Exploring Competitive Dynamics Between Pseudomonas Baetica And Salmonella In A Polymicrobial System, Braxton E.M. Stout

Electronic Theses and Dissertations

The global rise in antimicrobial resistance has catalyzed a greater focus on polymicrobial research aimed at characterizing microbial interactions and uncovering new therapeutic strategies. Though it has long been of interest, environmental soil-derived bacteria remain largely under-represented in research and thus uncharacterized in this field. This project aimed to identify soil microbes that display inhibitory mechanisms to potential nosocomial pathogens. Soil sample S1S3-2 displayed inhibitory phenotypes toward numerous bacteria and was identified as Pseudomonas baetica. In both planktonic and biofilm growth, P. baetica was able to inhibit Salmonella arizonae through a contact-dependent and temperature-dependent manner. Screening of a transposon insertion …

Function And Regulation Of Long Polar Fimbriae During Enterohemorrhagic Escherichia Coli Infection, Walter J. Galdamez

Dissertations and Theses (Open Access)

Enterohemorrhagic Escherichia coli (EHEC) is a foodborne pathogen that causes severe gastrointestinal disease and hemolytic uremic syndrome. EHEC employs multiple virulence factors to colonize the host intestine, including the locus of enterocyte effacement (LEE) encoded type III secretion system, intimin, and flagella, yet the role of long polar fimbriae (Lpf) in adhesions and infection remains less well understood. Long polar fimbriae can mediate bacterial attachment to host cells in vitro, yet the regulation and function of its two fimbrial operons, lpf1 and lpf2 in vivo remain poorly understood. Preliminary RNA-seq data from zebrafish infected with EHEC reveal that expression of …

Descriptive Comparative Analysis Of Bacteriophage And Auxiliary Metabolic Gene Diversity In Marine And Wastewater Environments, Andrew Crawford

Undergraduate University Honors Capstones

Bacteriophages (phages) are viruses that infect bacteria and play a role in bacterial evolution. Through horizontal gene transfer (HGT), phages integrate parts of their genomes into their bacterial hosts. While the molecular mechanisms of this process are well understood, the evolutionary impacts remain less certain. One evolutionary explanation is that auxiliary metabolic genes (AMGs) modulate host gene expression to favor phage reproduction or improve the host’s survival. AMG can persist in hosts' or phages' genomes across future generations, altering their contributions to the ecosystem and posing a concern for human and environmental health. The objective of this project is to …

Urea-Based Boronium Salts As Antimicrobial Agents, Gabriel Allen Merchant

Honors Theses

Quaternary ammonium compounds (QACs) are widely used in disinfectants due to their ability to inhibit the growth of and eliminate microbes. The potency, broad-spectrum activity, and low cost of QACs have made them a cornerstone of modem hygiene. In recent years, QACs have garnered many health and safety concerns due to their overuse and subsequent accumulation in the environment. The increased use of QACs has further led to an increase in antimicrobial-resistant bacteria, making the synthesis of novel antibacterial compounds vital to combat this growing threat. Recent advances in boronium salts offer a unique alternative to address these adverse effects. …

Genome-Wide Phenotypic Characterization Of Mycobacteriophage Mercurio, Tyler Downs

Departmental Honors & Graduate Capstone Projects

Bacteriophages, or phages, are being piloted as a supplemental or alternative therapeutic to antibiotics against drug-resistant Mycobacterium pathogens, such as M. tuberculosis, which pose a global public health crisis.  Characterizing bacteriophage genomes can provide insights into efficacy in phage therapy before implementation or elucidate new targets to manipulate bacterial growth.  Overexpression of individual phage genes is useful to study a gene product’s function independent of others.  Here, the results of phage Mercurio plasmid library overexpression in plate-based assays are described.  Mercurio infects nonpathogenic Mycobacterium smegmatis and is genetically related to bacteriophages infecting pathogenic Mycobacterium species.  Eleven gene products of …

Understanding The Role Of Toxs As A Bile Sensing Component Of The Toxrs Virulence Regulatory System In Vibrio Spp., Minje Kim

Dartmouth College Ph.D Dissertations

Pathogenic Vibrio bacteria, such as V. cholerae and V. parahaemolyticus, colonize in the human small intestine to cause severe gastrointestinal disease. During the infection, these bacteria encounter bile salts, antimicrobial cholesterol metabolites secreted into the intestine. Pathogenic Vibrio species have evolved to utilize bile salts as signals to regulate virulence. The signaling depends in part on ToxRS, a conserved co-component transmembrane transcription regulator. ToxRS consists of the transcription factor ToxR and its membrane-tethered binding partner ToxS. ToxS is required for ToxR stability and full transcriptional activity. Although bile salts are known to influence ToxRS-dependent virulence gene expression, the molecular …

Investigating The Synthesis And Antibacterial Activity Of A Main-Chain Cationic Polymer, Emily Smith

Honors Theses

Antibiotic resistance is a growing threat to public health. Due to the overuse of antibiotics in agriculture, the overprescription of antibiotics, and the misuse of antibiotics by patients, antibiotic resistance is spreading at an alarming rate. As antibiotic resistance spreads, the antibiotics we depend on to treat common infections become ineffective. Therefore, it is imperative to develop novel treatments for infections that do not increase the prevalence of antibiotic resistance. One treatment being explored is the use of synthetic polymers with antibacterial properties. Synthetic polymers are advantageous because they can be synthesized from widely available precursors and their structure is …

Garlic Breath And Beads Of Sweat: The Effects Of Garlic And Chili Peppers On The Growth And Ph Of Streptococcus Mutans., Lena Pitzer

Honors Projects

The purpose of this project is to provide a quantifiable and repeatable measurement of how the presence of garlic and chili pepper during the growth of a carious dentine strain of Streptococcus mutans affects the growth of the strain and surrounding pH level.This research project examines two possible alternative agents, garlic and chili peppers, due to the known antimicrobial effects of their active components, allicin and capsaicin. Prepared garlic and chili extracts were used during disk diffusion to assess and measure the zones of inhibition. The anticipated results are that there will be inhibition present with both the garlic and …

Elasmobranchii Oral Microbiome Diversity Within Southeast Florida: Implications Of Shark Zoonotic And Antibiotic Resistant Pathogens Associated With Human Interactions, Amanda Finnefrock

All HCAS Student Capstones, Theses, and Dissertations

Sharks are incredibly common in the Atlantic and Gulf waters surrounding Florida. Despite the prevalent nature of these animals, little research exists on the composition of their microbial communities (or “microbiomes”). Here we aim to determine the microbial makeup of the oral environment of sharks so that we can determine if there are any bacteria of clinical significance to humans, such as being antibiotic-resistant or having elevated capability for pathogenicity. A total of 41 samples were collected from the mouths and teeth of bull, Caribbean reef, great hammerhead, lemon, nurse, and sandbar sharks caught in Southeast Florida using sterile swabs …

Effects Of “Zero Sugar” Energy Drinks On Microbial Proliferation In Relation To The Gastrointestinal Microbiome, Madison Hines

Honors Theses

Energy drinks have rapidly increased in popularity and availability in recent years. With the rise of high-caffeine beverages, complications due to caffeine consumption have become more common in younger populations. The aim of this study was to use controlled laboratory methods to determine the effect of energy drinks on a variety of organisms commonly found in the gastrointestinal (GI) tract. The diverse and dynamic nature of microbes in the gut makes conditions of the GI tract difficult to replicate in a laboratory setting. As an alternative, isolates of bacteria commonly found as normal flora in the GI tract were plated …

Antibiotics And You: A Comprehensive Guide, Brady Haas

Senior Theses

Antibiotic resistance is a rapidly emerging issue within public health. As resistance grows, the effectiveness of traditional antibiotic therapies diminishes while risk of treatment grows. Alongside novel therapies, public knowledge is a strong combatant of the resistance-related risks of antibiotic usage. Through a comprehensive review of current literature, this work serves as an accessible guide to the mechanisms of antibiotics, bacterial resistance, and the challenges related to current antibiotic usage. Additionally, the ability of current policy and emerging novel treatments, such as nanoparticles and bacteriophage therapy, to fight antibiotic resistance is evaluated. This analysis highlights the importance of improving public …

Evolution Of Antibiotic Responses During Chronic P. Aeruginosa Infections In The Human Lung, David Frank Ritz

Dartmouth College Ph.D Dissertations

Typical antibiotic susceptibility testing (AST) of microbial samples is performed in homogeneous cultures in batch environments, which does not account for the highly heterogeneous and dynamic nature of antibiotic responses. The most common mutation found in P. aeruginosa lineages evolved during chronic cystic fibrosis infections in the human lung, a loss of function of repressor MexZ, increases basal levels of multidrug efflux MexXY, but does not increase resistance by traditional minimal inhibitory concentration (MIC) assays. Here, we use single cell microfluidics to show that P. aeruginosa’s response to aminoglycosides is highly heterogeneous, with only a subpopulation of cells surviving exposure. …

Biofilm Architecture Determines Proliferation Of Phages And Plasmids, James B. Winans

Dartmouth College Ph.D Dissertations

This thesis explores how biofilm architecture determines the spread and ecological consequences for the bacteria-dependent genetic elements phages and plasmids. Using Escherichia coli and Vibrio cholerae as model microbes, and the genetic elements T7 phages, λ phages, and conjugative plasmid pED208, we investigate how spatial structure influences phage infection dynamics, plasmid transfer, and interbacterial interactions within biofilms. We show that densely packed biofilms can protect sensitive bacteria from phage exposure and modulate competitive outcomes between obligately lytic and temperate phages. We find that entirely different outcomes can coöccur within microns of each other dependent on biofilm structure. We also demonstrate …

Coordinating The Layers: Regulation Of Peptidoglycan Synthesis And Cell Wall Assembly In Mycobacterium Smegmatis By Murj And Pgfa, Karen Emmanuella Samaga-De-Tembiwa

Biology Dissertations

The mycobacterial cell envelope consists of three covalently linked layers whose synthesis must be coordinated to maintain structural integrity during polar growth. While the biosynthetic enzymes for each layer are well characterized, the molecular mechanisms that coordinate synthesis across layers have remained poorly understood. This thesis investigates two essential transmembrane proteins, PgfA and MurJ, that regulate peptidoglycan metabolism in Mycobacterium smegmatis and provide new insight into how mycobacteria synchronize cell wall assembly.

We present evidence that PgfA functions as a bifunctional regulator that links peptidoglycan metabolism to the availability of trehalose monomycolate (TMM), a key mycolic acid precursor. Through epistasis …

Regulation And Localization Of Urease In Sporosarcina Pasteurii: Implications For Coastal Protection, Amar Kosovac

UNF Graduate Theses and Dissertations

Coastal erosion is a persistent problem exacerbated by global warming. As the climate changes, the southeastern coast is likely to experience an increased frequency and intensity of storms, which can significantly damage the coastline. The coast is crucial as it serves as a habitat for numerous animals, supports tourism, and underpins infrastructure. Microbially induced calcite precipitation (MICP) is a novel method to enhance erosion resistance in sandy soils using the non-pathogenic bacterium Sporosarcina pasteurii. S. pasteurii produces urease to catalyze urea into bicarbonate, which drives the precipitation of calcium carbonate. Maximal expression of urease is a limiting factor for …

Population Genomics And Evolution Of Pseudomonas Aeruginosa, Samara T. Choudhury

Electronic Theses & Dissertations (2024 - present)

Pseudomonas aeruginosa is a Gram-negative bacterium ubiquitous in diverse environments and an opportunistic pathogen in humans. It is a leading cause of chronic lung infections in cystic fibrosis patients and of hospital-acquired pneumonia and sepsis. With a large flexible genome and abundant mobile genetic elements, P. aeruginosa exhibits high levels of antimicrobial resistance (AMR), making it a significant public health threat. Evolutionary processes such as homologous recombination, and horizontal gene transfer generate extensive genomic diversity in this species and facilitate the spread of resistance genes. In this dissertation, I investigate the genetic and evolutionary factors shaping P. aeruginosa population structure …

Requirement Of Prepiilin Peptidase Activity For Variovorax Paradoxus Eps Flp/Fap Pilus Assembly, Jenny L. Lanthripp

Electronic Theses, Projects, and Dissertations

Variovorax paradoxus is a Gram-negative aerobic bacterium present in both soil and the human oral microbiome. This species contributes to biotransformation of xenobiotics and promotes plant growth. Interestingly, although the genome of strain EPS lacks the flagellum operon annotated in strain S110, the microbe remains motile, and flagella can be observed microscopically. To investigate this unexpected phenotype, motility mutants were enriched from a Tn5 mutant library using a liquid culture settling strategy. A total of 122 isolates were screened for motility defects, and 57 exhibited significantly reduced motility compared to the wild type. Rescue cloning revealed that over 60% of …

Functional Analysis Of Ftsa-Mediated Recruitment Of Ftsk In Escherichia Coli, Abbigale Perkins

Dissertations and Theses (Open Access)

Bacterial cytokinesis requires precise coordination between cytoplasmic and periplasmic components of the divisome to ensure that membrane constriction and chromosome segregation occur in synchrony. The actin-like protein FtsA plays a central role in this process by tethering FtsZ to the membrane and recruiting downstream division proteins. Despite its essential function, the mechanisms by which FtsA coordinates divisome activation and the recruitment of late-acting proteins remain incompletely defined. To address this, the role of FtsA in activating septal synthesis and recruiting the DNA translocase FtsK was examined using mutational analysis in Escherichia coli.

The FtsA^{M96E R153D} variant, which has …

Strategic Enhancement Of Biofuel Production Using Bacillus Subtilis As A Model Organism: A Dual Approach Of Gene Essentiality Mapping And Optimization, Angela A. Zebede

Electronic Theses and Dissertations

With rising global demand for renewable energy, enhancing microbial platforms for biofuel production is vital. This study engineered Bacillus subtilis to improve resilience to solvent stress by targeting membrane lipid biosynthesis pathways essential for integrity. Growth curve analysis (OD₆₀₀) showed that phosphatidylserine (PS) and phosphatidylethanolamine (PE) knockout strains grew significantly slower than wild type (168), indicating the importance of these lipids under stress. Laurdan fluorescence spectroscopy was used to assess membrane properties. Generalized polarization (GP) analysis revealed a concentration-dependent reduction in membrane order upon 1%–2% 1-butanol exposure. GP values declined progressively from control to 2% treatment, reflecting increased membrane fluidity …

Investigating The Mechanisms Of Microbial Interactions Using A Model Cystic Fibrosis Polymicrobial Community, Bassam El Hafi

Dartmouth College Ph.D Dissertations

Cystic fibrosis (CF) airway microbial communities are complex ecosystems where interspecies interactions influence pathogen survival and disease progression. We leverage a CF-relevant in vitro four-species model composed of Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sanguinis, and Prevotella melaninogenica, alongside a microbiome dataset with over 4,000 respiratory samples from publicly available sequencing data of CF patient samples, to explore the dynamics of microbial interactions in CF. On a broader scale, we performed microbial network analysis to examine how the latest modulator therapy, elexacaftor/tezacaftor/ivacaftor (ETI), might influence CF microbial communities. Our analysis revealed a reduction in node connections and …

Determining The Impact Of Surface Roughness On Disinfection Efficacy Of Commercial Products Against Pseudomonas Aeruginosa And Staphylococcus Aureus Wet Surface Biofilms, Kayley Stallings

All Theses

Biofilms are resistant to many stressors including disinfectant treatments. Disinfection may be further complicated by biofilms formed on damaged surfaces, as the damaged parts provide bacteria a better place to attach and grow. To better understand the risks, a new method to standardize surface scratching, to emulate worn surfaces via surface roughness changes was developed. These surfaces were used to grow biofilms with an adapted standardized EPA method to determine disinfection efficacy differences on scratched and non-scratched high-density polyethylene (HDPE) and stainless steel (SS) coupons treated with commercial disinfectants [hypochlorite (CL)-based, hydrogen peroxide (HP)-based, and quaternary ammonium (QA)-based]. Post-80 grit …

Elucidation Of A Role In Biofilm Production For The Tyrosine Catabolism Pathway In Vibrio Cholerae And Analysis Of Reversible Phase Variation In Vibrio Vulnificus, Aheli S. Mukerji

LSU Doctoral Dissertations

Biofilms produced by the cholera pathogen Vibrio cholerae not only enhance its ability to survive in the environment but also allow pathogenic success of the bacterium. This organism also undergoes phase variation, switching between smooth and rugose colonial phenotypes, the latter forming much more vibrio polysaccharide (VPS) resulting in more robust biofilms and subsequently having an increased level of persistence. In a previous study, many genes were found to be upregulated in the transition from the smooth to the rugose phenotype. Here, several of these upregulated genes were investigated for their potential role in biofilm production, and an additional gene, …

From Epidemics To Experimental Treatments: Amphibian Mass Mortality Events And A Potential Treatment For Chytridiomycosis, Daniel Callahan

Graduate Masters Theses

Worldwide, amphibian populations have experienced dramatic declines due to a variety of threats. Among them, disease has been particularly deleterious and continues to impact populations. In the United States and Canada, the three leading causes of amphibian mass mortality events are ranavirosis, chytridiomycosis, and severe perkinsea infection, all caused by infectious pathogens. While research and policy have helped populations recover from these diseases, more work needs to be done to develop practical and efficient treatments for these infections. Of these three diseases, chytridiomycosis has had the most devastating effects on amphibian populations globally. Caused by the chytrid fungi Batrachochytrium dendrobatidis …

Impacts Of Land Development On Soil Microdiversity And Antibiotic Production, Dennis Guillen Castro, Robert Garcia, Jonathan Castro, Davida Smyth

Masters Theses (Archived)

The impact of land development on soil microbial diversity and antibiotic production is critical due to industrial expansion and the scarcity of effective antibiotics. Low Impact Development (LID) aims to preserve ecosystems, but its effectiveness in maintaining microbial diversity is uncertain. This study compares soil samples from nine sites: undisturbed (UD), residential (RD), and Madla Greenway (GW) within the VIDA development area and Texas A&M University-San Antonio campus. Isolated microbes were screened for antibiotic production and genetically characterized. Preliminary findings indicate that UD sites harbor greater microbial abundance, and a higher proportion of antibiotic-producing microbes compared to GW and RD …

Intrinsic And Extrinsic Drivers Of Bioaerosol Decay: Investigating Pathogen Stability Of Bacteriophage Ms2, Sin Nombre Virus, And Sars-Cov-2 In Simulated Environments, Elizabeth A. Klug

Theses & Dissertations

The threat posed by a virus as a bioaerosol depends largely on its stability under various environmental conditions (relative humidity (RH), sunlight, ozone, etc.). This stability is typically studied through aerosol decay—how the virus' viability changes over time when exposed environmental conditions. The Goldberg rotating drum, a widely used tool for studying bioaerosols, has been the basis of such research (Goldberg et al., 1958). However, it has significant limitations, including an inability to measure initial pathogen infectivity loss and the use of small sample volumes. Additionally, it does not answer the question of what intrinsic factors (lipids, proteins, nucleic acids) …

Evaluation Of Phenotypic Antimicrobial Resistance From Bacterial Pathogen Isolates In Bison, Aleena M. Kallan

Honors Capstones

Bison, the American buffalo, are increasingly utilized for food consumption due to their high protein content. Shiga toxin-producing Escherichia coli (STEC) is an important food-borne pathogen that leads to severe clinical infections and becomes antimicrobial-resistant (AMR). Specifically, fluoroquinolone antibiotics can complicate human treatment when infected with resistant STEC. This study aims to determine the presence of STEC in bison reservoirs and their antimicrobial resistance. Fecal samples (n=320) from bison herds were collected, followed by specific culture-based isolation for STEC. Polymerase chain reaction (PCR) was employed for pathogen confirmation, with 25.6% prevalence. PCR targeting gene, gyrA (resistant to fluoroquinolone), was tested …

Phosphatase Activity And Structure Of The Spoiie Protein In Clostridioides Difficile, Kathryn Wootten

Biological Sciences Undergraduate Honors Theses

Clostridioides difficile is a major cause of severe gastrointestinal infections and diseases, particularly in healthcare settings. Because of its ability to produce infectious endospores by sporulation, the protein SpoIIE, which is known to play a role in the regulation of this process, is being explored as a potential therapeutic target. In order to gain better insight into the structure and function of this protein, a concentrated and purified sample of the protein must be obtained. The goal of this study was to determine the conditions that would yield the highest amount of SpoIIE. The density of the cultures of bacteria …

Decoding Bacterial Resilience: Srnas And Sigma Factors In Stress Adaptation And Persistence Of Salmonella, Anita Nguyen

Honors Theses

Small RNAs (sRNAs) are noncoding RNA molecules in bacteria that function primarily to regulate gene expression, including those associated with stress. The Borchert Lab has identified 173 sRNAs and > 500 sRNAs that are responsive to desiccation and carbon starvation (c-starvation), respectively. Prokaryotic transcription involves an RNA Polymerase (RNAP) that transcribes DNA into RNA. RNAP involves sigma factors, which recognize promoters for the initial steps of RNA synthesis. The Borchert Lab has determined that there are significant overlaps between sRNAs expressed in cells subjected to both short-term durations and long-term durations of carbon starvation. Salmonella enterica serovars can have outbreaks associated …

Pseudomonas Aeruginosa Exoenzyme Y Enzymatic Activity Inhibits Exoenzyme S-Induced Caspase Activation But Not Cytotoxicity In Pulmonary Microvascular Endothelial Cells, Connor Holm

Honors Theses

Pseudomonas aeruginosa (P. aeruginosa) is the most common cause of ventilator-associated pneumonia in intensive care unit patients. P. aeruginosa utilizes a type III secretion system that injects exoenzymes U, S, T, and/or Y into the host cell cytosol. A majority of clinically isolated P. aeruginosa strains express ExoY often in combination with ExoU and ExoT, or ExoS and ExoT. Host signaling mechanisms in response to intoxication with individual exoenzymes have been extensively studied, yet little is known about host cell response to co-intoxication. In this study, pulmonary microvascular endothelial cells (PMVECs) were infected with P. aeruginosa strains expressing different combinations …

Toxicity And Biodegradability Of Novel Boronium Vs Conventional Ammonium-Based Antimicrobial Compounds In Wastewater Treatment Systems, Noor Shalan

Honors Theses

Quaternary ammonium compounds (QACs) are highly effective as disinfectants, herbicides, and pesticides; thus, overuse causes elevated levels of residual toxicity in domestic and industrial wastewater. QACs can be toxic to essential bacteria breaking down pollutants in wastewater treatment plants (WWTPs) and can remain untreated in effluent, harming the environment, and contributing to antibiotic resistance, posing risks to human health. Novel boronium-based antimicrobial compounds have demonstrated efficacy in eliminating bacteria, fungi, and viruses. If the boronium compounds exhibit lower residual toxicity, they could offer a promising alternative to QACs. Because these compounds are still in development, their potential toxicity to the …