Microbiology Commons^™

Surveillance And Comparative Genomics Of Bacteria From Hospital And Human Reservoirs, Emily E. Benedict

WUSM Theses and Dissertations – All Programs

Bacteria are diverse and adaptable and, consequently, present in a wide variety of environments. They are capable of growing under intense pressures, including those brought on by the human immune system and disinfection strategies. To survive these pressures, bacteria develop resistances. Antimicrobial resistance, which occurs when a microbe is no longer responsive to the antibiotic intended to control it, is one such adaptation that presents an especially serious threat, as it limits treatment options for infections caused by antimicrobial resistant microbes. Similarly, the ability of bacteria to survive in environments subjected to heavy disinfection efforts, such as intensive care units …

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 …

Developing Field And Spaceflight Microscopy, Nikki Johnston

Dissertations and Theses

Designing for spaceflight favors the reduction of unnecessary features and cost-cutting, whether thisbe computation, hardware, or procedure. Resources are spent toward fortification and mission success over convenience. Such design goals paired with the relatively smaller budgets of academia lead us to do as much as we can in-house and use open-source as much as we can without compromising mission success. We also believe that thoroughly testing technology in extreme environments on earth is necessary for the success of a flight instrument. We focus on microscopy for life detection. I have spent my time here learning methods of hand-building microscopes to …

Host-Pathogen Dynamics Underpinning Staphylococcus Aureus Growth During Intracellular Osteoclast Infection, Luke D. O'Connor

WUSM Theses and Dissertations – All Programs

Bone infection is most commonly caused by the gram-positive bacterium Staphylococcus aureus. It has myriad ways in which it can circumvent or subvert killing by the host or antibiotics. Intracellular infection is one such niche that is protective from immune and antibiotic attack. In 2019, Krauss and colleagues discovered that infected osteoclasts (OCs) allow S. aureus to replicate intracellularly. There they found that the ability of S. aureus to grow inside the cell was tied to OC differentiation. The magnitude of overnight bacterial expansion positively correlated with OC maturity and duration cultured with the osteoclastogenic factor RANK ligand (RANKL). Bacterial …

Escherichia Coli Concentrations In Sand And Water At Tributary-Influenced Lake Michigan Beaches, Josie Elaine Kuhlman

Masters Theses

Contamination of public recreational water and sand is a human health concern, creating a management challenge for public health officials. Past research has shown that Escherichia coli can persist in sediment and can be washed into recreational water. Currently, beach monitoring practices only utilize E. coli concentrations in water samples to determine beach safety and do not consider potential exposure to sediment/sand concentrations. In this study, I investigated the relationship between E. coli concentrations in water and sand samples, which will aid public health officials in making more informed decisions about beach closures. I utilized culture-based measurements of E. coli …

Assessing Gene Expression Changes In The Octocoral Briareum Asbestinum Due To Vibrio Coralliilyticus Exposure, Hailey Poignant

All HCAS Student Capstones, Theses, and Dissertations

Coral reefs are an essential ecosystem home to tons of marine diversity that humans have also  learned to rely on, but they are harmed by climate change and the increasing prevalence of disease. While most studies focus on reef-building coral, octocorals also warrant attention to reveal how they respond to similar stressors. Octocorals share distant ancestry with reef-building corals, so there may be overlap in their immune responses which could provide insight into future restoration projects. To understand how octocorals respond to disease, the octocoral Briareum asbestinum was used as a model to examine gene expression changes caused by the …

Evaluating Pfas And Marine Microbial Interactions In Estuarine Sediments With Varying Urbanization And Assessments Of Microbial Responses To Pfos, Zachary J. Padgett

All Theses

Per- and polyfluoroalkyl substances (PFAS) are a diverse class of synthetic chemicals that have become globally distributed due to their extensive use in industrial and consumer products and their extraordinary resistance to environmental degradation. Their persistence and documented toxicity have made them a growing concern in coastal environments, particularly in estuaries where urban runoff, wastewater, and industrial discharges concentrate these compounds. Estuaries are unique in that tidal mixing and interactions with fine-grained sediments and organic matter promote PFAS retention, while the microbial communities living directly within estuarine sediments are positioned where PFAS preferentially accumulate, creating conditions for prolonged exposure and …

The Aggregation Of Microplastics By Enhancing Extracellular Polymeric Substance Production In Pseudoalteromonas Sp. Ncimb 2021 To Improve Removal Efficiencies In Environmental Matrices, Janelle L. Mercer

All Theses

Microplastics (MP) are ubiquitous in the natural environment and are a growing threat due to their small size and durability. Plastics are released into the environment through improper waste management, wastewater treatment outfalls, industrial spills, agricultural runoff, and landfills. These particles breakdown into secondary MP through degradation pathways. MP, less than 5 mm, require intricate removal techniques from water systems. Filtration techniques, though viable and effective, have implementation constraints due to high cost, maintenance demands, and filter fouling. By integrating coagulation and flocculation processes prior to filtration, MP removal efficiencies can increase, while minimizing operational challenges during filtration. Extracellular polymeric …

Understanding The Potential Sources Of Bacteria And Turbidity Pollution In The Edisto Island Watershed, Brynne Sumner

All Theses

Anthropogenic pollution introduces contaminants, such as pathogenic bacteria and turbidity, into coastal watersheds. These contaminants are the major contributors to water quality impairments in the three sub-watersheds encompassing Edisto Island and the Town of Edisto Beach (hereafter referred to as the Edisto Island Watershed), located within the ACE Basin, South Carolina, USA. With 18 locations impaired for fecal bacteria and 19 for turbidity on the 2024 South Carolina 303(d) list of impaired waters, the Edisto Island Watershed offers valuable insights into the water quality challenges rural coastal communities face.

This study aimed to identify the sources of fecal bacteria and …

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 …

Defining The Role Of Spxa1 And Spxa2 In Group A Streptococcus (Gas), Gretchen Anne Morrison

Dissertations and Theses (Open Access)

Group A Streptococcus (GAS) is a human-restricted pathogen whose global incidence has surged in the post-COVID era. The ability of GAS to shift from a colonizing to invasive phenotype depends on coordinated virulence gene regulation in response to host-imposed stressors. The paralogous global transcriptional regulators, SpxA1 and SpxA2, have emerged as central mediators of these adaptive responses; however, the mechanisms by which these regulators influence both global gene regulation in direct response to external stresses and the host response as a result of regulatory changes remain incompletely understood. Using an integrated multi-omic approach, we define the distinct yet interconnected regulatory …

Mutational Analysis Of Domain Functions In The Yeast Decapping Enzyme Dcp2, Jellisa Ewan, Ambro Van Hoof

Dissertations and Theses (Open Access)

In yeast, the major mRNA decay pathway involves deadenylation of the 3’ poly-A tail, followed by decapping of the 5’ m7Gppp cap and subsequent 5’ to 3’ degradation or 3’ to 5’ degradation. This is carried out by Pan2/Pan3 and Ccr4/Not deadenylases, the decapping enzyme Dcp2, and Xrn1 and  RNA exosome exoribonucleases, respectively. The eukaryotic mRNA decapping enzyme complex, Dcp1/Dcp2, is essential in yeast, and deletion of either gene is lethal. However, the deadenylases that act upstream and the 5’ exoribonuclease that act downstream of the decapping step are not, even though they are all highly conserved with no known …

Identification Of Conditionally Essential Genes Required For Salmonella Enterica Serovar Typhimurium Adaptation To The Chicken Cecal Extract Through Ex Vivo Modeling And Transposon Insertion Sequencing, Deborah Bukola Olubanjo

Graduate Theses and Dissertations

Salmonella enterica serovar Typhimurium (S. Typhimurium) remains a major foodborne pathogen associated with chicken, where it can persist in the intestinal tract without overt disease and contribute to zoonotic transmission. The chicken cecum represents a complex ecological niche shaped by microbial competition, host-derived substrates, short-chain fatty acids, oxygen limitation, extracellular components, and diverse metabolic gradients. Although transposon insertion sequencing (Tn-seq) has been widely used to define bacterial fitness determinants, limited work has examined genome-wide adaptation of S. Typhimurium in chicken ceca-derived ex vivo systems that preserve key features of the avian cecal environment. This dissertation investigated conditionally essential genes required …

Describing Propagation Of Carbapenem-Resistant Acinetobacter Baumannii Through Comparative Genomics And Phenotypic Analysis Of Modern-Day Clinical Isolates, Emma Graffice

ETDs from 2020-2029

Understanding the genomic structure of bacterial populations is essential for tracking antimicrobial resistance and informing public health strategies to prevent spread of multidrug resistant organisms. In this study, we investigated the diversity and distribution of carbapenem-resistant Acinetobacter baumannii (CRAb) lineages across a major healthcare system in the U.S. Deep South through both retrospective and prospective isolate collection. Our analysis revealed a heterogeneous population composed of multiple genotypically and phenotypically distinct lineages. To improve the resolution of lineage classification, we applied average nucleotide identity (ANI) as a high-resolution metric for comparative genomics. A ≥99% ANI threshold effectively delineated lineages, outperforming traditional …

Jnk Signaling Impacts Car-T Cell Effector Function, Charles Kuhlmann

ETDs from 2020-2029

The potent cytotoxic activity of T cells serves as a natural defense against cancers. Chimeric antigen receptor (CAR) T cell therapy represents a strategy for harnessing T cells against advanced tumors. CAR-T cell therapy has seen striking success against hematologic malignancies, prompting its application to new diseases. Ovarian cancer is a highly lethal disease characterized by frequent recurrence and aggressive nature, prompting the investigation of CAR-T cell therapy as a salvage regimen. However, like in other solid tumors, the early performance of CAR-T cell therapy in ovarian cancer is poor. While many strategies exist for improving the longevity of CAR-T …

Discovery Of Bmi-Associated Gut Microbiome Signatures In The Awi-Gen 2 Cohort, Meriem Yagoubi

Theses and Dissertations

Obesity is increasing across sub-Saharan Africa amid rapid dietary, environmental, and urbanization transitions, yet the gut microbiome features associated with adiposity in African populations remain under-characterized. This study investigated whether species-level gut microbiome composition is associated with body mass index (BMI) in the AWI-Gen 2 cohort, and whether BMI-associated microbial signals remain detectable after accounting for the dominant geographic structure of the microbiome. Gut microbiome community structure and diversity were characterized across 1,665 participants, and differential abundance analysis was used to identify taxa associated with BMI after controlling for study site. Machine learning models were then trained to assess how …

Microbial Literacy, Equity, And Sustainability At Cal Poly: A Policy Framework With University Housing As A Pilot Case, Joseph B. Fewel

Biological Sciences

Microorganisms play a fundamental role in human health, environmental systems, and the functioning of built environments, yet they remain largely absent from sustainability and public policy discussions. This project proposes a framework for integrating microbial literacy, equity, and health into institutional decision-making, using California Polytechnic State University (Cal Poly) as a case study and university housing as a pilot site for implementation. Drawing on interdisciplinary literature in microbiology, public health, environmental justice, and sustainability, as well as policy analysis and stakeholder interviews, this project examines how campus systems, including housing, ventilation, sanitation, food systems, and waste management, shape microbial exposure …

Exploring The Durability Of Marine Picocyanobacterial Microcolonies, Erik Swanson

University Honors Theses

Picocyanobacteria of the genus Synechococcus are widespread aquatic photoautotrophs that play essential roles in primary production and carbon cycling. Some Synechococcus strains form multicellular microcolonies, but the mechanisms of cell-to-cell attachments and structural durability of these microcolonies remain poorly understood. This research investigated the physical durability of microcolonies in two marine Synechococcus strains (CC9605 and CC9311) using physical disruption treatments. Cultures were subjected to vortexing and sonication treatments, and populations of single cells and microcolonies were quantified using flow cytometry based on differences in measures of size. Results indicated that strain CC9605 showed no significant treatment effect, whereas CC9311 displayed …

Protein Glycosylation In Natural And Synthetic Minimal Genome Mycoplasmas, John Sanford

ETDs from 2020-2029

Mycoplasmas are cell wall-less bacterial symbionts with remarkably streamlined genomes. Mycoplasmas offer two intriguing model organisms for studying concepts of minimal life. Mycoplasma genitalium has streamlined its genome to 580-kbp while maintaining virulence to suit its niche of parasitizing the human urogenital tract. The J. Craig Venter Institute has synthesized and transplanted a 543-kbp genome into a recipient cell, resulting in a non-pathogenic organism termed JCVI-syn3A. The conservation of a biological process in M. genitalium and JCVI-syn3A strongly implies an essential function in mycoplasmas, and potentially all life. Despite common thought of mycoplasmas being the simplest cells, much of their …

Marine Heatwaves And Fish Reproduction: Endocrine Responses In The Eurythermal Sheepshead Minnow (Cyprinodon Variegatus), Isabel Villafuerte

Master's Theses

Marine heatwaves associated with climate change are increasing in frequency and severity, posing significant threats to fish populations in shallow habitats such as estuaries and salt marshes. Because temperature is a primary regulator of fish reproduction, understanding how heatwaves affect reproductive physiology is critical for anticipating the biological consequences of ongoing climate change for coastal fishes. Here we examined how simulated heatwave conditions affect the reproductive hypothalamic-pituitary-gonadal (HPG) endocrine axis in the estuarine sheepshead minnow (Cyprinodon variegatus), a eurythermal fish well suited to studying thermal stress responses in estuarine environments. Adult sheepshead minnows acclimated to a daily oscillating …

Developing A High-Resolution Off-Axis Common-Mode Digital Holographic Microscope, Lucy Cook

University Honors Theses

Off-axis digital holographic microscopy (DHM) is a powerful tool for 3D, non-invasive live-cell tracking without moving parts. However, traditional setups face an inherent dilemma: split-path interferometers offer high spatial resolution but poor temporal stability, while more stable common-mode configurations are historically limited to lower numerical aperture (NA) regimes. This thesis bridges that gap by scaling a common-mode DHM architecture into a high-resolution benchtop instrument featuring NA = 0.65 objectives, paired with a high-power 520 nm laser source to combat transmission losses and sustain imaging frame rates across an expanded optical footprint. We map the multi-variable design space required to satisfy …

Immunomodulatory And Signaling Molecules From Plant-Associated Bacteria: Toll-Like Receptor 4 Agonist Adjuvants And Diketopiperazine-Mediated Communication, Marian Romaine

Dissertations, Theses, and Capstone Projects

Medicinal plants and their associated microbiomes constitute a rich source of bioactive natural products with applications in immunotherapy and microbial ecology. Herbal formulations have long been valued for safe immune enhancement, while bacterial signaling molecules govern community behaviors critical to pathogenesis, symbiosis, and environmental processes. Bacterial lipopolysaccharides (LPS) from plant-associated Gram-negative bacteria have emerged as potent TLR4 agonists, yet their endotoxic potential limits direct use, and diketopiperazines (DKPs) serve as versatile quorum-sensing mediators capable of modulating biofilms in mixed microbial systems.

The work in this thesis comprises two independent but complementary research strands. The first strand pursued the engineering of …

Evaluating Soil Health And Crop Yield In Louisiana Agricultural Systems: Impacts Of Best Management Practices And Prediction Models, Hector J. Mendoza Lagos

LSU Doctoral Dissertations

The adoption of conservation management practices is critical for improving soil health, enhancing nutrient use efficiency, and sustaining crop productivity in row crop systems in Louisiana. This study evaluated the role of conservation agronomic practices, soil biochemical indicators, and machine learning predictive models to improve soil nutrient dynamics, soil health indicators, microbial communities (MC), and crop productivity on a corn (Zea mays L.) research plot scale and in a commercial forty-hectare cotton (Gassypium hirsutum L.)-corn-soybean (Glycine max L.) rotation system in northeast Louisiana. The objectives of the study were to evaluate soil nutrient dynamics and MCs under …

Examining The Ligands, Location, And Function Of Toll-Like Receptor 10, Kiefer Keanu Tam

Master's Theses

Toll-like receptors are a class of innate immune pattern recognition receptors that detect pathogen-associated molecular patterns and regulate downstream inflammatory responses. Toll-like receptor 10 remains the only human TLR whose ligand specificity, cellular localization, and immunological function are not fully defined. Emerging evidence suggests that TLR10 may play an anti-inflammatory role and can heterodimerize with TLR2 to modulate immune signaling. Previous studies from our laboratory demonstrated that stimulation with heat-killed Mycobacterium tuberculosis promotes TLR2-TLR10 heterodimerization and trafficking to the cell surface. In this study, we expanded our ligand panel to include additional gram-positive bacteria, particularly anti-inflammatory probiotic species, to further …

Combating Β-Lactamase Resistance: From Inhibitor Design To Substrate Evolution, Lian M.C. Jacobs

USF Tampa Graduate Theses and Dissertations

β-lactamase production by bacteria is a major mechanism of antibiotic resistance. These enzymes hydrolyze β-lactam antibiotics, preventing them from binding to and inhibiting PBPs. Although new β-lactam scaffolds and inhibitors are continually introduced into the clinic, resistance often emerges within a few years. Therefore, the development of cross-class inhibitors with novel scaffolds is critical to mitigate this resistance. In parallel, a deeper understanding of the structural and mechanistic basis of β-lactamase resistance is essential. Together, these approaches provide an effective strategy for combating antibiotic resistance.

The first project addressed the need of effective cross-class β-lactamase inhibitors capable of targeting SBL …

Skin Of Frog And Scale Of Dragon: Nutritional Cues, Life Cycle Kinetics, And Secretome Dynamics In Batrachochytrium Dendrobatidis, Naomi C. Okada

UNLV Theses, Dissertations, Professional Papers, and Capstones

Nearly 50% of amphibian species are at risk of extinction, making them the most threatened group of vertebrates on the planet. A major driver of these declines is the pathogenic chytrid fungus Batrachochytrium dendrobatidis (Bd), which causes the fatal skin disease chytridiomycosis. Since its discovery in the late 1990s, Bd has been directly implicated in the extinction of 90 species of amphibians and the declines of hundreds more. Despite this devastating ecological impact, relatively little is known about its basic cellular biology.

Bd has a multi-stage asexual life cycle consisting of a motile and infectious zoospore, which encysts (into a …

Characterizing The Microbial Structure And Function In Black Soldier Fly Digested Dairy Manure And Subsequent Larvae, Branden N. Pierce

Theses and Dissertations

This work examined the microbial structure and gene expression found in Black Soldier Fly larval guts and their frass when reared on dairy cattle manure that had been amended with either R. rhodococcus 21198, P. polymyxa 8158, or both and compare the results to larvae reared on untreated manure. First an overview of literature surrounding projected global food supplies and the possible use of insects to either increase them or mitigate the environmental effect of producing said supply. A cellulose degradation assay was performed to assist in determining which bacterial species to use as amendments. Characterization of the microbial communities …

Impacts Of Salinity On Microbial Enzyme Activity In Coastal Waters, Natali Ariyoshi

Honors Theses

Microbial extracellular enzymes are critical for the breakdown of organic matter and nutrient cycling in aquatic ecosystems. Extracellular enzyme activity serves as an indicator of nutrient turnover rates, metabolic states, and nutrient limitations within an ecosystem. Coastal ecosystems are especially dynamic as the influx of freshwater from inland runoff or seawater intrusion from storm surges can lead to fluctuations in salinity which can restructure microbial communities and alter enzymatic activity. Despite the ecological significance of these changes, few studies have explored the effects of short-term salinity shifts on microbial extracellular enzyme activity in coastal waters. This study investigated the effects …

Antibiotic Resistance Patterns In Bacterial Isolates From Mississippi Gulf Coastal Environments, Lawler F. Horn

Honors Theses

Coastal environments host diverse microbial communities that play essential ecological roles but may also serve as reservoirs for antibiotic-resistant bacteria. This study investigated patterns of antibiotic resistance in microbial isolates collected from public beaches along the Mississippi Gulf Coast. A total of 143 bacterial isolates exhibited growth and were included in antibiotic susceptibility screening. High levels of antibiotic resistance were observed, with 137 of 143 isolates showing growth on vancomycin, 124 on amoxicillin, and 102 on erythromycin. Resistance to kanamycin (19/143 isolates) and tetracycline (33/143) was less common. Multidrug resistance was widespread, with 101 isolates (70.6%) resistant to three or …

An Investigation Of Entamoeba Histolytica Chitin Synthases And Other Encystation Factors In Early Encystation, John N. Talledo

All Theses

Entamoeba histolytica is a food-and-water-borne human protozoan pathogen that relies on a two-stage life cycle for successful proliferation outside of the host. E. histolytica exists in its dormant cyst form while outside of its host and converts to the motile trophozoite (amoeba) form in the small intestine. The trophozoites colonize the large intestine to cause symptomatic disease in ~10% of infections, resulting in ~100 million cases of amoebic dysentery each year. Trophozoites can convert back to the cyst form, which is shed in feces to continue the infection cycle.

Currently, there is a lack of understanding of the exact molecular …