Microbiology Commons^™

Of Mice And Men: The Regulation Of Herpes Simplex Virus 1 Latency In Mouse And Human Neurons, Paige N. Canova

Dartmouth College Ph.D Dissertations

Herpes simplex virus 1 (HSV-1) establishes latent infections in sensory neurons, from which HSV sporadically reactivates, often due to external stress and other stimuli. Latency and reactivation are commonly studied using in vivo and ex vivo models in a variety of hosts, as well as in vitro models including primary mouse neurons and neurons derived from human pluripotent stem cells (iPSCs). The criteria for authentically modeling HSV latency include the ability to easily manipulate host genetics and biological pathways, as well as mimicking the immune response and viral pathogenesis in human infections. Presently, there remains a pressing need for …

Molecular Interactions Between The Shellfish Pathogen Vibrio Coralliilyticus Re22 And The Probiont Phaeobacter Inhibens S4sm, Jessica Coppersmith

Open Access Dissertations

Oyster larvae aquaculture is an important industry, both economically and environmentally, helping to create sustainable food systems by supplying seed oysters to farms, and also to restoration projects aimed at building coastal resilience and improving water quality by rejuvenating wild populations. However, oyster larvae are highly susceptible to rapid mortality events, crashes, which can seriously impact the industry. One source of these crashes in hatchery systems is vibriosis, caused by pathogenic species of Vibrio bacteria that are ubiquitous in temperate coastal waters, and with rising surface water temperatures their prevalence and virulence are increasing. To prevent these larval crashes from …

Wasting Disease Of A Marine Foundation Species Links Community Interactions To Disease Dynamics, Lillian R. Aoki, Olivia J. Graham, Reyn M. Yoshioka, Rebecca Maher, Lindsay Alma, Eileen E. Hofmann, Colleen A. Burge, Drew Harvell, Maya L. Groner

CCPO Publications

Infectious disease plays a key role in shaping marine communities, including in seagrass meadows, which form biodiverse coastal habitats. Eelgrass (Zostera marina) is the most widespread seagrass species and is susceptible to seagrass wasting disease, caused by the protist Labyrinthula zosterae. As a foundation species, eelgrass strongly influences ecosystem structure, function and services; recent work has begun to explore the links between critical community interactions and seagrass wasting disease. Here, we highlight recent advances about how the eelgrass community regulates and responds to seagrass wasting disease, from the microbiome to herbivores and filter feeders. We further show …

Valorizing Municipal Solid Waste For Sustainable Aviation Fuel And Polyhydroxyalkanoate Bioplastics: Pyrolysis And Microbial Pathways, Emon Das

Theses and Dissertations--Biosystems and Agricultural Engineering

The escalating global burden of municipal solid waste (MSW), projected to reach 3.88 billion tons annually by 2050, calls for innovative valorization strategies to mitigate environmental impacts and promote a circular bioeconomy. This thesis investigates the conversion of MSW into two high-value products: sustainable aviation fuel (SAF) and polyhydroxyalkanoate (PHA) bioplastics. Chapter one presents comprehensive physicochemical characterization and pyrolysis-GC/MS analysis of MSW feedstocks. The physicochemical results reveal that densification enhances handling and storage properties, while pyrolysis-GC/MS analysis indicates that plastic-rich MSW streams produce bio-oils with favorable hydrocarbon profiles suitable for SAF production, potentially contributing to decarbonization efforts in the aviation …

Backyard Chimeric Microbiomes: K-12 Participatory Science, Abigail Saucier

Honors Theses and Capstones

The US education system has seen a recent push for more secondary school curriculum to include STEM (Science, Technology, Engineering, and Mathematics) materials and activities. Middle and high school is a pivotal time when academic and personal experiences affect the development of student attitudes towards STEM (Christensen et al., 2015; Moreno et al., 2016). Teachers often utilize hands-on activities to promote student engagement with science curriculum (Brooks & Poles, 2021; Christensen et al., 2015). Hands-on activities improve student learning, but impacts vary by type of activity. When students work towards a known outcome they can feel disconnected from the work …

Microbial And Plant Biodiversity In Appalachian Agroecosystems And Their Implications For Soil Health, Kinsey Reed Close

Graduate Theses, Dissertations, and Problem Reports (ETD)

The sustainability of agricultural landscapes depends on understanding the complex interactions between plants, soil, and microbes. In Appalachia, a region shaped by complex terrain and long histories of human and ecological interaction, small family farms produce hay, livestock, and row crops. These agroecosystems, though often treated as “artificial” by many ecologists, have the potential to support both food production and biodiversity conservation if managed with an understanding of ecological complexity. This dissertation examines how plant and microbial diversity interact with soil and management to influence nutrient cycling, soil health, and long-term resilience in Appalachian agricultural systems. A literature review revealed …

Effects Of Liraglutide On The Gut Bacterial Community, Jami Anne Bull

Graduate Theses/Dissertations

Overweight and obesity are major health concerns associated with metabolic disorders and gut dysbiosis. Treatment options such as GLP-1 receptor agonists, like liraglutide, promote weight loss and improve insulin sensitivity; however, their impact on the gut bacterial community remains unclear. This study investigated the effects of liraglutide on the gut bacterial community of diet-induced obese (DIO) mice using Illumina DNA sequencing of the bacterial 16S rRNA gene. My study used twelve-week-old male C57BL/6J DIO mice. They were placed on a high-fat diet and treated with liraglutide (0.2 mg/kg) via daily subcutaneous injection for 14 Days. High-fat and low-fat diets control …

The Influence Of Flower-Microbe Interactions On Bumble Bee Behavior And Gut Microbiome Composition, Success Chiamaka Ekemezie

Graduate Theses/Dissertations

This thesis examines how microbial interactions in floral nectar and environmental variation influence bumble bee (Bombus spp.) foraging behavior and gut microbiome composition. Pollen germination experiments and behavioral assays in the lab tested whether Metschnikowia reukaufii (yeast) and Acinetobacter nectaris (bacteria) induce pollen germination and bursting in nectar and affect bee behavior subsequently. Both microbes reduced intact pollen, but bees did not alter flower preference. Furthermore, the study also assessed how floral and bee community composition shaped gut microbiome composition across six Missouri prairies. Using amplicon-sequenced fungal ITS and bacterial 16S rRNA genes, I found that fungal microbiome composition varied …

Spatial And Temporal Shifts In Bacterial Communities And Nutrient Removal In Two Springfield Wastewater Facilities, Rubina Sherchan

Graduate Theses/Dissertations

Bacterial communities play a central role in the biological nutrient removal and overall performance of wastewater treatment plants (WWTPs). However, very few is known about the spatial and seasonal dynamics of these communities. This study explores the spatial and seasonal variations in bacterial community composition across multiple treatment stages in two municipal WWTPs—Southwest (SWTP) and Northwest (NWTP)—in Springfield, Missouri. Using 16S rRNA gene amplicon sequencing, I analyzed 87 samples collected during summer and winter of 2024 from influent, sludge, aeration basins, clarifiers, and final effluent stages. I retrieved 16.4 million (summer) and 3.2 million (winter) sequences. Proteobacteria dominated both seasons …

Inoculating Soybean Plants At Different Growth Stages: Selecting Bradyrhizobium, Sinorhizobium, Or Both, Matthew R. Knoll

Graduate Theses/Dissertations

Soybean plants rely on nitrogen for growth, however atmospheric nitrogen (N2) is not a usable form and needs to be converted into different forms that are available to the plant. Nitrogen fixing bacteria such as rhizobia form symbiotic relationships with Soybeans in exchange for shelter and excess plant sugars. As a result, the plant can get the nitrogen it needs. There are four main genera of rhizobia that can form root nodules on Soybean including Bradyrhizobium, Sinorhizobium, Mesorhizobium, and Rhizobium. At this point, the effect that age of the host plant has on the selection of …

Genomic And Metabolic Network Properties In Thermophiles And Psychrophiles Compared To Mesophiles, Amal Saeed Alblooshi

Theses

Thermophiles and psychrophiles are extremophilic microorganisms that thrive in harsh conditions. Thermophiles are mostly located in hot springs, prosper in high temperatures. Psychrophiles thrive in extremely cold environments, including polar regions and deep-sea habitats. Although they play a crucial role in biotechnology and environmental research, their mechanisms of adaptation are still not well understood. The main objective of this thesis is to understand the genomic characteristics and metabolic network features in thermophiles and psychrophiles compared to mesophiles. The genomes of 59 species among thermophiles, psychrophiles, and mesophiles were collected from the NCBI database. These genomes were used to analyze their …

Deciphering Genetic Contributions To Antibiotic Persistence: Insights From Multi-Gene Knockout Studies, Elise K. Schweer

Electronic Theses and Dissertations

Antibiotic resistance is a critical global health challenge, complicating efforts to treat bacterial infections effectively. Antibiotic persistence plays a significant role in driving resistance. Persisters are a subpopulation of non-dividing bacterial cells that often evade lethal antibiotic treatment. Once antibiotics are removed, these cells "resurrect," resuming growth and may lead to relapsing infections. Notably, the progeny of persister cells exhibit a heightened tendency to acquire mutations or incorporate antibiotic resistance genes, further compounding the challenge of antibiotic resistance. In our recent study, we knocked out seven hypothetical genes and observed a significant reduction in persister levels. Compared to the wild …

Biotransformation Of Camelina Meal Via Pretreatment And Fermentation For Functional And Nutritional Upgrading, Ram Kumar Bhattarai

Electronic Theses and Dissertations

Camelina sativa, an oilseed crop of the Brassicaceae family, has seen increased cultivation in North America in response to the rising demand for biofuels over the past two decades. With this growth, camelina meal, a byproduct of oil extraction, has emerged as a promising yet underutilized resource, particularly for applications in animal nutrition. This study aimed to evaluate the potential of camelina meal as a substrate for submerged fungal fermentation and to examine how this bioconversion affects its physicochemical and nutritional properties. The influence of mild pretreatments (unwashed, washed only, and washed/dried and ground) on fermentation outcomes was also assessed. …

Microbial Mavericks: Turning Hazards Into Snacks, Alison G. Blanton

Biology Dissertations - Archive

Symbiotic associations with microbes are widespread across life and provide hosts with essential and beneficial functions. A growing concern in pest management is symbiont-mediated detoxification (SMD), a form of metabolic resistance to insecticides. The best-known example of SMD involves the bean bug Riptortus pedestris, where an environmentally acquired but obligate Caballeronia symbiont confers resistance to the organophosphorus insecticide fenitrothion. Motivated by this model, I began my work in another known bug-Caballeronia symbiosis: Leptoglossus phyllopus, native to the United States. I then expanded the study to include two additional U.S.-native hosts, Leptoglossus zonatus and Anasa tristis. Representative …

Microbiological Examination Of Yellow Mealworm (Tenebrio Molitor) Larvae Under Various Processing And Storage Conditions As Potential For Human Consumption, Rachel Midkiff

Graduate Theses, Dissertations, and Problem Reports (ETD)

Yellow mealworm (Tenebrio molitor) larvae have gained attention as a sustainable and nutritionally balanced food source, yet their high natural bacterial load raises food safety concerns. This study investigates the impact of pre-processing, processing, and storage conditions on microbial load and diversity in mealworms, comparing thermal (hot) and non-thermal (cold) treatments. These treatments include freeze-drying, wet heat treatments, dry heat treatments, and the combination of wet and dry heat treatments against untreated controls. Microbial loads were quantified by plate counts after day 0, day 10, and day 28 of vacuum-sealed refrigerated (4°C) storage. Water activity (Aw), pH, and moisture content …

Bacterial Two-Hybrid Systems Evolved: Innovations For Protein-Protein Interaction Research, Rebecca M. Richardson, Steven M. Pascal

Chemistry & Biochemistry Faculty Publications

Bacterial two-hybrid (B2H) systems offer a versatile platform for detecting protein-protein interactions (PPIs) in vivo. Originally developed to study bacterial transcriptional regulators, these systems have evolved to support a wide range of applications, including interaction mapping, domain analysis, and high-throughput screening. This review surveys the development and expansion of B2H systems across diverse biological contexts. We highlight technical considerations, platform-specific innovations, and recent adaptations that extend the utility of B2H systems in both prokaryotic and eukaryotic protein interaction research environments. By comparing different B2H variants and discussing their integration with complementary approaches, we provide a framework for leveraging these …

Nucleotide-Derived Bacterial Alarmones Attenuate The Induction Of Type-I Interferon Responses In A Murine Macrophage Reporter Cell Line, Ryan P. Kilduff, Erin B. Purcell, Lisa M. Shollenberger

Chemistry & Biochemistry Faculty Publications

The stringent response is a well-studied phenomenon in many bacterial systems and regulates resource-consuming activities such as transcription, translation, and replication. The stringent response is a well-conserved signaling framework, as are the nucleotide-derived signaling mediators, collectively referred to as (p)ppGpp or as alarmones. There is a wealth of research evaluating nucleotide-derived alarmone signaling in bacterial models, however, their potential to modulate innate immune signaling has not yet been evaluated. Several common pathogen-synthesized molecules, such as lipopolysaccharide (LPS) and cyclic-di-AMP (c-di-AMP), act as pathogen-associated molecular patterns (PAMPs), which are common patterns that alert the innate immune system of bacterial infection. The …

Caveolin-Mediated Endocytosis: Bacterial Pathogen Exploitation And Host-Pathogen Interaction, Dibyasri Barman, Rishi Drolia

Biological Sciences Faculty Publications

Within mammalian cells, diverse endocytic mechanisms, including phagocytosis, pinocytosis, and receptor-mediated endocytosis, serve as gateways exploited by many bacterial pathogens and toxins. Among these, caveolae-mediated endocytosis is characterized by lipid-rich caveolae and dimeric caveolin proteins. Caveolae are specialized microdomains on cell surfaces that impact cell signaling. Caveolin proteins facilitate the creation of caveolae and have three members in vertebrates: caveolin-1, caveolin-2, and caveolin-3. Many bacterial pathogens hijack caveolin machinery to invade host cells. For example, the Gram-positive facultative model intracellular bacterial pathogen Listeria monocytogenes exploits caveolin-mediated endocytosis for efficient cellular entry, translocation across the intestinal barrier, and cell–cell spread. Caveolin …

Analyzing Microbial Communities In Porites Astreoides, Sanaa Caldwell, Katie Parker, Daniel Barshis

Biological Sciences Faculty Publications

Coral reefs are vital marine ecosystems that support many different species and ecosystem services through protecting coastlines from storms and erosion, providing raw materials for medication, and facilitating diversity amongst marine species. Anthropogenic climate change is causing ocean temperatures to exceed the range of coral thermal tolerance resulting in more coral bleaching events globally. However, some corals have the capacity to withstand high temperatures through different thermal tolerance strategies. A balanced microbial community plays a critical role in coral health and recent studies have indicated that a balanced microbiome is associated with temperature-stress tolerant corals. Yet, there is a severe …

Impacts Of Tick Parasitism On The Rodent Gut Microbiome, Robert J. Brinkerhoff, Joshua Pandian, Meghan Leber, Isabella D. Hauser, Holly D. Gaff

Biological Sciences Faculty Publications

Host microbiota may impact disease vector behavior and pathogen transmission, but little is known about associations between ectoparasites and microbial communities in wildlife reservoir species. We used Illumina metagenomic sequencing to explore the impacts of tick parasitism on the rodent fecal microbiome in both a field and laboratory setting. We found that tick parasitism on wild hosts was associated with variation in the fecal microbiota of both the white-footed deermouse, Peromyscus leucopus, and the southern cotton rat, Sigmodon hispidus. In a lab experiment, we detected significant changes to the fecal microbiome after experimental exposure to immature ticks in …

Interactions Between Microplastics, Biofilms, And Antimicrobials In Freshwater Streams, Ryan Thomas Krantz

Dissertations

Microplastics (MPs) are ubiquitous contaminants in freshwater ecosystems that could be hotspots for the interaction of antimicrobial compounds and surface-attached microbial biofilm communities. MPs and antimicrobials are both common in wastewater and urban freshwaters and MPs can adsorb contaminants like antimicrobials to their surface. Within aquatic habitats, MPs also support colonization by microbial biofilms. Therefore, we hypothesized that the adsorption of antimicrobials to MP surfaces would affect microbial communities colonizing MPs, altering their diversity, composition, and antimicrobial resistance. We investigated the effects of these interactions across two studies. The first study, discussed in Chapter 2, used a microcosm approach to …

Antibody-Induced Multicellular Behaviors Of Salmonella Typhimurium, Samantha K. Lindberg

Electronic Theses & Dissertations (2024 - present)

Salmonella enterica is a globally distributed bacterial pathogen that is commonly acquired through consumption of contaminated food and water. The enterica subspecies includes over 1500 unique subvariants, or serovars, that are classified by antigen presentation. Due to its global environmental prevalence, broad host range, and increasing pathogenicity, serovar Typhimurium is of particular concern for human and animal health, as well as food safety. Once in the gastrointestinal tract, Salmonella Typhimurium (STm) exploits host immune mechanisms, implements an arsenal of virulence factors, and outcompetes the microbiota to invade the intestinal epithelium. While STm infections are generally self-limiting and relatively mild, emerging …

The Role Of Fruiting Bodies In Protecting A Community Of Myxococcus Xanthus Spores From The Environment, Dave Lall

Wayne State University Dissertations

Environmental microorganisms have evolved a variety of strategies to survive fluctuations in environmental conditions, including the production of biofilms and differentiation into spores. Myxococcus xanthus are ubiquitous soil bacteria that produce starvation-induced multicellular fruiting bodies filled with environmentally resistant spores (a specialized biofilm). Isolated spores have been shown to be more resistant than vegetative cells to heat, ultraviolet radiation, and desiccation. The evolutionary advantage of producing spores inside of fruiting bodies is not clear. Here, we examine a hypothesis that the fruiting body provides additional protection from environmental insults. We developed a high-throughput method to compare the recovery (outgrowth) of …

The Chemical Ecology Of A Caribbean Boulder Coral During Restoration And The Interplay Between Fish Predation And Microbiome Variation, Catherine E. Raker

Open Access Dissertations

Coral reefs are one of the most biodiverse and productive ecosystems on the planet. In recent decades, however, climate change and other global threats have caused severe declines in live coral cover worldwide. Coral propagation, or “gardening,” is a popular strategy to attempt to restore healthy corals to degraded reefs. Slow-growing boulder corals are often restored using microfragmentation, where cutting coral colonies into roughly 1 cm² fragments can increase their growth rates up to 5x. However, extreme early mortality of fragments has been observed in the field, which has been at least partially attributed to predation. It has been …

“What’S Supp” Developing An In Vitro Model For Healthy Oral Biofilms, Alex Labossiere

Open Access Dissertations

The study of oral plaque has largely been influenced by the study of pathogens. Here in Chapter 1, I will discuss how this pathogenic focus has been dominant until the onset of microbiome research and begin to explain microbiomes in the context of supragingival plaque in homeostatic communities. From there we will then discuss the possible roots where dysbiosis may arise from plaque to cause disease and ways in which we can study healthy supragingival plaque by in vitro models.

In chapter 2, I will discuss molecular commensalism and how it can be viewed as a tool to further understand …

Characterizing Agroecosystem Effects Of Industrial Hemp On A Rotational Row Cropping System And Microbial Communities, Kent D. Pham

Theses and Dissertations--Plant and Soil Sciences

The implementation of crop rotation on a farm can have many benefits for agroecosystem health and production. This practice can potentially reduce nutrient amendments, disrupt pest and disease cycles, and increase crop yields. In Kentucky, one common rotation consists of either corn or soybean grown the first year, followed by the other crop, repeated every two years. Industrial hemp, grown for fiber or grain, is an emerging crop that has shown promise as a rotation alternative, although not much is known about its effects on soil health, agroecosystem functioning, and microbial communities. To better characterize hemp’s role within American agriculture, …

Sars-Cov-2 Variants Of Concern: Biological Implications Of Immunogenicity And Comorbidity, Jacob Nichols

Theses and Dissertations (ETD)

When coronavirus disease 2019 (COVID-19) emerged in human populations in late 2019, there was nothing known about the virus, SARS-CoV-2, besides that it had a high degree of similarity to severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV). The prior published research on these viruses set a strong foundation for the research approaches needed to quickly stand-up medical countermeasures for treatment of COVID-19. However, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) soon revealed a high propensity to evolve new variants that could engage host cell receptors with greater affinity and escape host immunity. With each wave …

Characterization Of Novel Hantaviruses In Paraguay, Ifebuche Nnamani

Theses and Dissertations (ETD)

The genus Orthohantavirus, is a group of tripartite, negative-sense RNA viruses of which some members are the etiologic agents for hemorrhagic fever with renal syndrome (HFRS) or orthohantavirus cardiopulmonary syndrome (HCPS) in the Old and New Worlds, respectively. Sampling of wild rodents for these viruses has increased our knowledge of their host range and continues to lead to the discovery of new orthohantaviruses species and strains. HFRS and HPS have case fatality rates of up to 15% and 40%, respectively. And in some years, morbidity rates of up to 100,000 cases can be reached, globally. The epidemiological evidence of human-to-human …

Gut Microbial Community Structure Of The Adult Citrus Root Weevil Diaprepes Abbreviatus, Imilce A Rodriguez-Fernandez, Tasha M Santiago-Rodriguez, Paola G Figueroa-Pratts, Keislamarí Cintrón-Berríos, Nichole D Rodriguez-Cornier, Gary A Toranzos

Faculty, Staff and Students Publications

Diaprepes abbreviatus is an agricultural pest known to affect around 270 plant species across the Caribbean and the United States, posing significant challenges to pest management. Chemical control dominates management, but environmental and health concerns motivate microbiome-informed alternatives. However, limited information exists on the gut anatomy, physicochemical environment, and microbial composition of D. abbreviatus. In this study, we provide the first comprehensive characterization of the gut morphology, pH, and microbiota of adult D. abbreviatus in both females and males collected in Puerto Rico. Using dye-based gut tracing, we identified foregut, midgut, and hindgut or posterior gut compartments, and confirmed the …

Transposable Element Activity Captures Human Pluripotent Cell States, Florencia Levin-Ferreyra, Srikanth Kodali, Yingzhi Cui, Alison R S Pashos, Patrizia Pessina, Justin Brumbaugh, Bruno Di Stefano

Faculty, Staff and Students Publications

Human pluripotent stem cells (hPSCs) exist in multiple, transcriptionally distinct states and serve as powerful models for studying human development. Despite their significance, the molecular determinants and pathways governing these pluripotent states remain incompletely understood. Here, we demonstrate that transposable elements act as sensitive indicators of distinct pluripotent cell states. We engineered hPSCs with fluorescent reporters to capture the temporal expression dynamics of two state-specific transposable elements, LTR5_Hs, and MER51B. This dual reporter system enables real-time monitoring and isolation of stem cells transitioning from naïve to primed pluripotency and further towards differentiation, serving as a more accurate readout of pluripotency …