Document Type


Date of Degree

Spring 2019

Access Restrictions

Access restricted until 07/29/2021

Degree Name

PhD (Doctor of Philosophy)

Degree In


First Advisor

Grobe, Justin L

First Committee Member

Grobe, Justin L

Second Committee Member

Kirby, John R

Third Committee Member

Smith, Richard J

Fourth Committee Member

Braun, Terry A

Fifth Committee Member

Klingelhutz, Aloysius J


Bioinformatics is a unique field in that it incorporates many different disciplines, including biology, computer science, and statistics, to study biological data. There is a vast array of techniques that utilize bioinformatics, including pangenomics, RNASeq, whole genome metagenomics, and 16S sequencing.

To study bacterial interactions, we used a model system of species interactions, Myxococcus xanthus. M. xanthus is a soil bacterium that is a known predator of other bacteria. It has one of the largest repertoires of two component systems (TCS) to respond to external stresses. TCS are a pair of proteins, one that senses environmental stress (histidine kinase, HK) and another that usually acts as a transcriptional regulator (response regulators, RR). We studied a class of RRs, NtrC-like, reliant on an alternative sigma factor, sigma54. The oligomerization of NtrC-like RRs is regulated to modulate activation of the protein, which would change the bacterium’s ability to respond to its environment. We studied HsfA, a NtrC-like RR that regulates specialized metabolites. Specialized metabolites are used in bacterial interactions. In predation interactions they are used to kill prey. Our goal was to find genes that might be involved in specialized metabolite production that would aid in predation. We used prediction tools to find putative binding sites of HsfA to find potentially new metabolites. We used two motifs to attempt to predict if the oligomerization of these response regulators is positively or negatively regulated. We found that the presence of a motif in the receiver domain to be associated with negative regulation of oligomerization, but further studies are needed to experimentally confirm this finding.

One environment in which bacterial interactions occur is in the gut. The gut microbiome is the consortium of organisms and their genomic content in the gastrointestinal tract. The gut microbiome is sensitive to aspects of a person’s lifestyle, such as diet and medication. Here we studied the effect of two different diets and two drugs on the gut microbiome.

Risperidone, an antipsychotic used to treat schizophrenia and bipolar disorder, has been shown to cause obesity and diabetes. We studied the effect of diet and risperidone usage on weight gain and the microbiome using a C57Bl/6J female mouse model. Our results show that diet has a strong impact on the microbial composition of the gut in response to risperidone. As many mental health patients stop and restart their medication, we examined the effect of stopping and restarting risperidone on the microbiome. When risperidone is stopped the microbiome reverts to a state similar to the control group but diverges into a different microbial composition upon restarting treatment. Interestingly, mice did not gain significantly more weight than their control group upon the second risperidone treatment. Further studies are needed to examine the functional changes occurring with the stop and restart of risperidone to determine the mechanism of mice resisting weight gain during the second round of treatment.

Captopril is used to treat hypertension, a very common disease in the United States. Here we studied the effect of captopril on weight gain, metabolic phenotypes, and the gut microbiome. Our results showed that captopril caused an increase in resting metabolic rate (RMR) in mice. This occurred through an increase in energy expenditure. This increase in RMR had the effect of captopril-treated mice being resistant to weight gain. Our group has previously shown that the gut microbiome can directly affect RMR. Therefore, we studied the gut microbiome of captopril-treated mice. We observed a shift in their gut microbiome to organisms Akkermansia muciniphila and Lactobacillus, associated with lean body mass. Captopril therefore has the potential to be a better medication to treat patients with both hypertension and obesity. Further studies are needed to determine the effect of captopril on the microbiome in a hypertension mouse model.


Bioinformatics, Captopril, Microbiome, Risperidone, Sequencing


xv, 130 pages


Includes bibliographical references (pages 86-101).


Copyright © 2019 Samantha Nicole Atkinson

Available for download on Thursday, July 29, 2021