Digital Commons Network^™

Cultivating Excellence: A Literature Review On Harnessing The Power Of The Gut Microbiome For Athletic Performance, Maya Katharine Dean

Honors Projects

The interplay between our gut microbiome and health is immense. This literature review analyzes the current research assessing the interplay between gut microbiome and athletic performance. Knowing how to improve gut microbial diversity via nutrition and supplementation can take athletic performance to the next level; namely improvements in immune, mental, and physical health.

Pathogenicity Of Acinetobacter Calcoaceticus, Kaitlan A. Sullivan

MUSC Theses and Dissertations

Acinetobacter is a genus of gram-negative bacteria that have been appearing frequently in hospitals contributing to infections in the blood, lungs, urinary tract, and other parts of the body. It infects patients with weakened immune systems that are placed on ventilators, after the use of catheters, or have any other open wounds produced by prolonged hospital stays. This genus of bacteria is problematic due to its high probability of becoming resistant to multiple classes of antibiotics. Thus, we are determining the pathogenicity of clinical isolates of Acinetobacter calcoaceticus using the organism Caenorhabditis elegans as a model.

We are testing …

Understanding The Kinetics Of Laser-Induced Nanowelding Of Nanoparticles And The Motility Of Bacteria When Faced With Obstacles, Ariel Rogers

Graduate Theses and Dissertations

This dissertation has two focus areas: nanoparticle nanowelding and bacteria motility in the presence of micrometer sized structures. There are two main projects for the nanoparticle nanowelding studies: “Real-time imaging of laser-induced nanowelding in solution” and “Two-color laser-induced nanostructure shape modulation.” For the real-time imaging project, I used a fluorescence microscope, a 405 nm laser, and various python packages to quantify the average size of nanowelded nanostructures as a function of time and found that the average nanostructure growth over time fit the parameters of A¯(t) ∝ c0(1−e−t/τ), where c0 represents the initial concentration of nanoparticles in the solution and …

The Interplay Between Lung Adenocarcinoma, Nutrient Availability, And The Microbiome., Alexis A. Vega

Electronic Theses and Dissertations

Lung cancer is one of the most common forms of cancer diagnosed, and has the highest lethality rate across all other forms of cancer in the U.S. While current therapeutic options include chemo-, immuno-, and radio-therapy, the benefits of caloric or nutrient restriction on cancer cells has also been investigated. Due to the many biological functions associated with methionine, many have proposed a methionine restricted diet would lead to favorable outcomes when combating cancer. Although our cells are incapable of synthesizing methionine, the bacteria found in our microbiome can. Furthermore, recent discoveries suggest an independent microbiome found within tumors that …

Opening The Black Box: Soil Microbial Communities In Field-Based Plant-Soil Feedback Experiments, Julia Kate Aaronson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Plant-soil feedback is a process through which plants modify the properties of their associated soils, affecting their growth. PSF can play a key role in regulating plant growth and communities including altering plant invasion, rarity, and abundance. However, our understanding of the soil organisms that drive these plant growth responses is limited. Most studies treat soils as a ‘black box’ and do little to reveal which specific microbes or microbial communities may be responsible. This chapter examines two recent large PSF field experiments conducted in Minnesota, USA, and Jena, Germany. These experiments revealed that plants altered their soils, changing subsequent …

Characterization Of Lps As A Virulence Factor In Burkholderia Cepacia During Plant And Human Infection, Jack Klahr, Elizabeth Danka

Biology Senior Theses

Burkholderia cepacia is a gram-negative bacterium first characterized as the causative agent of sour skin in onion crops. More recently, B. cepacia has become a clinical concern as an opportunistic pathogen that can colonize the upper respiratory tract of cystic fibrosis patients and increase mortality in these patients. Infection is exacerbated by the intrinsic resistance to antibiotics found in this genus of organisms. Additional virulence factors help the bacteria persist in the host during infection. However, few of these factors have been described. In this work, we characterized a putative virulence factor that was first identified through an onion infection …

The Role Of Cerium(Iii) In Bacterial Growth And The Microbial Transformation Of Aromatic Hydrocarbons, Shruti Sathish

Honors Theses

Biofilms are communities of surface-attached bacterial cells encased in an exopolymeric matrix. In this state, they are more resistant to antimicrobial treatment and can have adverse effects in medical, agricultural, and industrial settings. Whereas, as biocatalysts, biofilms from nonpathogenic bacteria enhance their performance and stability in catalysis. Unfortunately, there are several challenges when using bacteria in organic transformations due to their complex cellular chemistry. Trivalent lanthanide metals were discovered to serve regulatory roles in some bacterial catalytic processes, including those of Pseudomonas putida KT2440 (P. putida), a non-infectious Gram-negative bacterium. The main goal of our research is to use cerium(III) …

Investigating The Effectiveness Of Microplastic Removal And The Relationship Between Microplastics, Bacterial Communities, And Nitrogen Cycling In The Natural Treatment Systems At The Arcata Wastewater Treatment Facility, Fiona Connor

Cal Poly Humboldt theses and projects

This thesis addressed two challenging aspects of microplastic research, including the quantification of microplastics in organic-rich water, and the investigation of how microplastics impact microorganisms and related nutrient-cycling. Two projects were designed and executed to address specific research objectives relating to these broad topics. The first objective was to develop and implement methods to determine the effectiveness of microplastic removal across the natural treatment systems at the Arcata Wastewater Treatment Facility (AWTF). The second objective was to observe how microplastics found in domestic wastewater impact the bacterial communities and nitrogen cycling in freshwater treatment wetland sediment through a bench-scale experiment, …

Study Of Microbial Load In Water Samples From Hydraulic Fracturing Adjacent Streams, Anthony W. Ruocco

Senior Projects Spring 2023

Hydraulic Fracturing, also known as “fracking,” is an oil and gas extraction method in which a mix of water, sand, and chemicals are shot at high pressures into subterranean areas. This process has the potential to not only damage landscapes and impact wildlife, but also to pollute groundwater and surface water, as well as streams. Water collected near fracking sites may show the effects of hydraulic fracturing on microbial communities, and examination of bacterial growth can possibly give indication of habitat degradation or the effect of inorganic compounds introduced by the hydraulic fracturing process. Samples collected by a Jude Lab …

Analysis Of Experimental Antimicrobial Prevention Strategies Against Microbial Contamination Of Locally Harvested Poultry And Produce In West Virginia, Rebecca Breanne Stearns

Graduate Theses, Dissertations, and Problem Reports

Fresh produce and poultry have been associated with several foodborne illness outbreaks. Strategies to mitigate these risks are a much-needed research priority; therefore, five experiments were conducted to analyze pathogen cross-contamination capabilities on produce and poultry. Microbial contamination prevention and reduction strategies were also studied.

In Chapter Two, three antimicrobial delivery methods in combination with increasing concentrations of hydrogen peroxide-peroxyacetic acid (H₂O₂-PAA) (0.05-0.25 ml/dL) were compared to evaluate their ability to reduce and prevent cross-contamination of Listeria monocytogenes (L. monocytogenes) and Listeria innocua (L. innocua) on inoculated apples. Apples have been …

A Metagenomic Analysis Of The Microbial Communities Associated With Different Hydrothermal Vent Chimneys, Laura Murray

WWU Graduate School Collection

Hydrothermal vents host a diverse community of microorganisms that utilize chemical gradients from the venting fluid for their metabolisms. The venting fluid can solidify to form chimney structures that these microbes adhere to and colonize. These chimney structures are found throughout many different locations in the world’s oceans. In this study, comparative metagenomic analyses of microbial communities on five chimney structures from around the Pacific Ocean were elucidated focusing on the core taxa and genes that are characteristic for each of these hydrothermal vent chimneys, as well as highlighting differences among the taxa and genes found at each chimney due …

Detection And Diagnosis Of Bacterial Pathogens In Blood And Urine Using Laser-Induced Breakdown Spectroscopy, Emma J.M. Blanchette

Electronic Theses and Dissertations

The aim of this thesis is to expand on and improve the existing techniques used for detecting and identifying bacterial pathogens in clinical specimens with laser-induced breakdown spectroscopy (LIBS). Specifically, the existing experimental procedures, including bacterial sample preparation and data acquisition, as well as the data analysis with chemometric algorithms were investigated. Substantial reductions in LIBS background signal were achieved by implementing rigorous cleaning steps and the introduction of the use of ultrapure water. Following this, a database of LIBS spectra was acquired from specimens of E. coli, S. aureus, E. cloacae, M. smegmatis, and P. …

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 …

Principles Of Aaa+ Proteases, Samar Mahmoud

Doctoral Dissertations

ATPases associated with diverse cellular activities (AAA+) proteases in bacteria help maintain protein homeostasis by degrading misfolded and regulatory proteins. While a handful of protein targets for these proteases have been identified in Caulobacter crescentus and other organisms, more research is needed to elucidate mechanisms that govern substrate specificity. In the second chapter of this thesis, I will elaborate on how AAA+ substrate specificity is less rigid than previous work has suggested and how limiting ATP or mutations can alter substrate preferences of the ClpXP protease. In the third chapter, I will highlight our efforts to use a quantitative proteomics …

A Bioinformatics Analysis Of Microbial Diversity And Its Correlation With Human Lifestyle, Diet, And Health Variables, Alivia Ankrum, Kate Cooper

Theses/Capstones/Creative Projects

The abundant impact of microbiota on human physiology suggests a need for exploration into their impact on human health and disease. The American Gut Project (AGP) was established to aggregate microbiome sequencing data as well as health, diet, and lifestyle metadata. This study proposes to identify taxonomic species and build a phylogenetic tree representation from the AGP participant sample collection as well as find their respective alpha and beta diversity of all metadata variables based on patient questionnaire data. Additionally, this study will involve a chimeric sequence extraction from the 16S rRNA sequences of the AGP. The expected results are …

Reproductive Ecology And Microbial Communities From Wood Duck Nest Boxes In Georgia And Florida, Jake Shurba

All Theses

Wood ducks (Aix sponsa) are an important game species throughout the Atlantic Flyway that was nearly extirpated by the early 20^th century due to overhunting and the loss of habitat. Wood ducks are secondary cavity-nesters that utilize artificial nest boxes and natural cavities. It is reported that the use of nest boxes is likely what led to re-establishment of the species in North America. Where boxes are numerous, overuse of boxes by multiple hens throughout a nesting season can occur and result in a buildup of bacteria, parasites and other potentially detrimental pathogens that can impact egg …

Effects Of Surface Topography On Macrophages And Bacterial Cells, Joseph Carnicelli

Theses - ALL

An association has been found between the texture of breast implants and anaplastic large cell lymphoma, which led to some textured implants to be withdrawn from the market in 2019. There is evidence that these cancers are associated with the harboring of bacteria on the surfaces of the textured implants. It is possible that specific topographic features hinder the removal of attached bacteria by inhibiting macrophage phagocytosis or promoting biofilm formation. Here we examine how bacteria and macrophages interact with recessive surface topographies as analogs to the surfaces seen on textured breast implants. Changes in bacteria morphology were observed among …

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 …

The Spatial, Temporal, And Ecological Constraints Of Plant-Host Associated Microbial Communities, Jonathan Dickey

Doctoral Dissertations

With the development of next generation sequencing technology, ecologists have recently been able to describe microbial communities across a wide array of niches at an accelerated pace. De-novo-based patterns in richness and relative abundance have been described for bacterial and fungal communities in terrestrial, aquatic, and host-associated microhabitats. A recent synthesis has shown that these communities exhibit similar geographical patterns that have been traditionally described for plant and animals. Yet, there is a lack of hypothesis-based research for host-associated microbial communities. Throughout this dissertation, I will address how spatial scale, sequencing resolution, and manipulative rainfall exclusion govern host-associated microbial communities …

Effects Of Protein Concentration And Beta-Adrenergic Agonists On Ruminal Microbial Communities In Finishing Beef Heifers, Alison P. Pfau

Masters Theses

To improve animal performance and modify growth by increasing lean tissue accretion, beef cattle production has relied on use of growth promoting technologies such as beta-adrenergic agonists. These synthetic catecholamines, combined with the variable inclusion of rumen degradable (RDP) and undegradable protein (RUP), may improve feed efficiency and rate of gain in finishing beef cattle. However, research about the impact of beta-adrenergic agonists and protein level and source on the ruminal microbiome is limited. The objective of this study was to determine the effect of different protein concentrations and beta-adrenergic agonist (ractopamine hydrochloride; RAC usage) on ruminal bacterial communities in …

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 …

Evaluation Of Selected Nuproxa Feed Additives For Protection Against Lameness And Improving The Wellbeing Of Broilers In A Lameness Challenge Model, Jaren Hernandez

Biological Sciences Undergraduate Honors Theses

A common concern in commercial industries profiting from broiler chickens is their inability to yield a completely healthy flock. Bacterial Chondronecrosis with Osteomyelitis poses a threat to these companies by impairing the birds' proximal and distal tibial and femoral heads. In 2000, roughly 17.3% of broiler chickens were affected by Bacterial Chondronecrosis with Osteomyelitis which caused a substantial economic loss in the industry (McNammee et al., 2000). BCO cannot be tied to a particular bacterial species; this experiment focuses on evaluating the efficacy of certain commercial feed additives while determining the bacterial species causing BCO in this set of the …

Antimicrobial Assay Of Sagebrush Roots, Lauren Rachel (Moody) Mcfadden

Undergraduate Honors Capstone Projects

Plants produce secondary metabolites for various functions, one of which is antibacterial activities. Sagebrush has historically been used by Native Americans for different medicinal purposes, suggesting that it may have secondary metabolites that would have medicinal values, including antimicrobial activities, and can be a natural source for antibiotics. This study aims to carry out the antimicrobial activity of Sagebrush root extract against a handful of bacteria. We tested the antimicrobial activity of root extract of Sagebrush against six bacteria such as Bacillus subtilis, Bacillus cereus, E. coli DHSα (Lab cloning strain), Agrobacterium tumefaciens GV3101 (Lab cloning strain), Pseudomonas …

Structural Formation And Functionality Of The Spoiie Protein In Clostridium Difficile, Rachel Siebenmorgen

Biological Sciences Undergraduate Honors Theses

My research efforts were directed toward the structure and functionality of a protein, designated SpoIIE [11], which previously has been shown to regulate C. difficile peptide utilization in addition to sporulation and toxin release. The SpoIIE protein is found in all spore-forming gram-positive bacteria and is a crucial component in activation of transcription factors and septum formation thus affecting the regulation and timing of spore development [11,12]. A truncated form of the SpoIIE protein named SpoIIE∆TM was used in an effort to determine the structure of an important but uncharacterized linker domain of the protein. If the structure and specific …

Diversity Of Bacteriophage In Burkholderia Species, Abigail Price

Honors Projects

Bacteriophages are viruses that infect and replicate within bacteria and offer the potential of a therapeutic alternative to chronic infections that do not respond to antibiotic-based therapies. B. vietnamiensis is one of a number of Burkholderia species involved with chronic drug resistant infections in the lungs of individuals with compromised respiratory systems, as found in those with chronic obstructive pulmonary disease and, most especially, are of particular significance in patients with cystic fibrosis. The diversity of the Burkholderia species is explored by using online databases and looking at bacteriophage or phage-encoding viruses found in B. vietnamiensis. The open reading frames …

Degradation And Nitrogen Cycling In The Context Of Biodiversity-Ecosystem Function Relationships In The Inquiline Bacterial Community Of Darlingtonia Californica, Megan Teigen

Cal Poly Humboldt theses and projects

Biodiversity-ecosystem function (BEF) research aims to explain how species and their environments interact with each other. Microbial communities engage in vital biogeochemical pathways in a variety of natural ecosystems, and yet there are large knowledge gaps about the specific metabolic pathways in which they are involved. Degradation specifically contributes to nitrogen cycling globally through the breakdown of large organic nitrogen compounds into small inorganic nitrogen that is necessary for the survival of many other organisms. In this study, I focused on the degradative function of the inquiline microbial communities found within the carnivorous pitcher plant, Darlingtonia californica. Darlingtonia grows in …

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 …

Microbial Community Analysis: Biofilm Inhibition & Algae Associated Community Structure, Michelle V. Fong

University of the Pacific Theses and Dissertations

Natural products chemistry is the pursuit of bioactive small molecules from living organisms. These can be classified as primary metabolites if they are essential to survival, and secondary metabolites if they are accessory, playing a role in communication, defense, recruitment, etc.. Natural products have made a significant contribution to society – of 1,881 FDA-approved drugs from 1981 to 2019, 4% were pure natural products, 19% were natural products derived, and 3% were synthetic drugs with a natural products pharmacophore targeting a wide range of diseases and infections (Newman & Cragg, 2020). Pharmacophores are structural components of drugs that are responsible …

Restricted Microbial Presence, Activity, And Community Structuring Within Dry Valley Soils Of Antarctica, Scott Fillerup George

Theses and Dissertations

The McMurdo Dry Valley region is the largest ice-free area of Antarctica. Harsh abiotic conditions of the polar desert ecosystem, including extreme cold, aridity, and limited nutrient availability select for unique taxa. The comparatively simple terrestrial ecosystem is well-suited for investigating edaphic influences on microbial presence, activity, and community structuring. The Dry Valleys are viewed as a useful analog for Mars astrobiology investigations. However, most biotic investigations have been focused on lower elevations, where an understanding of edaphic effects on microbial communities within its generally more favorable conditions has emerged. Transiently wetted Dry Valley water tracks may be analogous to …

The Flavoprotein Rcla Is A Hypothiocyanous Acid Reductase, Irina Chapman

Masters Theses

Reactive chlorine species (RCS) - hypochlorous acid (HOCl), hypothiocyanous acid (HOSCN), and chloramines - are powerful antimicrobial oxidants generated by the innate immune system. Bacteria developed defense mechanisms against RCS, which are highly toxic for invading pathogens. One such defense system involves RclA, an enzyme from the flavin disulfide reductase family, which is massively upregulated upon exposure of Escherichia coli to RCS. Recent research suggests that RclA functions as a Cu(II) reductase to provide resistance against RCS. However, the exact mechanism used by RclA was subject to debate. In this study, we demonstrate that RclA is unlikely to function as …