygdalinum, comb. nov., and Lacriformis guttoideum, comb. nov. A second genus, Enterocloster, includes Clostridium clostridioforme, Clostridium bolteae, Clostridium citroniae, Clostridium lavalense, Clostridium aldenense, and Clostridium asparagiforme, reclassified as Enterocloster clostridioforme, comb. nov., Enterocloster bolteae, comb. nov., Enterocloster citroniae, comb. nov., Enterocloster lavalense, comb. nov., Enterocloster aldenense, comb. nov., and Enterocloster asparagiforme, comb. nov.

We then propose reclassification of another group of cellulolytic and hemicellulolytic Clostridium species. One genus, Cellulospecium, gen. nov., includes Cellulospecium herbivorans, comb. nov., Cellulospecium populeti, comb. nov., and Cellulospecium polysaccharolyticum, comb. nov., formerly Clostridium herbivorans, Clostridium populeti, and Clostridium polysachharolyticum. Another genus, Leschinia, houses Leschinia phytofermentans, comb. nov., formerly Clostridium phytofermentans. We also describe a novel species, Anaerocolumna spermata.

We propose the classification of a novel genus and species, Kineothrix alysoides, a highly motile anaerobic spore-former with broad saccharolytic capabilities. It produces butyrate as a major fermentation product and appears to be able to fix nitrogen.

We end with the microcosm from which the novel taxa were isolated. With the most abundant members isolated, we were able to approach the question of the rare biosphere through synthetic ecology. Rather than culling out diversity with toxins, we were able to remove diversity by leaving members out. These rare members had a significant positive effect on plant degradation, though nutrient limitation had a more pronounced effect. This approach is especially useful for comparative and perturbation studies.

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