Other Microbiology Commons^™

Detection And Control Of Environmentally Transmissible Viruses, Anand R. Soorneedi

Doctoral Dissertations

Viruses, owing to their ubiquitous nature and ability to infect almost every other species, have long been a subject of interest for scientists. Some of the virus species can be very deadly to humans and animals alike and can impose a huge economic and health burden across the world. The recent CoVID-19 pandemic underscores the importance of timely detection for developing effective intervention strategies. Unfortunately, some of the virus species that cause significant health and economic impacts do not have robust and reliable detection methods due to several reasons. In some cases, despite having gold standard methods for detection of …

Effect Of Authentic Kefir And Nigella Sativa On Broilers Challenged By Coccidia And Clostridium Perfringens, Julian E. Nixon

All Dissertations

Black seed oil concentrations of 0%, 0.1%, 1% and 5% were added to milk inoculated with kefir grains and incubated at 25°C for 22 h. The pH and microbial count indicated 1% black seed oil caused low inhibition (P > 0.05) of fermentation, but 5% black seed oil caused significant inhibition of the kefir microorganisms (P < 0.05).

Cobb 500 male chicks (n = 256) were distributed in a randomized block design and received one of four treatments: CTRL1 (Non-medicated, no kefir, no Clostridium perfringens), CTRL2 (Non-medicated, no kefir, C. perfringens inoculated), CTRL3 (BMD medicated, no kefir, C. perfringens inoculated), KTRT (Non-medicated, …

Characterization Of Antimicrobial Properties Of Excrement And Functional Microbiome Of Black Vultures (Coragyps Atratus), Bridgette Gray

Theses

Black vultures, Coragyps atratus, are obligate scavenging birds that consume and dispose of decaying carcasses and carrion. They fulfill a key ecological niche in the environments in which they live. It has been observed that these vultures sometimes excrete bodily waste onto their legs. This adaptive behavior could help aid them in controlling bacteria and other microbes they encounter while stepping into a carcass to eat. This study directly examined the antimicrobial properties of the excrement of black vultures across various bacterial species utilizing a zone of inhibition test and a nematode species utilizing a survival assay. The black vulture …

The Influence Of Microorganisms On Human Health, Tiffany Bui

University Honors Theses

The purpose of this thesis is to explore the interplay between the environment, lifestyle, and composition of human microbiomes across different communities, with a specific focus on immune and digestive health. This literature review investigates three distinct types of communities: isolated/traditional, transitional, and urban/industrialized communities, each characterized by unique environments, societal structures, and interactions. These factors contribute to the distinct microbial populations and compositions within each community. It is impossible to avoid contact with microorganisms as they are present in every aspect of our lives, from the air we breathe, the water we drink, the soil we walk on, the …

The Effects Of Aloe Vera On The Human Gut Microbiome, Samantha Leon

Honors Theses

The human gut microbiome is a diverse community of bacteria influenced by multiple factors including host age, geographical location, and diet. This study observed the effects of aloe vera juice on the human gut microbiome. Fecal samples were taken every two weeks over a period of one year; the subject consumed aloe vera juice in alternating cycles of consumption “on” and abstaining “off” with each cycle lasting for eight weeks. The bacterial community in each sample was characterized using 16S rRNA gene sequencing. Sequences were identified and their relative abundances were used to look for patterns distinguishing “on” and “off” …

The Stringent Response In Pseudomonas Aeruginosa Influences The Phenotypes Controlled By The Gac/Rsm System, Michael Shawn Hooker

Electronic Theses and Dissertations

Pseudomonas aeruginosa is a ubiquitous, opportunistic pathogen that causes acute and chronic infections. Infection is typically initiated via motile and virulent strains. After exposure to stressors, acute infections make both genotypic and phenotypic switches to a chronic, sessile strain. This is due to intricate regulatory networks directing gene expression in response to stressors. One network, GacA/GacS, has been established to control virulence factors. The stringent response of bacteria is mediated by alarmones produced primarily by RelA which responds to starvation.

To study the effect of the stringent response on the virulence switch. A series of experiments were run in both …

Effect Of Temperature On The Microbiome Of A Laboratory-Reared Colony Of Haemaphysalis Longicornis Ticks, Brianna L. Mitchell

Undergraduate Honors Theses

Haemaphysalis longicornis ticks are invasive to the United States with potential to transmit several tick-borne pathogens that are native to the United States. Based on existing locations of H. longicornis in its native regions in Asia, as well as its invasive populations that are established in the United States, several geographic range prediction models have been produced to help understand future range expansion and distribution of this invasive tick in North America. Unfortunately, these models do not all agree and there is uncertainty associated with the potential geographic range expansion of H. longicornis ticks in North America. Climate can affect …

The Effects Of Salt And Temperature On Three Methanogen Species: Implications For Mars, Katy Dunlap

Biological Sciences Undergraduate Honors Theses

The question of whether life has ever existed on Mars – either in the past or currently – has been pursued for decades. This debate has been prompted by a variety of discoveries regarding similarities between Mars and Earth and more recently concerns over human extinction. Mars, like Earth, once had large amounts of water, a key ingredient for life. H₂O exists on Mars in various forms now, and it is theorized that there is liquid water beneath the surface as well. Mars also contains salt and is very cold at its surface, pointing researchers towards the idea …

Determining The Effects Of Maternal Adiposity On Preterm Neonatal Microbiome And Short Chain Fatty Acid Profiles, Dalton James, William A. Clark Phd, Kristy L. Thomas

Undergraduate Honors Theses

The gut microbiota and its metabolites have vast impacts on the human digestive system, immune system, and health outcomes. Short chain volatile fatty acids (SCVFAs) present in feces can be representative of the interactions of the microbiota present in the gut. Low microbiota diversity in the human gut is highly associated with obesity and adverse health outcomes. Furthermore, the maternal microbiome has a direct impact on neonatal microbiota through various pathways such as environment, skin flora, breast milk composition, and vaginal secretions. This study is aimed to further understand the associations between various factors (maternal adiposity, gestational time, length of …

From Micro To Macro: Examining Potential Microbiome Mediated Influences On Human Growth And Health Outcomes Through Breastfeeding And Antibiotic Exposures, Nicole K. Phillips

Electronic Thesis and Dissertation Repository

Human microbiome research has rapidly developed over the past two decades yet absent from most research is the composition and dynamics of microbiomes within human populations. Given the limitations in longitudinal studies which requires decades of repeated microbe taxonomic testing of a population sample, an alternative option is to examine microbiomes and their influences via proxies using pre-existing health datasets. This research demonstrates preliminary associations between presumed disrupted and supportive microbiomes dynamics proxied by antibiotic and breastmilk exposure respectively. Using health record data across the life span from approximately 500,000 U.K. participants, this research demonstrates variable altered growth and health …

Effects Of Microcystin-Lr On Channel Catfish (Ictalurus Punctatus) Susceptibility To Microbial Pathogens (Aeromonas Hydrophila And Edwardsiella Piscicida), Alison Marchant

Theses and Dissertations

Microcystin-LR is a hepatotoxin produced by cyanobacteria. Aeromonas hydrophila and Edwardsiella piscicida infections are leading causes of losses in market-sized channel catfish (Ictalurus punctatus). These older fish should have natural immunity in place and a predisposing factor is likely a prerequisite for these disease outbreaks. While microcystin-LR rarely causes mortality in warm-water aquaculture, we believe it may be a predisposing factor that leads to bacterial disease outbreaks during the summer months due to its ability to damage the liver. Our study investigated microcystin-LR’s effects on channel catfish susceptibility to these pathogens. We found that a sublethal dose of microcystin-LR induced …

Antibiotic-Resistant Bacteria In Freshwater Crayfish, Colby Finch

Honors Theses

The presence of antibiotic-resistant bacteria is increasing in natural aquatic environments. Alongside this, organisms that live in these ecosystems are increasingly harboring antibiotic-resistant bacteria. In this study, I analyzed the capacity for the crayfish species Procambarus vioscai paynei to harbor antibiotic-resistant bacteria. Crayfish, as well as water and sediment, were sampled from a pond at the University of Mississippi Field Station. The guts of crayfish were plated on TSA agar, as well as agar containing vancomycin, erythromycin, penicillin, tetracycline, or ciprofloxacin. Following incubation, counts of bacteria were determined. Selected bacterial isolates were tested for multiple antibiotic-resistance. Bacterial isolates were also …

A Comparison Of Heterotroph Isolation And Sequencing Methods From Various Cyanobacterial And Algal Microbiomes, Victoria Starks

Honors Theses

Cyanobacteria have provided a vast, new source of natural products to be utilized in drug development. Because of their non-axenic nature, cyanobacteria typically have an abundance of symbiotic heterotrophs living in association with them. These bacteria can play significant roles in the survival of its cyanobacterial host as well as provide the potential production of unique compounds. The possibility of unknown natural products is only increased by the flexible nature of these bacteria, as altering its environmental state can change the activity of biosynthetic pathways and even activate novel production. Our research team’s intent is to isolate cyanobacterial strains from …

Metagenome-Wide Associations And Metabolic Modeling To Predict The Biomarkers For Colorectal Cancer, Nagavardhini Avuthu

Theses & Dissertations

Colorectal cancer (CRC) is the most common malignancy and the second most common cause of cancer-related deaths in the world. It is a multifactorial disease mediated by genetic, environmental, and lifestyle factors. Over time, the accumulation of genetic and epigenetic changes results in the activation of oncogenes and deactivation of tumor suppressor genes in the colon and rectal region which finally leads to tumor development. The gut microbiome is the main factor linking the effects of diet and environmental factors to host metabolism. Several studies showed the dysbiosis of gut microbiota in CRC patients with an increased proportion of pathogenic …

Multi-Omic Systems Biological Analysis Of Host-Microbe Interactions, Piet Jones

Doctoral Dissertations

Systems biology offers the opportunity to understand the complex mechanisms of various biological phenomena. The wealth of data that is produced, at an increasing rate, provides the potential to meet this opportunity. Here we take an applied approach to integrate multiple omic level data sources in order to generate biologically relevant hypotheses. We apply a novel analysis pipeline to model both, in concert, the microbial and transcriptomic signature from COVID-19 positive patients. We show patients may suffer from an increased microbial burden, with an increased pathogen potential. Gene expression evidence further shows patients may exhibit a compromised barrier immunity, owing …

Native And Non-Native Ant Impacts On Soil Microbes, Hannah A. Stewart

Biology Theses

Organisms produce chemical weapons for defense, but target organisms can develop resistance. In their introduced range, non-native species may bring “novel weapons” against which native organisms have not co-evolved resistance. The invasive European fire ant (Myrmica rubra) may have brought antimicrobial secretions to the Northeastern United States that are novel weapons against native fungal and bacterial soil organisms. I hypothesized that M. rubra would better inhibit seed pathogens resulting in greater emergence of native myrmecochorous Viola sororia seeds and, as a side effect, more strongly inhibit arbuscular mycorrhizal fungi than a native seed dispersing ant (Aphaenogaster picea …

Identification Of Critical Points For Bacterial Contamination In The Microbrewery Environment, Alex Ryan Thompson

All Theses

There are 8,884 craft breweries producing over 23 million barrels of beer in the United States as of 2020. These 23 million barrels of craft beer account for 12.3% of the United States beer consumption in 2020. The American craft beer industry is substantial and needs to protect its product from bacterial contamination.

Overall, beer is a microbially stable product. Beers pH, ethanol levels, CO₂ concentrations, the presence of hop-derived antimicrobial compounds, and low levels of O₂ make beer a highly unfavorable environment for most bacterial species. Furthermore, the brewing process, which involves heat treatments and chemical sanitizers …

Locked Nucleic Acid Aptamer And 10 Nm Gold Nanoparticles Increases The Sensitivity Of A Prion Protein Detection Assay, Haley Channell

Chancellor’s Honors Program Projects

No abstract provided.

The Role Of Stm1987 And Arti In Arginine Response Of Salmonella Typhimurium, Deeba Mohseni

Undergraduate Honors Theses

Cyclic-di-GMP, a common bacterial second messenger, has been thought to help develop virulence and biofilms in bacteria, most specifically in Salmonella Typhimurium. By being able to dysregulate cyclic-di-GMP production, virulence may be better combatted. STM1987, an L-arginine-responsive diguanylate cyclase with a periplasmic sensory domain, dimerizes and generates the bacterial second messenger cyclic-di-GMP in response to the amino acid L-arginine in a pathway that also requires the periplasmic L-arginine-binding protein ArtI. Their biochemical responses to L-arginine and when they dimerize could help clarify this pathway, so I sought to develop a periplasmic dimerization sensor to better monitor these biochemical interactions. Similar …

Biodegradation Of Rubber Particles In Soil: Using Acclimated Bacteria Isolated From Kansas Soil To Degrade Cryogrinds In Slurry, Shane Graham

Williams Honors College, Honors Research Projects

This study investigated the viability of bioremediating rubber cryogrind using enriched indigenous bacteria. To begin the experiment, soils from three highway roadside locations in Kansas, KS 96 and West, KS 400 and 143^rd, and 199^th, were collected and transported to the lab to be studied. An initial soil characterization was run on the soil samples using distilled (DI) water mixture and 0.01 M CaCl₂ to assess conductivity. The soils were tested to gather a baseline of the relationship between pH and conductivity and the impact of its distance from the roadside. Bacteria were isolated from …

Exploration Of Lignin-Based Superabsorbent Polymers (Hydrogels) For Soil Water Management And As A Carrier For Delivering Rhizobium Spp., Toby Adjuik

Theses and Dissertations--Biosystems and Agricultural Engineering

Superabsorbent polymers (hydrogels) as soil amendments may improve soil hydraulic properties and act as carrier materials beneficial to soil microorganisms. Researchers have mostly explored synthetic hydrogels which may not be environmentally sustainable. This dissertation focused on the development and application of lignin-based hydrogels as sustainable soil amendments. This dissertation also explores the development of pedotransfer transfer functions (PTFs) for predicting saturated hydraulic conductivity using statistical and machine learning methods with a publicly available large data set. A lignin-based hydrogel was synthesized, and its impact on soil water retention was determined in silt loam and loamy fine sand soils. Hydrogel treatment …

Modification Of Culture Medium And Identification Of Microbial Contaminants For Improved In Vitro Propagation Of Freshwater Mussels, Raquel M. Wetzell

Theses and Dissertations

In vitro propagation efforts play an essential role in conserving and restoring threatened freshwater mussel populations by circumventing the need for a fish host. Across a broad range of taxa, transformation is induced with an artificial M199 medium and rabbit serum. However, such formulation may not be sufficient in culturing critical species with more specific physiological requirements. In this study, multiple serum mixtures were tested to improve in vitro transformation of two freshwater mussel species: yellow lampmussel (Lampsilis cariosa) and tidewater mucket (Atlantaconcha ochracea). These species were selected because they parasitize similar fish host species but …

Investigating Antimicrobial Properties Of Snake Venoms Against B. Cereus, B. Subtilis, E. Coli, And P. Vulgaris, Savannah Berger

Honors Program Theses and Research Projects

The increasing incidence of antibiotic resistant bacterial infections has provoked the attention of health officials and scientists as a major threat to global public health. Antibiotic resistance is the product of overprescription by doctors, ineffective or shortened dosing by the patient, and more. When a bacterial infection is ineffectively treated as such, persistent pathogenic cells are given the opportunity to proliferate and spread their resistance to other cells. With bacteria utilizing such tools to fight and ultimately resist our current treatment methods, investigation towards the next novel mechanism of inhibition is essential. Venom is of particular interest to many scientists …

Toward Lignin Valorization: Development Of Rhodococcus Opacus Pd630 As A Chassis For Triacylglycerol (Tag) Production From Recalcitrant Aromatic Feedstocks, Rhiannon R. Carr

McKelvey School of Engineering Theses & Dissertations

The advent of the industrial era was precipitated by the discovery of fossil fuels, and ushered in unprecedented changes for humanity included but not limited to the development of rapid transit and communications, improvements to food distribution and preservation, the mass production of goods, and a radical rearrangement of communities from relatively small enclaves to metropolises. With all the benefits, however, come considerable costs, especially to the global environment. Greenhouse gas emissions, built up over centuries of unregulated combustion, have precipitated a rate of global temperature change unparalleled in the 4.5 billion-year history of this planet. In order to preserve …

Developing A Toolbox To Engineer Quantitative Trait Variation In Legume Species Using Crispr/Cas Technologies., Petar Miletic

Electronic Thesis and Dissertation Repository

The impact of intensive agriculture on the environment is immense. This is especially dire with regard to the natural nitrogen (N) cycle, where the human driven interference, primarily associated with industrial fertilization, has reached unsustainable levels. Unlike cereals, legumes, such as soybean, alfalfa and common bean, have the ability to use atmospheric nitrogen, which limits the need for industrial fertilization. A more wide-spread use of legumes could alleviate some of the negative impacts on the biogeochemical cycle while also providing a useful alternative to meat consumption, an important factor in sustainability. To reach this goal, further improvements of legume crops …

The Role Of Low-Molecular Weight Fungal Metabolites In Eutypa Dieback Grapevine Trunk Disease, Dana Sebestyen

Masters Theses

Eutypa dieback, one of several grapevine trunk diseases (GTDs), is of serious concern to the grape industry globally. This disease is caused by the fungus Eutypa lata but it is often seen in consortia growth with Phaeoacremonium minimum and Phaeomoniella chlamydospora. It is vital to understand the mechanisms for how this disease functions to develop control measures to combat it. Brown rot fungi are able to use a complex of low molecular weight (LMW) metabolites to induce a Fenton reaction to deconstruct woody tissue. These metabolites are part of a chelator mediated Fenton (CMF) chemistry that produces reactive oxygen …

Structure-Function Studies Of The Trypanosome Mitochondrial Replication Protein Polib, Raveen Armstrong

Masters Theses

Trypanosoma brucei and related protists are distinguished from all other eukaryotes by an unusual mitochondrial genome known as kinetoplast DNA (kDNA) that is a catenated network composed of minicircles and maxicircles. Replication of this single nucleoid involves a release, replicate, and reattach mechanism for the thousands of catenated minicircles and requires at least three DNA polymerase (POLIB, POLIC and POLID) with similarity to E. coli DNA polymerase I. Like other proofreading replicative DNA polymerases, POLIB has both an annotated polymerase domain and an exonuclease domain. Predictive modelling of POLIB indicates that it has the canonical right hand …

Fishing For The Right Probiotic: Investigating The Mechanism Of Mucosal-Bacterial Interactions At The Interface Of Health And Productivity In Salmonid Aquaculture, Luana Langlois

Electronic Thesis and Dissertation Repository

Aquaculture is vital for the global food supply, but the high incidence of infectious diseases threatens the industry’s productivity. The intestinal mucosa is a key port of entry for pathogens and provides an extensive interface for host-microbe interactions. Tight junctions are at the core of gut barrier function and the mucosal health of finfish. Disruption of these complexes gives rise to sepsis, which leads to systemic inflammation and death. The present study employs a combinatorial approach that integrates in vitro and in vivo analyses to gain actionable insights into the mechanism of microbial-mediated modulation of host health. The experiments outlined …

Understanding The Adhesion Mechanism In Mycelium-Assisted Wood Bonding, Wenjing Sun

Electronic Theses and Dissertations

The increasing environmental awareness has led to an increased interest in developing more sustainable materials as alternatives to petroleum-derived products. Among different nature-based products, fungal-mycelium-based bio-composites have gained considerable attention in various applications. Multiple materials with different densities and structures and potential applications can be fabricated by inoculating filamentous white-rot fungi in lignocellulosic materials and other substrates. Different from lower-density as-grown foam-like mycelium composites, higher-density mycelium-lignocellulosic panels have the potential to replace commercial particleboard and fiberboard bonded by petroleum-based resins. This kind of composite can be produced by directly adding heat and pressure to the low-density foams or by assembling …

Generation And Characterization Of An In Vitro Organotypic Foreskin Model For Future Study Of The Penile Microbiome, Geoffrey J. Rempel

Electronic Thesis and Dissertation Repository

The foreskin is a site of HIV-1 acquisition in heterosexual males. The lack of relevant in vitro models that mimic the foreskin microenvironment, including innate immune and barrier functions, has limited our understanding of susceptibility at this site. We hypothesize that we can establish organotypic in vitro foreskin that mimics in vivo tissue. Organotypic foreskin models were generated and are composed of stratified cell layers that express E-cadherin suprabasally, filaggrin apically, and expressed TLR1, TLR2, and β-defensin-1 mRNA similar to in vivo foreskin. Preliminary results suggest organotypic foreskin tissues retain the ability to respond to LPS. Lastly, organotypic foreskin permeability …