Microbiology Commons^™

Effects Of Fasting On The Oral Microbiome, Youyuan Wang, Leonard Moreno, Fernando Reyes

Humboldt Journal of Microbiology

Humans are mostly made up of microbes. Multiple studies have estimated that bacterial cells outnumber human cells in the body, with our digestive systems harboring the highest concentrations of bacterial life. The oral microbiome is densely populated and of significant physiological importance. These microbial communities maintain tooth and gum health, aids in pre-digestion of foods, and even plays a defensive role — guarding their host from external threats that may lead to oral and systemic pathologies. Studies have shown that fasting can affect the gut microbiome, but there is currently insufficient research on how fasting intervals can affect the oral …

Diatom Abundance And Diversity Across The Arcata Wastewater Treatment Plant And Wildlife Sanctuary, Rhiannon Red Bird, Anna K. Curry, Brandy R. Ayon, Kellie N. Pierson

Humboldt Journal of Microbiology

Wastewater management is an essential component of modern society that is necessary for reducing human environmental impact, particularly in aquatic ecosystems. In Humboldt County, California, the Arcata Wastewater Treatment Plant and Wildlife Sanctuary (Arcata Marsh) is a model for other wastewater treatment plants worldwide to treat waste naturally, reducing the use of chemicals. This wastewater is then discharged into the Humboldt Bay. It is well known how treatment helps remove harmful waste materials, but it has not been investigated how phytoplankton diversity is affected before, during, and after treatment. Phytoplankton are primary producers that are responsible for carbon sequestration and …

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Humboldt Journal of Microbiology

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Kirby-Bauer Disc Diffusion Method Indicates Absence Of Antimicrobial Properties In Ariolimax Columbianus Mucus, Elsa Balfe, Elizabeth Kowalski, Stephanie A. Leavitt

Humboldt Journal of Microbiology

Antibiotic resistance is a rapidly accelerating epidemic demanding novel approaches. Gastropod mucus has been shown to possess antimicrobial properties and could potentially be used as an ingredient in antibiotic development. However, whether the mucus of Ariolimax columbianus, the banana slug, also displays antimicrobial properties is unknown. In this study, we investigated whether the mucus of A. columbianus is resistant to Escherichia coli (E.coli), Streptococcus aureus (S.aureus), and Klebsiella pneumoniae (K.pneumoniae), three medically relevant strains of bacteria. Specimens were collected from a coniferous forest and isolated for downstream mucus extraction. We spread uniform concentrations of our bacteria on Mueller-Hinton agar plates …

Testing Ssa4:Ade3 Reporters For Mcs Screening, Karah Edmonds, Rebecca Adams

Science University Research Symposium (SURS)

In eukaryotic cells, after transcription, mRNA is escorted from the nucleus to the cytoplasm to be translated. This process, called mRNA export, is essential for gene expression. However, when the cell exists in stressful conditions, mRNA export becomes regulated, and only select transcripts, including the stress-responsive SSA4 mRNA, can be exported. This project aims to uncover the mechanism of selective SSA4 mRNA export by generating a reporter that enables phenotypically visible expression under stressful conditions. Specifically, the ADE3 ORF was placed under the regulatory sequence of SSA4, which was anticipated to induce a red color for colonies only following stress. …

Environmental Toxicants And Human B Cells: Insights From Crispr Editing And Genomic Sequencing, Clayton Allex-Buckner

Browse all Theses and Dissertations

The human immunoglobulin heavy chain gene locus (IGH) has two 3 prime regulatory regions (3’IGHRR), each containing three enhancers (hs3, hs1.2, hs4). In animal models, the 3’IghRR regulates IgH expression and class switch recombination (CSR) to different Ig isotypes. The 3’IGHRR hs1.2 enhancer in humans is polymorphic in that an invariant sequence (IS) can be repeated one to four times in tandem. The hs1.2 polymorphism is of interest due to its association with several human autoimmune disorders and its potential sensitivity to exogenous substances such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD or dioxin). In mouse models, TCDD inhibits the hs1.2 enhancer and 3’IghRR …

Surveillance And Monitoring Of Amphibian Pathogens And Evaluating The Impacts Of An Associated Course-Based Undergraduate Research Experience (Cure), Jennifer Perez

EWU Masters Thesis Collection

Amphibians are a highly diverse class of vertebrates and crucial for natural ecosystems, inhabiting both aquatic and terrestrial environments at different life stages. However, amphibians are facing devastating declines largely due to the disease chytridiomycosis, caused by the fungal pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal). This disease can lead to population declines, biodiversity loss, and species extinction. However, resources to study and mitigate this disease are limited and an opportunity to assist in these efforts has been created in the form of a course-based undergraduate research experience (CURE). Chapter 1 of my thesis used Roger's Diffusion of Innovations …

Evaluating Efficacy Of Anti-Batrachochytrium Dendrobatidis Probiotic Treatment On Pacific Chorus Frogs (Pseudacris Regilla) At Current And Modeled Climate Change Temperatures, Autumn N. Holley

EWU Masters Thesis Collection

Amphibian populations are declining due to a variety of threats, including the chytrid fungal pathogen, Batrachochytrium dendrobatidis (Bd), the causative agent of the disease chytridiomycosis. Climate change and other stressors can have complicated interactions with amphibian disease. Some amphibian populations are less susceptible to chytridiomycosis due to factors such as symbiotic skin microbes that may inhibit Bd through secondary metabolites. There have been several attempts to develop probiotics from these symbiotic, antifungal bacteria to provide protection against Bd infection, but these studies have had mixed success. Our study evaluated anti-Bd bacteria isolated from the skin of Pacific chorus frogs (Pseudacris …

Characterisation Of Selected Microbes In Terrestrial And Simulated Extraterrestrial Habitats: Human Health And Environmental Applications, Daniel Joseph Keaney

Theses

The rapid development of the Space industry and associated technologies over the past decade is leading to the inevitable consideration of establishing human-based colonies on extra-terrestrial bodies such as the moon and Mars. With Mars being the focus of not only this body of work, but current New Space Age travel (NASA and SpaceX), a significant issue posed by Martian colonists includes establishing a safe and sustainable food source. Owing to its constantly evolving prehistoric landscape, the soils of Mars are contaminated with sodium perchlorate, a water-soluble salt that is toxic to humans, leftover from once inferred brine seeps that …

Bioprospecting For And The Applications Of Halophilic Acidophiles In Bioleaching Operations, Melissa K. Corbett, Elizabeth L. J. Watkin

Research outputs 2022 to 2026

The economic recovery of metals from sulfide ores has become a topic of increasing interest due to the escalating demand for critical minerals and the reducing grade of available ores. Bioleaching is the use of acidophilic iron and sulfur-oxidising microorganisms to facilitate the extraction of base metals from primary sulfide ores and tailings. One significant issue limiting the use of bioleaching is the availability of freshwater due to the sensitivity of these microbes to chloride. The use of saline tolerant acidophilic iron- and-sulfur oxidising microorganisms will go a long way to addressing this issue. There are three possible means of …

Implications Of Intraspecific Variation In Soil Microbes On Solidago Performance, Yazeed Alshammari

Masters Theses

This study explored the implications of intraspecific variation in soil microbes on the performance of Solidago altissima, a North American species that has become invasive across several continents. This research explored how different clones of Solidago altissima were associated with bacterial and fungal soil microbial communities, which influenced plant performance. In a common garden of 24 Solidago altissima clones, I analyzed the relationship between soil microbial communities, foliar chemistry, clone genetic relatedness, and plant performance. My methods included analysis of soil microbial communities (bacterial and fungal), genetic distances among clones to assess relatedness, and measures of plant performance (light …

Investigating The Impact Of Nonenzymatic Lysine Acetylation On The Function Of The Bacterial Ribosome, Sarah Caldwell Feid

Dissertations

An under-investigated target of lysine acetylation is the bacterial ribosome. Although lysine acetylations on the ribosome are common and conversed in diverse bacterial species, little work has been done to understand how lysine acetylation affects the bacterial ribosome. The goal of this work is to determine if lysine acetylation has functional impact on the bacterial ribosome.I have identified in vitro and in vivo effects of nonenzymatic, AcP-dependent lysine acetylation on translation and the ribosome. In vitro acetylation of transcription-translation reactions causes a translation-specific defect that is unaffected by the addition of the CobB deacetylase. This suggests certain AcP-sensitive residues that …

Metabolic Engineering Of Escherichia Coli For N-Acetyl-Glucosamine Production, Anica Tasnim Protity

Graduate Research Theses & Dissertations

Glucosamine (GlcN) and GlcN-based supplements, such as N-acetyl-glucosamine (GlcNAc), are commonly used by osteoarthritis patients to relieve pain and maintain the health of bone joints. However, the current production methods for GlcN-based products are not eco-friendly and pose risks to individuals with shrimp allergies. Microbial cell-based systems have been explored to address these issues as an eco-friendly alternative for GlcN and GlcNAc production. This study focused on developing an Escherichia coli (E. coli) strain for GlcNAc fermentation. E. coli has an endogenous pathway for peptidoglycan biosynthesis involving GlcNAc-1-P. However, altering this pathway could affect cell growth and integrity. Therefore, two …

In Silico Analyses Of Diversity And Dissemination Of Antimicrobial Resistance Genes And Mobile Genetics Elements, For Plasmids Of Enteric Pathogens, Suad Algarni, Jing Han, Dereje D. Gudeta, Bijay K. Khajanchi, Steven C. Ricke, Young Min Kwon, Douglas D. Rhoads, Steven L. Foley

Animal Science Faculty Publications and Presentations

Introduction: The antimicrobial resistance (AMR) mobilome plays a key role in the dissemination of resistance genes encoded by mobile genetics elements (MGEs) including plasmids, transposons (Tns), and insertion sequences (ISs). These MGEs contribute to the dissemination of multidrug resistance (MDR) in enteric bacterial pathogens which have been considered as a global public health risk.

Methods: To further understand the diversity and distribution of AMR genes and MGEs across different plasmid types, we utilized multiple sequence-based computational approaches to evaluate AMR-associated plasmid genetics. A collection of 1,309 complete plasmid sequences from Gammaproteobacterial species, including 100 plasmids from each of the following …

Pancreatic Ductal Adenocarcinoma And New Treatments In Development, Melissa J. Moisan

Biology and Microbiology Graduate Students Plan B Research Projects

Pancreatic ductal adenocarcinoma (PDAC) is the most frequently mutated (95%) 5exocrine pancreatic cancers. Patients with PDAC are also the least likely to survive more than 5 years with only 8% overall survivability. The median survival for patients with distant metastasis is less than one year. Most pancreatic ductal adenocarcinoma occurs in the pancreatic head, and the remainder can be found within the body (5% to 15%) or tail (10% to 15%) (14). This extremely aggressive cancer has an increasingly large metastatic dissemination rate to surrounding organs such as the liver, lung, and peritoneum, or can be seen as distant metastases …

Investigating The Impacts Of Ammonium Phosphate-Based Fire Retardants On Cyanobacteria (Anabaena) Growth, Gavin Sutter, Brenda Gonzalez Flores, Grace Laskey, Shane Jurak

Humboldt Journal of Microbiology

In recent years the effects of climate change have taken a devastating toll on ecosystems around the world. With high temperatures and extreme droughts, wildfires have become increasingly common. In order to combat these natural disasters wildland firefighters, drop millions of gallons of fire retardant on public lands and forests. These fire retardants consist of between 80%-100% ammonium phosphate which are incredibly effective as fire suppressants yet is more commonly known for its use in fertilizer. Ammonium phosphate fertilizers can lead to stream eutrophication and undesirable environmental impacts. Our research aims to address the effects of fire retardant on growth …

Essential Oils And Their Antimicrobial Effect On Serratia Marcescens, Seren C. Davies-Hughes, Patricia I. Marquez, Henna N. Schulz, Laura S. Sanchez

Humboldt Journal of Microbiology

S. marcescens is a gram-negative, facultatively anaerobic bacterium that is particularly aggressive in its growing capability. It is a concern in medical fields as well as home environments due to its resistance to most antibiotics, high mortality rate, and easy ability to colonize on soap and other fatty substances. Although testing of natural cleansers such as lemon juice, vinegar, and ammonia has been done on S. marcescens and essential oil efficacy has been tested on Escherichia coli and Staphylococcus aureus, no literature has been published on the effect of essential oils on S. marcescens growth. The purpose of this experiment …

Sex-Dependent Effects Of Induced Acute Inflammation On Glucose Homeostasis And Rna Editing Enzymes, Christian A. Rivas

Graduate Theses/Dissertations

The first line of defense against bodily insults, like pathogen invasion, is the innate immune system. Innate immunity sets in motion countless cascades that result in inflammation. Inflammation simultaneously affects multiple biological processes like metabolism and gene expression. Males and females react differently to inflammation. To understand both molecular and physiological sex differences in inflammation, we examined how inflammation affects gene expression and glucose metabolism. Adenosine deaminase acting on RNA (ADAR1) is upregulated by inflammation and catalyzes RNA editing, a process where nucleotides encoded by the genome are modified. ADAR1 also controls the innate immune reaction by decreasing activity of …

Application Of Nitrate To An Anaerobic Subsurface Bioremediation, Cassie Marie Roberts

Masters Theses

"The highly contaminated subsurface matrix of the Baird and McGuire Superfund site is currently threatening the health and safety of the surrounding environment of Holbrook, MA. Contaminants of significant concern due to high concentration are inorganic arsenite and petroleum hydrocarbons, such as naphthalene. Parsons Corporation and the Massachusetts Department of Environmental Protection have implemented a bioremediation pilot to attempt to degrade the hydrocarbons and arsenic with the application of nitrate. The nitrate would act as an electron acceptor for biodegradation of the hydrocarbon contaminants, produce nitrite that would oxidize reduced iron, and iron oxides would sequester arsenic. Preliminary data showed …

Characterizing The Rhizosphere Microbial Community Of Food Crops In A Changing Climate, Samuel Snider

Theses and Dissertations (Comprehensive)

In recent years, there have been increased occurrences of food-borne illness in Canada, which is not directly associated with animal-related products but is caused by the increasing prevalence of pathogenic outbreaks in fresh produce. This can have health and economic impacts on the agriculture industry in Canada. As such, it is essential to better understand the plant-microbe interactions of crops grown in Canada and determine how climate change may alter the relationship. Plants can promote the growth of beneficial bacteria in the rhizosphere, which can create protective competition between beneficial and pathogenic bacteria. Changes in the environment of the rhizosphere …

Functional Residues Of Cjpata, Robert Lamont

Theses and Dissertations (Comprehensive)

Antibiotic resistance in pathogenic bacteria continues to challenge clinicians and threaten the lives of infected individuals. For this reason, new classes of antibiotics or new targets for antibiotic therapy are needed to circumvent this global health crisis. In Gram-negative bacteria, the enzymes peptidoglycan O-acetyltransferase A and B (PatA and PatB), are responsible for adding acetyl groups to the C-6 hydroxyl group of N-acetyl muramic acid (MurNAc) in peptidoglycan (PG). These acetyl groups are responsible for inhibiting the activity of lysozyme from host organisms that hydrolyze the β1-4 glycosidic linkage between MurNAc and N-acetylglucosamine (GlcNAc). The acetyl groups …

Characterization Of The Clostridioides Difficile Glycosyl Hydrolase Ccsz, Brian Lowrance

Theses and Dissertations (Comprehensive)

Bacteria inhabit many of the harshest environments on Earth; persisting and thriving in conditions thought to be unsuitable for life. One common strategy to withstand these environments is the formation of a biofilm. Biofilm composition varies greatly, depending on the underlying community that produces it. Cellulose, a polymer consistently prevalent in biofilms, has been identified as a virulence factor in many pathogens and is suspected to be involved in pathogenesis by Clostridioides difficile. C. difficile is the #1 cause of hospital acquired diarrhea, which can range from mild to life-threatening infections. Biofilm formation is hypothesized to be involved in …

Identification Of New Substrates From Pseudomonas Aeruginosa Exos, Adam V. Thota

Master's Theses

Pseudomonas aeruginosa is a gram-negative environmental bacterium that uses its intrinsic and acquired antibiotic resistance to infect patients with compromised epithelium, such as cystic fibrosis and burn wounds, and corneal keratitis. In order to cause disease, most strains of P. aeruginosa use the type three secretion system (T3SS) to disrupt cellular signaling and integrity. However, P. aeruginosa may also secrete exotoxins after invading host cells, which prolongs host cell death and maintains an intracellular niche. Of the T3 secreted effector toxins, ExoS, specifically the ADP-ribosyltransferase activity of ExoS, was shown to delay the death of invaded corneal cells, but it …

Investigating Structural And Biochemical Characteristics Of A Peptidase Required For Staphylococcus Aureus Virulence, Sagar Bhusal

Master's Theses

Staphylococcus aureus is an opportunistic Gram-positive pathogen that transiently colonizes 30% of the population at any given time. Upon breaching host skin or mucosal barriers, S. aureus can infect and cause disease in nearly all host tissues. Once inside the host, S. aureus expresses a plethora of virulence factors, mostly regulated by the Accessory Gene Regulatory (Agr) quorum sensing system, which facilitates the evasion of immune responses or directly promotes pathogenesis. The S. aureus Agr system relies on the production of a small peptide known as an auto-inducing peptide (AIP) to control virulence gene expression in response to cell density. …

Investigating Putative Toxin-Immunity Pairs From A New Class Of Rhs Proteins In Pseudomonas Aeruginosa, Syed Faieq Imam

Master's Theses

Pseudomonas aeruginosa is a gram-negative, opportunistic pathogen that is ubiquitous in nature, especially in human/animal impacted environments. One of the reasons for this is the arsenal of protein systems and toxins that P. aeruginosa utilizes to mold its environment to suit its needs. Recently, we discovered a novel locus in the P. aeruginosa genome, which resembles other loci that are known to mediate interbacterial competition. Our bioinformatic analysis found this locus to be enriched in a rearrangement hotspot (rhs) motif which led us to ad-interim term the three ORFs of the loci as rhsB, rhsC, and rhsI. Furthermore, we have …

Multipatch Stochastic Epidemic Model For The Dynamics Of A Tick-Borne Disease, Milliward Maliyoni, Holly D. Gaff, Keshlan S. Govinder, Faraimunashe Chirove

Biological Sciences Faculty Publications

Spatial heterogeneity and migration of hosts and ticks have an impact on the spread, extinction and persistence of tick-borne diseases. In this paper, we investigate the impact of between-patch migration of white-tailed deer and lone star ticks on the dynamics of a tick-borne disease with regard to disease extinction and persistence using a system of Itô stochastic differential equations model. It is shown that the disease-free equilibrium exists and is unique. The general formula for computing the basic reproduction number for all patches is derived. We show that for patches in isolation, the basic reproduction number is equal to the …

Trends In Antibiotic Susceptibility Of Staphylococcus Aureus Isolates In A Pediatric Hospital: An Analysis Of The Impact Of The Sars-Cov-2 Pandemic, Juan Miguel S. Gonzalez Rivero

Honors Undergraduate Theses

Infections caused by the organism Staphylococcus aureus are one of the most common causes for community-associated and healthcare-acquired infections (HAI). Isolates of this bacterium found within the healthcare setting often demonstrate a higher prevalence of antibiotic resistance making these infections difficult to treat. Historically, considerable focus has been placed on methicillin-resistant S. aureus (MRSA), which are strains resistant to β-lactam antibiotics like penicillin, oxacillin and cephalosporins; however, methicillin-sensitive (MSSA) strains may also possess resistance to several first-line antibiotics. Resistance to antibiotics can be acquired through horizontal gene transfer (HGT) by means of mobile genetic elements or by random DNA mutations …

Comparison Of Groundwater Chemistry And Associated Biodiversity Of Sulfidic Karst Habitats In Southcentral Kentucky, Kendall Wheeler

Mahurin Honors College Capstone Experience/Thesis Projects

In most ecosystems, primary production is conducted by plants or photosynthetic microbes; however, extremophilic sulfur-oxidizing bacteria can use hydrogen sulfide gas (H2S) as an electron donor to produce metabolic energy in a type of metabolism called chemoautotrophy. These ecosystems are a prominent feature of some karst landscapes, and two have been observed in the Mammoth Cave system, Sulphur River in Parker Cave and Marianne’s Pass in Mammoth Cave National Park respectively.

Sulfidic water is ubiquitous in southcentral Kentucky and is strongly associated with hydrocarbon deposits. This oil boom of the 1880s in this region predates most environmental regulation and records …

Investigation Of Key Mechanisms Of Contact Dependent Growth Inhibition Systems In Burkholderia Cepacia Complex Species, Zaria K. Elery

Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics

Burkholderia cepacia complex is a group of closely related environmental bacteria that can exacerbate disease in immunocompromised individuals. B. cepacia bacteria are equipped with an arsenal of mechanisms to cooperate and compete for nutrients in various polymicrobial environments. Contact-dependent growth inhibition (CDI) systems are antagonistic mechanisms widespread among proteobacteria. CDI systems consist of Two Partner Secretion pathway proteins that function to deliver the toxic C-terminal portion of the large effector exoprotein (termed ‘BcpA’ in Burkholderia-type CDI systems) to the cytoplasm of a compatible recipient bacterial cell upon direct cell to cell contact. The translocation of BcpA out of the …

Substrate Selection And Effector Gating In The Helicobacter Pylori Cag Type Iv Secretion System, Mackenzie E. Ryan

Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics

Helicobacter pylori is a recognized carcinogen and gastric colonization by strains that harbor the cag type IV secretion system (1) is the strongest known risk factor for stomach malignancy. Gastric adenocarcinoma is the fourth leading cause of cancer-related deaths world-wide ( > 700,000 deaths annually), with H. pylori directly contributing to the development of more than one million new cases of cancer per year accounting for 5.5% of all malignancies. H. pylori exploits cag T4SS activity to alter the mucosal microenvironment by delivering diverse immunostimulatory cargo into target gastric epithelial cells. Currently, the mechanisms by which the cag T4SS …