Other Microbiology Commons^™

Staphylococcus Aureus Oleate Hydratase Produces Ligands That Activate Host Ppara, Christopher D. Radka, Matthew W. Frank, Tyler S. Simmons, Cydney N. Johnson, Jason W. Rosch, Charles O. Rock

Markey Cancer Center Faculty Publications

Commensal gut bacteria use oleate hydratase to release a spectrum of hydroxylated fatty acids using host-derived unsaturated fatty acids. These compounds are thought to attenuate the immune response, but the underlying signaling mechanism(s) remain to be established. The pathogen Staphylococcus aureus also expresses an oleate hydratase and 10- hydroxyoctadecanoic acid (h18:0) is the most abundant oleate hydratase metabolite found at Staphylococcal skin infection sites. Here, we show h18:0 stimulates the transcription of a set of lipid metabolism genes associated with the activation of peroxisome proliferator activated receptor (PPAR) in the RAW 264.7 macrophage cell line and mouse primary bone marrow-derived …

Do Duckweeds Adapt To Water And Microbes?, Ava M. Rose

Honors Theses and Capstones

Organisms in their home environment sometimes outperform transplanted individuals native to other areas, in a phenomenon termed local adaptation. While local adaptation is traditionally considered to be driven by the abiotic factors of an environment, scientists have recently increased consideration of biotic factors. Specifically, of interest to many is host-associated microbiomes, which can alter host trait expression. As the desire to commercialize microbiome treatments for agriculture and medicine grows, it is important to analyze the potential value of local microbiomes, which may be adapted to their hosts, or to which local hosts may have adapted. Using Lemna minor (duckweed) as …

Social Interactions And Spatial Structure Drive Community Assembly Of Bacterial Biofilm, Matthew C. Bond

Dartmouth College Ph.D Dissertations

Despite the critical nature which microbial communities play in the natural world and human civilization, the breadth of understanding remains shallow. Challenged by scale, high variability between environments, and extensive diversity, microbial ecologists strive to understand connections between a community’s structure and function, as well as the ecological and evolutionary mechanisms underlying observed natural patterning of communities. Biofilms are the predominate mode of growth for microbial communities—characterized by cellular attachment to a surface via a self-produced matrix and heterogeneous structure, often resulting in a primary growth front along the biofilm surface due to differential access to bulk nutrients (cite). This …

Determination Of Spore Viability In Concrete Across Several Factors Using Most Probable Number, Samuel Boyer

Williams Honors College, Honors Research Projects

To determine the lowest concentration of spore added to polyurethane-cement composite (PUCCO) particles that can still germinate after curing in concrete. This research project is a small addition to the larger research project being undertaken by Mirza Mohammed Rashiduzzaman for his Masters. The larger project involves the use of fungal spores added in concrete to act as a self-healing component when cracks form in the concrete structure over time. These spores are suspended in a protective oil and loaded into small, hardened sponge-like PUCCO cubes to act as growth points when water and air can reach the PUCCO in the …

The Development And Evaluation Of A Method For Complete Collagenase I Digestion Of Bos Taurus Bone Samples, Reilly Price

Master of Science in Forensic Science Directed Research Projects

Current methods for processing aged forensic bone samples for DNA analysis involve pulverization and organic extraction, which further destroys already degraded DNA and uses large amounts of limited samples. Additionally, the success rates for this type of analysis vary widely as homogenization incorporates PCR inhibitors into the sample. Little research has explored how pulverization results in DNA damage in profiles obtained from skeletal remains. This study proposes an enzymatic digestion method to separate osteocytes from PCR inhibitors in the extracellular bone matrix to improve the quality and quantity of DNA isolated from aged bone samples. The technique described here used …

Effects Of Subchronic Oral Pfos Exposure Via Drinking Water On Gut Microbiota Composition, Emma Ann Loder

Graduate Theses/Dissertations

Perfluorooctanesulfonic acid (PFOS) has been phased out of production in the United States, but because of its resistance to degradation and its persistence in the environment, PFOS can be found in drinking water across America. Oral exposure to PFOS has been linked to adverse developmental, immunological, hepatic, and endocrine health. Oral PFOS exposure may alter the gut microbiota and cause dysbiosis, which is implicated in the pathology of inflammatory diseases like Crohn’s disease, diabetes, and ulcerative colitis. The goal of the study was to investigate the effects of subchronic oral PFOS exposure on the composition of the gut microbiota. Adult …

The Sewage Microbiome Dynamics Of Different Serving Neighborhoods In Charleston, Illinois, Sandra Chiamaka Okoye

Masters Theses

The complex microbial ecosystem within sewage systems holds significant implications for environmental and public health. Unlike studies on wastewater treatment plant microbiomes, upstream sewage systems have not been studied widely. This research investigated the dynamic sewage microbiome across diverse serving neighborhoods in Charleston, Illinois, encompassing residential, hospital, industrial, and university areas. Drawing upon recent advancements in microbiome research, the study aimed to unravel the spatial and temporal variations in microbial structures. Three times between June to December 2023 sewage samples were collected from manholes in the areas mentioned above. Community DNA was extracted and sequenced for the V4-V5 region of …

Erwinia Amylovora Phage Therapy: Biocontrol Formulation, Receptor Identification, Resistance Mechanisms, Nassereldin Ibrahim

Theses and Dissertations (Comprehensive)

Fire blight is known as a disease of Rosaceae and it displays infection symptoms in about 200 species in 40 rosaceous genera. The most economically important crops that are affected by fire blight are apples and pears. Fire blight can cause severe outbreaks and a single fire blight outbreak can disrupt orchard production for years. The bacterium that causes this disease is indigenous in North America, and according to Statistics Canada, economic losses in apples and pears were valued at an estimated $4 million in 2005, which is approximately 5% of the total production. In addition, production costs can increase …

The Potential Of Endophytic Bacteria As The Biocontrol Agents Of Fusarium Proliferatum, Rima Ernia, Nisa Rachmania Mubarik, Lisdar Idwan Sudirman

Makara Journal of Science

Fusarium proliferatum decreases the productivity of shallot (Allium cepa L.). Endophytic bacteria are potential biocontrol agents in controlling the growth of F. proliferatum. This study aimed to select and characterize endophytic bacteria producing bioactive compounds that inhibit the growth of F. proliferatum. The endophytic bacteria used were isolated from the roots, stems, leaves, and soil of shallot plants from healthy and diseased shallot farming fields. The endophytic bacteria were selected using the dual culture method and extracted using ethyl acetate solvent. The results of the 16S rRNA identification suggested that isolate ABP5.2 is similar to Pseudomonas …

Intestinal Microbiome, Fecal Fermentation Profile, And Health Indices In Hiv Infected Men Versus Non-Infected Controls, Mary Andreae, Mary C. Andreae Mrs

Electronic Theses and Dissertations

Many HIV-positive (HIV+) males on Highly Active Anti-Retroviral Therapy (HAART) experience metabolic abnormalities, including Non-Alcoholic Fatty Liver Disease (NAFLD) and lipodystrophy. The intestinal microbiota and short chain fatty acids (SCFA), participate in bidirectional communication with their host. Dysbiosis in HIV+ males on HAART demonstrate a Prevotella-rich enterotype shaped by multiple factors including, medications, adiposity, diet, intestinal permeability, and lifestyle; our objective was to investigate these factors. 19 HIV+ and 21 HIV- males were enrolled. BMI and hip-to-waist ratio (H:W) were obtained, and FibroScan for liver health. Intestinal permeability markers Claudin-21, flagellin, and intestinal fatty acid binding protein (IFABP) in …

Bactericidal Effects Of Chlorine And Bacteriophages On Mycobacteria In Conventionally Treated Water., Max Kevane-Campbell

ORBioM (Open Research BioSciences Meeting)

Introduction

Mycobacteria are members of the order Actinomycetales and the only genus in the family Mycobacteriaceae. The distinguishing characteristics that are found in mycobacteria include acid-fastness and the presence of mycolic acids. Mycobacteria can be commonly classified as non-spore-forming, aerobic, slender rod-shaped, and are slow-growers. Natural reservoirs that mycobacteria can be found in are aquatic and terrestrial environments. Recent studies have shown that mycobacteria that can cause skin lesions, immune and/or pulmonary dysfunctions and chronic diseases, i.e., Mycobacterium avium subsp. Paratuberculosis, M. kansasii, and M. xenopi, can be isolated from common household tap water. Tap water can originate from …

What Is Microbial Dormancy?, Mark D. Mcdonald, Carlos Owusu-Ansah, Jared B. Ellenbogen, Zachary D. Malone, Michael P. Ricketts, Steve E. Frolking, Jessica Gilman Ernakovich, Michael Ibba, Sarah C. Bagby, J. L. Weissman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Life can be stressful. One way to deal with stress is to simply wait it out. Microbes do this by entering a state of reduced activity and increased resistance commonly called ‘dormancy’. But what is dormancy? Different scientific disciplines emphasize distinct traits and phenotypic ranges in defining dormancy for their microbial species and system-specific questions of interest. Here, we propose a unified definition of microbial dormancy, using a broad framework to place earlier discipline-specific definitions in a new context. We then discuss how this new definition and framework may improve our ability to investigate dormancy using multi-omics tools. Finally, we …

Protocol For Optimizing Production And Quality Control Of Infective Ecohiv Virions, Hammodah Rawhi Hammodah Alfar, Daphne N. Pariser, Harry Chanzu, Smita Joshi, Daniёlle M. Coenen, Joshua Lykins, Kanakanagavalli Shravani Prakhya, Mary Jane Potash, Wei Chao, Jennifer Kelschenbach, David J. Volsky, Kelly Metcalf-Pate

Saha Cardiovascular Research Center Faculty Publications

EcoHIV is a model of HIV infection that recapitulates aspects of HIV-1 pathology in mice. However, there are limited published protocols to guide EcoHIV virion production. Here, we present a protocol for producing infective EcoHIV virions and essential quality controls. We describe steps for viral purification, titering, and multiple techniques to analyze infection efficacy. This protocol produces high infectivity in C57BL/6 mice which will aid investigators in generating preclinical data.

Understanding And Quantifying Bioaerosol Fate Within The Aerobiological Pathway: Physical Transport, Environmental Decay, And Mitigation, Sean Kinahan

Theses & Dissertations

The recent COVID-19 pandemic has highlighted the need for better tools to understand and characterize phases of the aerobiological pathway, a model for understanding how infectious bioaerosols are sourced, generated, transported, deposit, and affect human health. This dissertation presents validation of methodologies for studying transport of airborne biological agents and variations on their consequences, especially focusing on their physical and chemical fate. Chapter 1 focuses on a parallel comparison of two methods of aging bioaerosols in real-world outdoor environments with complex sunlight, atmospheric chemistry, and pollutants. Both capture on microfibers and the use of Goldberg rotating drums to keep a …

The Unique Gut Microbiome Of Giant Pandas Involved In Protein Metabolism Contributes To The Host's Dietary Adaption To Bamboo, Feilong Deng, Chengdong Wang, Desheng Li, Yunjuan Peng, Linhua Deng, Yunxiang Zhao, Zhihao Zhang, Ming Wei, Kai Wu, Jiangchao Zhao, Ying Li

Animal Science Faculty Publications and Presentations

Background

The gut microbiota of the giant panda (Ailuropoda melanoleuca), a global symbol of conservation, are believed to be involved in the host’s dietary switch to a fibrous bamboo diet. However, their exact roles are still largely unknown.

Results

In this study, we first comprehensively analyzed a large number of gut metagenomes giant pandas (n = 322), including 98 pandas sequenced in this study with deep sequencing (Illumina) and third-generation sequencing (nanopore). We reconstructed 408 metagenome-assembled genomes (MAGs), and 148 of which (36.27%) were near complete. The most abundant MAG was classified as Streptococcus alactolyticus. A …

Exploring Experimental Design And Multivariate Analysis Techniques For Evaluating Community Structure Of Bacteria In Microbiome Data, Kelsey Karnik

Department of Statistics: Dissertations, Theses, and Student Research

The gut microbiome plays a crucial role in human health, and by working collaboratively with microbiologists, we aim to further our understanding of the human gut and its impact on human health. Promoting a diverse microbiome is emphasized throughout microbiology literature, and involving a statistician in designing experiments to relate gut bacteria and some measured health outcome is crucial for ensuring valid and accurate results. By adopting new experimental design and analysis methods, researchers can begin to gain a deeper understanding of how the genetics of our food affect the composition of taxa within the gut microbiome. This dissertation is …

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 …

Enhancing Lovastatin Biosynthesis In Oyster Mushrooms (Pleurotus Ostreatus) Using Phytohormones, Fransisca Astrid Mustafa, Mamat Kandar, I Nyoman Pugeg Aryantha

Makara Journal of Science

The biosynthesis of lovastatin, the anti-cholesterol compound, in oyster mushrooms (Pleurotus ostreatus), has the potential to be enhanced by utilizing phytohormones, which activate the expression of certain genes. This research aimed to determine the best type and concentration of phytohormone among auxin, gibberellin, and cytokinin, as well as the best mycelial colonization percentage in F2 medium to realize the greatest increase in lovastatin biosynthesis in oyster mushrooms. Lovastatin was extracted from the fruiting bodies and mycelia and analyzed by spectrophotometry. The analysis of CYP450 linked to lovastatin biosynthesis was conducted by quantitative polymerase chain reaction (qPCR) using samples containing …

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 …