Life Sciences Commons^™

More Than The Sum Of Their Parts: Building A Framework For Understanding Host-Microbe Interactions In Medicago Sativa, Katherine Mackenzie Moccia

Doctoral Dissertations

This dissertation seeks to understand plant-microbe interactions in the agriculturally relevant plant Medicago sativa from three distinct vantage points within microbiology. Within the plant microbiome, we examine how primer usage and the application of peptide nucleic acids impacts 16S and 18S rRNA gene sequencing. In doing so, we design a novel peptide nucleic acid, PNA, and test its impact using multiple primers and sequencing protocols. Once microbial sequencing methodology is established, we generate a synthetic consortium of bacterial isolates from M. sativa leaves and modulate nitrogen levels to better understand microbial structure. Drop out communities, where we remove one member …

Extracting Detailed Metabolic Information And Connections From Mammalian Gut Microbiomes Via Metaproteomics, Jose A. Blakeley-Ruiz

Doctoral Dissertations

A diverse community of bacteria populates the mammalian gastrointestinal tract. These populations exist in a balance with the host assisting with key functions, particularly metabolism of intractable fibers and immune modulation. Disruption of this balance can lead to diseases such as infection, inflammatory bowel syndrome, and obesity. Common symptoms include chronic pain, chronic inflammation, and altered metabolism. Several taxonomic classifications of bacteria have been associated with these diseases, but Recent studies have indicated that these finding are not always statistically valid. An explanation for this is that microbial communities between individuals and even across time can vary substantially even when …

Microbial And Metabolomic Biomarkers Of Feed Efficiency In Angus Cattle, Brooke Ashley Clemmons

Doctoral Dissertations

In Tennessee and the United States, cattle account for a significant proportion of the livestock agricultural sector. In the beef cattle industry, 40-70% of the total cost of production comes from feed costs, resulting in billions of dollars going towards feeding cattle. Thus, identifying methods for improving feed efficiency is imperative for reduced feed input costs and more effective use of environmental and economic resources. The rumen microbiome contributes a vast amount of nutrients for the host ruminant, including approximately 70% of energy precursors as well as vitamins, proteins, and other nutrients. These microbes produce metabolites that are then available …

Assessment Of Next Generation Sequencing Technologies For De Novo And Hybrid Assemblies Of Challenging Bacterial Genomes, Sagar Mukund Utturkar

Doctoral Dissertations

In past decade, tremendous progress has been made in DNA sequencing methodologies in terms of throughput, speed, read-lengths, along with a sharp decrease in per base cost. These technologies, commonly referred to as next-generation sequencing (NGS) are complimented by the development of hybrid assembly approaches which can utilize multiple NGS platforms. In the first part of my dissertation I performed systematic evaluations and optimizations of nine de novo and hybrid assembly protocols across four novel microbial genomes. While each had strengths and weaknesses, via optimization using multiple strategies I obtained dramatic improvements in overall assembly size and quality. To select …

Genetic And Ecological Characterization Of Indigoidine Production By Phaeobacter Sp. Strain Y4i, William Nathan Cude

Doctoral Dissertations

The Roseobacter clade is a widely distributed, abundant, and biogeochemically active lineage of marine alpha-proteobacteria. Members of the Roseobacter lineage are prolific surface colonizers in marine coastal environments, and antimicrobial secondary metabolite production has been hypothesized to provide a competitive advantage in colonization. In this work, Phaeobacter sp. strain Y4I was found to produce the water soluble, blue pigment indigoidine via a nonribosomal peptide synthase-based biosynthetic pathway encoded by a novel series of genetically linked genes, termed igiBCDFE. Comparison of wildtype, non-pigmented, and hyper-pigmented Y4I insertional mutants demonstrated a perfect correlation between indigoidine production and the inhibition of Vibrio …

Characterization Of Uncultured, Human Oral Microbiota Using A Targeted, Single-Cell Genomics Approach, Alisha Gail Campbell

Doctoral Dissertations

Microbial communities associated with the human oral cavity are complex, and many oral microbes have yet to be cultured. These uncultured community members are of interest ecologically and phylogenetically, and a number of uncultured species have been positively correlated with oral diseases such as periodontitis. Thus, an approach was adapted to selectively separate single cells from mixed populations of oral bacteria and obtain genomic information for uncultured community members. A combination of fluorescent labeling, cell sorting with flow cytometry and multiple displacement amplification was used to obtain sufficient genomic material for whole-genome pyrosequencing.

The first targets were from uncultured oral …