Microbiology Commons^™

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 …

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 …

Mapping The Tar Vrna Interaction With Hiv-1 Integrase, Jian Sun, Rahul Yadav, Tolga Catmakas, Luke Fisher, Nicholas C. Fitzkee, Jacques J. Kessl

Faculty Publications

A series of critical interactions within the viral core between viral RNA (vRNA) and HIV-1 Integrase (IN) has previously been reported. In these studies, contact points between vRNA and IN were identified using RNA-seq and MS-based protein foot-printing approaches. Several IN amino acids located in its C-terminal domain (CTD) were found to be essential for vRNA binding, and their alanine substitution severely impacted the correct morphogenesis of the mature viral core. Here, we have used the TAR element to extend these studies by performing a comprehensive mapping of the interaction by deploying RNA crosslinking and NMR methodologies. Together, these approaches …

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 …

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 …

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 …

Synergies Of Microecology And Macroecology Elicit Insights For Creation Care, David Warners, John T. Wertz

University Faculty Publications and Creative Works

This article reports on a collection of microecological and macroecological insights that emerged from extended conversations between Calvin University professors David Warners, a botanist concentrating in restoration ecology, and John Wertz, a micro-biologist specializing in microbial ecology. Classic descriptions of ecology identify biological interactions as happening at the ecosystem, community, or population level. And yet, ecological interactions are very much occurring at the microbial level as well. Furthermore, microbial-level interactions frequently influence the quality and character of macroecological relationships and vice versa. Allowing ecological principles to be applied across all life forms broadens our comprehension of interactions that are happening …

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 …

Assessment Of The Bioremediation Potentials Of Biosurfactant-Producing Bacterial Strains Recovered From Spent Engine Oil-Contaminated Environments In Southwest Nigeria, Nafisa Mohammed Babayola, Nasiru Bright Lecky, Chinweizu Obioma Onumaegbu, Olufunmiso Olusola Olajuyigbe, Martins Ajibade Adefisoye

Journal of Environmental Science and Sustainable Development

Environmental pollution from hydrocarbons and their derivatives is predominantly of anthropogenic origin, occurring mainly during mining, transportation, and storage. This often in an annual release of substantial amounts of pollutants into the environment. The effective restoration of petroleum-contaminated environments requires a series of interventions to remediate soil to its natural state. This study aimed to isolate and characterize biosurfactant-producing bacterial strains with potential bioremediation capabilities to assess the potential application for remediating soils polluted with spent engine oil in the Remo district, Ogun State. Bacterial isolates were recovered from soil samples collected from spent engine oil contaminated sites, using standard …

Urobiome Composition Varies With Vesicoureteral Reflux Grade And History Of Febrile Urinary Tract Infection, Theresa C. Barrett, Kelvin Li, Adam Fitch, Asha Patel, Bhanu Sharma, Jacqueline Holden, Kermina Abdelsayed, Nina N. Kowalewski, Sridhar Narla, Daniel Bushnell, Barbara A. Methé, Catherine S. Forster

Department of Medicine Faculty Papers

Vesicoureteral reflux (VUR) is a risk factor for urinary tract infection (UTI). However, data describing the urobiome in children with VUR are limited. Here, we characterized the urobiome in children with and without VUR to better understand its potential role in VUR pathogenesis. Catheterized urine samples were obtained from children who presented for voiding cystourethrogram (VCUG) between 12/1/2020 and 10/3/2023. Children were excluded if they had any surgical procedures of the genitourinary tract in the 30 days prior to VCUG or were on treatment antibiotics at the time of VCUG. 16S rRNA gene sequencing and taxonomical classification identified the urobiome. …

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 …

Impact Of The Dose And The Number Of Transmitted/Founder Viruses On Siv Dynamics, Sunil Maity, Vitaly V. Ganusov

Biology and Medicine Through Mathematics Conference

No abstract provided.

The Influence Of Prosthetic Obturators On Quality Of Life In Individuals With Maxillectomy Defects, Minseok Kim

Oral Health

Abstract

Introduction: In recent years, there has been a growing focus on understanding the impact of oral cancer on patients' quality of life. Prosthetic rehabilitation techniques, such as maxillary obturators, often in conjunction with reconstructive surgery, have emerged as interventions to address the challenges posed by post-maxillectomy abnormalities.

Objective: This study aims to systematically review and evaluate the effectiveness of maxillofacial prosthetic rehabilitation using obturators in enhancing the quality of life of patients following maxillectomy.

Methodology: Systematic review of identified literature spanning the timeframe from 2000 to 2020 was used. The comprehensive search encompassed widely recognized databases including PubMed, …

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 …

Acquisition Behavior Response: Investigating The Ability Of Leptoglossus Phyllopus To Choose Between A “Good” Versus “Sub-Optimal” Strain Of Caballeronia, Irene L. Pham

2026 Spring Honors Capstones Projects

Leptoglossus phyllopus is a polyphagous pest that primarily feasts on citrus, tomatoes, and legumes. They must form a mutualistic symbiosis with Caballeronia every generation by ingesting the bacterium from their environment. However, not all species of Caballeronia confer the same fitness on the L. phyllopus host, raising the question of whether L. phyllopus possesses a partner choice mechanism that would allow it to distinguish between a good (GAOX1) and a suboptimal (Lep1P3) symbiosis partner. This was examined by conducting a choice experiment in which the two symbionts (GAOX1 vs. Lep1P3) were placed in a plastic box, and the bug’s roaming …