Microbiology Commons^™

The Effect Of Tryptamine Producing Bacteria On Gut Motility In Mice, Emilia Sofia Norberg

Graduate College Dissertations and Theses

It has become increasingly clear that there is bidirectional communication between the microbes that exist in the lumen of the gastrointestinal (GI) tract and the nervous system. Research within the last 20 years has revealed GI bacterial metabolites to have a significant effect on gut motility, and some of these actions involve influencing serotonin signaling in the epithelial layer of the intestines. Serotonin, abbreviated as 5- HT, has many functions within the gut including propulsive and segmentation motility, vasodilation, and epithelial cell secretion. There are several bacterial species that have been discovered to synthesize one of 5-HT’s precursory molecules, including …

Metagenomic Insights Into The Full-Scale Anaerobic Digestion Of Cow Manure And Pre-Treated Food Waste, Amy Camille Decola

Graduate College Dissertations and Theses

Anaerobic digestion provides many benefits, such as diverting organic waste from landfills, promoting nutrient recovery, reducing greenhouse gas emissions, and producing renewable energy. A complex community of microorganisms is responsible for the anaerobic digestion process that converts organic matter into biogas, a renewable energy source. The start-up phase of an anaerobic digester is considered a crucial point in solidifying the core microbial community that will ensure a stable anaerobic digester. A full-scale anaerobic digester that co-digests cow manure and pre-treated food waste from a hydrolysis tank was studied from start-up through stable performance in order to better understand the dynamics …

Dengue Virus Modulation Of Genome Instability In Vero E6 Cells, Erica Nicole Lamkin

Graduate College Dissertations and Theses

Dengue virus (DENV) is the fastest-spreading arthropod-borne virus in the world. Dengue is characterized as a major global public health challenge in tropical and subtropical nations by the World Health Organization. The number of dengue cases globally has increased 8-fold in the past two decades, with 100 to 400 million cases occurring annually. While most patients with dengue fever are asymptomatic, dengue infection carries the possibility of severe and potentially fatal febrile illness. Approximately 1 in 4 individuals infected with dengue virus develop symptomatic dengue infection, often presenting as mild to moderate, nonspecific, acute febrile illness. A smaller subset of …

The Microbiome As An Environmental Risk Factor For Multiple Sclerosis, Theresa Montgomery

Graduate College Dissertations and Theses

Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system. The etiology of MS is complex and poorly understood; however, disease risk is likely combinatorial due to the effects of both genetics and environmental risk factors. A recently identified environment risk factor for MS is the gut microbiome. However, the specific gut microbiota associated with disease risk, onset and/or progression, their mechanisms of action, and impact of host genetics remain unclear. Leveraging the primary autoimmune mouse model of MS, experimental autoimmune encephalomyelitis (EAE), in a genetically diverse mouse model consisting of 29 unique genotypes, combined with gut …

Biofilm Sanitizer Tolerance Of Vermont Dairy Listeria Monocytogenes, Emily C. Forauer

Graduate College Dissertations and Theses

Listeria monocytogenes is a foodborne pathogen found in biofilms on surfaces and equipment in the food processing environment. Sodium hypochlorite (SH) and quaternary ammonium compounds (QAC) are readily available and commonly used sanitizers. However, due to the structure and additional organic material produced in a biofilm, killing bacteria within the biofilm may be a challenge for one or both of these sanitizers.

The objective of this work was to determine if immature and mature biofilms from L. monocytogenes isolated from Vermont artisan dairy environments were more tolerant to QAC and SH compared to planktonic cultures’ tolerance. To determine sanitizer minimum …

Microevolution In Staphylococcus Aureus: Does Exposure To Sub-Lethal Levels Of Cinnamon Bark Oil Lead To Changes In Antimicrobial Susceptibility?, Heather Sandra Schuettner

Graduate College Dissertations and Theses

The emergence of antibiotic-resistant and multi-drug resistant bacteria presents a growing global health issue recognized by the World Health Organization and the Centers for Disease Control and Prevention. Infections caused by drug-resistant bacteria are associated with longer hospital stays, higher treatments costs, and increased mortality compared to infections caused by antibiotic-susceptible pathogens. The global increase in antibiotic resistance is driven in part by the misuse and overuse of antibiotics in healthcare and agriculture. Staphylococcus aureus can infect humans and animals, and strains that are resistant to one or more antibiotics are common. Many plant essential oils have antimicrobial properties. Essential …

Microevolution In Staphylococcus Aureus: Does Exposure To Sub-Lethal Levels Of Cinnamon Bark Oil Lead To Changes In Antimicrobial Susceptibility?, Heather Sandra Schuettner

Graduate College Dissertations and Theses

The emergence of antibiotic-resistant and multi-drug resistant bacteria presents a growing global health issue recognized by the World Health Organization and the Centers for Disease Control and Prevention. Infections caused by drug-resistant bacteria are associated with longer hospital stays, higher treatments costs, and increased mortality compared to infections caused by antibiotic-susceptible pathogens. The global increase in antibiotic resistance is driven in part by the misuse and overuse of antibiotics in healthcare and agriculture. Staphylococcus aureus can infect humans and animals, and strains that are resistant to one or more antibiotics are common. Many plant essential oils have antimicrobial properties. Essential …

Characterization Of Higher Order Chromatin Structures And Chromatin States In Cell Models Of Human Herpesvirus Infection, Michael Mariani

Graduate College Dissertations and Theses

Human herpesviruses are ubiquitous pathogens worldwide with 90% of the global population infected with one or more Human herpesviruses (HHV’s) by adulthood. All herpesviruses have three unique life cycle stages. Upon resolution of a primary acute stage infection, they can establish a latent stage infection within the host cell nucleus. This stage is characterized primarily by transcriptional quiescence of the viral genome. Specific physiological conditions (e.g., cell stress) can cause the latent virus to enter the reactivation stage, often many years after resolution of the acute infection, in which the virus becomes replicationally active again. HHV’s are known to cause …

Network And Ecological Methods To Study Enteric Pathogen Co-Infections, Connor L. Klopfer

Graduate College Dissertations and Theses

Diarrhea remains a leading cause of childhood morbidity and mortality, especially inchildren under 5 years of age. Enteric pathogen co-infection has been found to cause increased diarrheal severity and some pathogens may work in tandem to enhance infection. It is important to identify patterns of pathogen co-infection and their impact on diarrhea to inform intervention strategies for improving child health. In this thesis, I use data from the MAL-ED and PROVIDE birth cohort studies in Bangladesh to generate bipartite networks that represent the relationship between stool samples and pathogens. I randomly rewire the network while preserving connectivity to randomize the …

Sarracenia Purpurea As A Model System For Aquatic Ecosystem State Changes And Their Impact On Bacterial Communities, Amanda Claire Northrop

Graduate College Dissertations and Theses

Aquatic ecosystems can undergo abrupt and long-lasting transitions from one state to another, often with negative ecological and economic consequences. With anthropogenic enrichment, aquatic ecosystems such as lakes and ponds may shift rapidly from an oligotrophic, clear water state to a eutrophic, turbid state. These shifts, or state changes, generally occur due to a phenomenon called hysteresis in which the relationship between a driving variable and ecosystem variable depend on the current state of the ecosystem. Such dynamics often make recovery difficult or impossible. Though state changes in aquatic ecosystems have been studied extensively since the 1970s, there have been …

Metarhizium Anisopliae, Metarhizium Brunneum And Beauveria Bassiana Formulations For Biological Control Of Larval Winter Ticks, Dermacentor Albipictus, Cheryl Sullivan

Graduate College Dissertations and Theses

There is a critical need to develop effective, high-quality, fungal-based biopesticides for use against ticks. Dermacentor albipictus Petch (Acari: Ixodidae), the winter tick, is a one-host tick. They commonly infest large ungulates, particularly moose, Alces alces L. (Artiodactyla: Cervidae) on which they cause significant physiological and metabolic stress on densely parasitized individuals. Heavily infested calves can be killed. Entomopathogenic fungi in the genera Metarhizium (Hypocreales: Clavicipitaceae) and Beauveria (Hypocreales: Cordycipitaceae) are promising tick biological control agents. The larval stage of D. albipictus aggregates on the ground in a prolonged, quiescent state during the summer and then quests for hosts in …

Analysis Of Host Factors Involved In Regulating Hiv-1-Induced Syncytium Formation, Emily Elizabeth Whitaker

Graduate College Dissertations and Theses

Human Immunodeficiency Virus type 1 (HIV-1) is a retrovirus and the causative agent of Acquired Immunodeficiency Syndrome (AIDS). HIV-1 can spread through multiple modes of transmission including cell-to-cell transmission between CD4+ T cells at a transient junction known as the virological synapse (VS). The VS forms upon HIV-1 Envelope (Env) on the surface of an infected (producer) cell binding CD4 on an uninfected (target) cell. While the VS typically resolves with complete cell separation and transfer of virus particles, Env can occasionally facilitate cell-cell fusion at this site, forming a multinucleated infected cell (syncytium). Excessive syncytium formation is prevented by …

Assessing Growth And Methods Of Decontamination Of Listeria Monocytogenes In Brushes And Brines Used For Production Of Washed-Rind Cheese, Rosalind Grace Neale

Graduate College Dissertations and Theses

Washed-rind, or smear-ripened, cheeses are considered high-risk for contamination with Listeria monocytogenes due to favorable growth conditions on the cheese rind and multiple points for contamination during post-production cheese care and aging. Foodborne illness outbreaks have implicated wash solutions and washing tools as potential vectors for transmission of L. monocytogenes. In order to evaluate the risk posed by the wash solutions and cheese brushes independently, a three-objective study was developed to investigate the growth potential of L. monocytogenes in cheese washing solutions (Objective I) and the transfer potential of L. monocytogenes between wash solution and cheese brush bristles of three …

Pathological Consequences Of Pdi Oxidoreductase Activity On Viral Protein Maturation, Nicolas Chamberlain

Graduate College Dissertations and Theses

The influenza A virus (IAV) causes severe respiratory illness in humans. Current treatments are rapidly becoming ineffective due to the emergence of viral resistance to available therapies such as oseltamivir and zanamivir. Given the impact of this virus there is an urgent need to explore novel targets for new treatments less susceptible to viral mutation; targeting host proteins utilized by the virus may avoid these limitations. It has been shown in vitro that interactions with host ER based protein disulfide isomerases (PDIs) are required for specific IAV proteins to reach their functional conformations. The viral proteins hemagglutinin (HA) and neuraminidase …

The Utilization Of Host-Derived Compounds By Gram-Negative Bacteria, Lauren Alexandra Hinkel

Graduate College Dissertations and Theses

The increase in multidrug resistance (MDR) among bacterial pathogens is an ongoing threat to public health, with the CDC estimating more than 2.8 million MDR infections in the United States each year, and greater than 35,000 deaths annually. Gram-negative bacteria possess intrinsic mechanisms to resist available therapeutics and are frequently responsible for difficult-to-treat nosocomial, blood stream, and soft tissue infections. In addition to biophysical and genetic MDR mechanisms, Gram negatives are metabolically versatile, enabling them to utilize host-derived nutrients to promote proliferation and colonization within the host. The metabolic versatility of Gram-negative bacteria is due, in part, to the transcription …

A Chemical Genetics Approach To Understand The Regulation Of Cryptosporidium Sexual Differentiation, Md Mahmudul Hasan

Graduate College Dissertations and Theses

Cryptosporidium species are eukaryotic intracellular parasites belonging to the phylum Apicomplexa. C. hominis and C. parvum cause diarrhea in humans which is self-limiting in immunocompetent adults but can have severe consequences in immunocompromised individuals and malnourished children. In developing countries, Cryptosporidium is one of the leading causes of moderate to severe diarrhea in children under five years of age. There is an urgent need for novel therapeutics against this parasite as the current treatment option is inadequate to treat the most vulnerable population to Cryptosporidium infection. Better understandings of the biology of Cryptosporidium would greatly enhance our capability to design …

Comparison Of Methods For Detection Of Listeria On Wooden Shelves Used For Cheese Aging: Challenges Associated With Sampling Porous Surfaces, Gina Christine Frontino

Graduate College Dissertations and Theses

This thesis examined the efficacy of various sampling and detection methods used for environmental monitoring of Listeria species on wooden surfaces used for cheese aging. Government agencies including the Food and Drug Administration (FDA) and United States Department of Agriculture (USDA) recommend enrichment methods coupled with use of environmental sponges and swabs. Our study compared efficacy of sponge swabs manufactured by 3M™ and World Bioproducts. There is a lack of research validating the best performing swab type and enrichment method combination that is sensitive when used on rough, porous surfaces. The sensitivity of these environmental sampling tools and methods are …

An Analysis Of Between-Cow Variation In Innate Immunity In Relation To Mastitis Severity, Filiz Korkmaz

Graduate College Dissertations and Theses

Bovine mastitis remains one of the costliest diseases affecting the dairy industry. Individual susceptibility to mastitis and severity of infection varies between animals and can only be partially explained by genetics. As such, understanding how genetic predisposition coordinately interacts with epigenetic modifications and environmental exposures is necessary to bridge the gap in missing heritability. The role of DNA methylation in regulating the response to bacterial lipopolysaccharide (LPS) was first determined by performing reduced representation bisulfite sequencing on fibroblasts isolated from heifers at 5- and 16-months of age that exhibit an age-dependent up-regulation in LPS-responsiveness. More than 14,000 differentially methylated sites …

Identification And Characterization Of Gatase1-Like Arac-Family Transcriptional Regulators In Burkholderia Thailandensis., Adam Michael Nock

Graduate College Dissertations and Theses

The ability of bacteria to detect their surroundings and enact an appropriate response is critical for survival. Translation of external signals into a coherent response requires specific control over the transcription of DNA into RNA. Much of the regulation at this step is accomplished by transcriptional regulators, proteins that bind to DNA and alter gene expression. A wide-spread variety of regulators in bacteria is the AraC-family. These regulators are divided into two conserved domains and respond to a variety of compounds owing to different N-terminal domains. A subfamily of these regulators, GATase1-like AraC-family transcriptional regulators (GATRs), is described. These proteins …

Genotypes And Phenotypes Of Staphylococci On Selected Dairy Farms In Vermont, Robert Mugabi

Graduate College Dissertations and Theses

The genus Staphylococcus contains at least 47 species and 23 subspecies. Bacteria in this genus are ubiquitous; many are commensals on human and animal skin and can be opportunistic pathogens. In dairy cattle, staphylococci are the leading cause of intramammary infections (IMI) and mastitis. Mastitis is the inflammation of the mammary gland, and is one of the leading infectious diseases causing production losses in the dairy industry. Based on the ability to clot blood plasma in vitro, members of the genus can be divided into two groups: coagulase positive staphylococci (CPS) and coagulase negative staphylococci (CNS). In the dairy industry, …

Evaluating The Resistome And Microbial Composition During Food Waste Feeding And Composting On A Vermont Poultry Farm, Korin Eckstrom

Graduate College Dissertations and Theses

While commonly thought of as a waste product, food scraps and residuals represent an important opportunity for energy and nutrient recapture within the food system. As demands on production continue to increase, conservation of these valuable resources has become a priority area. In the wake of new legislation in Vermont, Act 148, the Universal Recycling Law, the fate of microbial species in food waste, scraps and residuals is increasingly important. The presence of antimicrobial resistance genes in all types of foods calls for an increased need to estimate risk of antibiotic resistance transfer and maintenance across all segments of food …

Methods To Identify And Develop Drugs For Cryptosporidiosis, Rajiv Satish Jumani

Graduate College Dissertations and Theses

Cryptosporidiosis is a common diarrheal disease caused by intestinal infection with the apicomplexan parasite Cryptosporidium, in humans usually either with C. hominis or C. parvum. Unfortunately, given a large burden of disease in children and immunocompromised people like AIDS patients, the only currently approved treatment, nitazoxanide, is unreliable for these patient populations. To address the urgent need for new drugs for the most vulnerable populations, large phenotypic screening efforts have been established to identify anti-Cryptosporidium growth inhibitors in vitro (hits). However, in the absence of a gold standard drug, the in vitro and in vivo characteristics that should be used …

Detection Of The Lung Environment By Multi-Drug Resistant Gram-Negative Bacterial Pathogens, Graham Geier Willsey

Graduate College Dissertations and Theses

Nosocomial lung infections are a growing concern in the United States, with more than 300,000 cases reported annually. More than 30 % of which are caused by the Gram-negative bacteria, Pseudomonas aeruginosa and Klebsiella pneumoniae. Similarly, Gram-negative bacteria establish chronic infections in individuals with cystic fibrosis (CF) that are difficult or impossible to eradicate.P. aeruginosa has historically been one of the most prevalent pathogens of adults with CF. However, as antipseudomonal therapy has improved, more antibiotic resistant species have taken hold, including Stenotrophomonas maltophilia, which now colonizes more than 10 % of individuals with CF. Regardless of …

Rumen Microbial Ecology And Rumen-Derived Fatty Acids: Determinants Of And Relationship To Dairy Cow Production Performance, Laura Marie Cersosimo

Graduate College Dissertations and Theses

Rumen microbiota enable dairy cattle to breakdown fiber into useable energy for milk production. Rumen bacteria, protozoa, and fungi ferment feedstuff into volatile fatty acids (VFA), the main energy source, while methanogens utilize fermentation by-products to produce methane. Milk fat contains several bioactive rumen-derived fatty acids (FA), including odd-chain FA (OCFA) and branched-chain FA (BCFA), important for maintenance of human health. The overarching dissertation goal was to determine which factors affect rumen methanogen and protozoal community structures and their metabolism products, while defining relationships between rumen microbiota and animal performance. Results presented contribute to the goals of providing new knowledge …

Key Virus-Host Interactions Required For Arenavirus Particle Assembly And Release, Christopher Michael Ziegler

Graduate College Dissertations and Theses

Viruses are infectious agents that must infect the cells of living organisms in order to reproduce. They have relatively simple genomes which encode few proteins but can compensate for their simplicity by hijacking components of their cellular hosts. Arenaviruses, a family of zoonotic viruses carried by rodents, encode only 4 proteins. One of these proteins, Z, is responsible for several functions during the virus life cycle including driving the formation and release of new virus particles at the plasma membrane of infected cells. Relatively little is known about how this viral protein is regulated or the complement of host proteins …

Target Identification Strategies For Mmv Malaria Box Inhibitors Of Toxoplasma Gondii Growth, Jenna Elizabeth Foderaro

Graduate College Dissertations and Theses

Small molecule screening is commonly used to discover lead compounds for drug development, but it can also be a powerful way to identify chemical probes for studying biological mechanisms. Our lab uses small molecules to study the mechanisms by which the protozoan parasite Toxoplasma gondii infects and replicates within its hosts. In this work, we employed a fluorescence-based assay to screen the Medicines for Malaria Venture (MMV) Open Access Malaria box for compounds that affect T. gondii growth. The box contains 400 previously identified small-molecule inhibitors of the related parasite, Plasmodium falciparum. We identified 79 hits, including a 2,4-diaminoquinazoline (MMV006169; …

Functional Consequences Of Ama1-Ron2 Interaction During Host Cell Invasion By Toxoplasma., Shruthi Krishnamurthy

Graduate College Dissertations and Theses

T.gondii is a model organism of the phylum Apicomplexa that infects one third of the human population. While the majority of infections are asymptomatic or manifest with mild flu-like symptoms, toxoplasmosis can be fatal in immunocompromised individuals and in the developing fetus. The lytic cycle of tachyzoite-stage parasites causes damage to the host by repeated rounds of host cell invasion, intracellular replication and lysis of the host cell upon egress.

Invasion is a key step for the parasite to maintain its intracellular lifestyle. Apical Membrane Antigen 1 (AMA1) is an adhesin released from a unique set of secretory organelles called …

Ecological Dynamics In Compost-Amended Soils And The Resulting Effects On Escherichia Coli Survival, Anya Cutler

Graduate College Dissertations and Theses

Escherichia coli (E. coli) are common and typically innocuous copiotrophic bacteria found in the mammalian gut microbiome. However, over the past 30 years, pathogenic E. coli have been responsible for several outbreaks of foodborne illness linked to contaminated produce. The introduction of Escherichia coli to an agricultural soil, via contaminated water, compost, or raw manure, exposes the bacterium to a medley of ecological forces not found in a mammalian gut environment. This study assesses a variety of abiotic and biotic soil factors that influence the ability of an "invasive" copiotrophic coliform bacterium to survive in compost-amended agricultural soil. The study …

Identification Of Regulatory Factors That Control Clostridium Difficile Sporulation And Germination, Kelly Ann Fimlaid

Graduate College Dissertations and Theses

Clostridium difficile is a Gram-positive spore-forming strict anaerobe that can cause severe colitis in humans. C. difficile is best known as the leading cause of nosocomial-acquired diarrhea, particularly in people undergoing antibiotic therapies, since it is naturally resistant to most antibiotics. A clinical feature that makes C. difficile infection, or CDI, particularly difficult to treat is the organism's inherent ability to resist antibiotic therapies while in its spore form. Since oxygen is toxic to C. difficile, spores are the major transmissive form; they are also resilient to most disinfectants, which makes them extremely difficult to eliminate to prevent additional …

Hiv-1-Induced Cell-Cell Fusion: Host Regulation And Consequences For Viral Spread, Menelaos Symeonides

Graduate College Dissertations and Theses

Human immunodeficiency virus type 1 (HIV-1) is a human retrovirus of the lentivirus subgroup which primarily infects T cells and macrophages, and causes acquired immune deficiency syndrome (AIDS). Since its emergence in the early 1980s, HIV-1 has caused a global pandemic which is still responsible for over one million deaths per year, primarily in sub-Saharan Africa.

HIV-1 has been the subject of intense study for over three decades, which has resulted not only in major advances in cell biology, but also in numerous drug treatments that effectively control the infection. However, cessation of treatment always results in reemergence of the …