Microbiology Commons^™

Diversity Of Navel Microbiome In Young Adults, Shreya Shah, Teresa Donze-Reiner, Vishal Shah

Biology Faculty Publications

Introduction. Human skin microbial communities represent a tremendous source of genetic diversity that evolves as a function of human age. Microbiota differs between regions of oily and moist skin, and appears to stabilize with age.

Aim. We have a minimal understanding of the time frame required for the stabilization of skin microbiota, and the role played by gender. In the current study, we examined the microbiota present in the navel region of college-attending young adults in the age group of 18–25 years and investigated if diversity is associated with gender (male and female).

Method. The study involved 16 female and …

Rapid Antibiotic Susceptibility Testing Platform For Direct Clinical Samples, Terrance Zhang

Honors Scholar Theses

Infectious diseases and septicemia are two of the major causes of death in the U.S., necessitating rapid treatment of septic patients with proper, efficacious antibiotics. Unfortunately, the emergence and spread of multidrug-resistant bacteria are continuously being aggravated by an abuse in antibiotic prescription at a clinical and agricultural level. It is known that antibiotic resistance evolves through the sequential accumulation of multiple mutations in bacteria, which is accentuated by prolonged exposure of bacteria to ineffective antibiotics when implementing traditional septicemia treatment. The goal of this project is to develop a novel, easy-to-use AST platform for rapid antimicrobial susceptibility profiling to …

Possible Role Of N-Acetylglucosamine For Induction Of Polyhydroxybutyrate Depolymerase In Streptomyces Sp. Sfb5a, Morgan Todd

Honors Projects

Streptomyces sp. SFB5A is a filamentous, Gram-positive bacterium that makes a polyhydroxybutyrate (PHB) depolymerase to degrade PHB for energy usage. Its life cycle begins as spores germinate to form vegetative mycelia. Starvation prompts formation of aerial mycelia and ultimately spores after 5-7 days. During starvation, Streptomyces may use peptidoglycan hydrolases to degrade its own cell walls, releasing N-Acetylglucosamine (NAG). PHA depolymerase activity is detected during growth of strain SFB5A on NAG as the sole carbon source, suggesting that NAG induces PHA depolymerase synthesis. To test this hypothesis, strain SFB5A was grown for 4 days on PHB, and a colorimetric assay …

Glycogen Accumulation By Wild Type And Bald Mutant Strains Of Streptomyces Sp. Sfb5a During Growth On 3-Hydroxybutyrate, Mackenzie Francis

Honors Projects

Previous research has shown that Streptomyces sp. SFB5A produces PHA depolymerase and forms aerial hyphae, while the bld4 mutant of this species forms aerial hyphae very poorly and does not produce PHA depolymerase. This effect may be due to the mutant’s inability to sense starvation. Therefore, we hypothesized that the bld4 may also be deficient in formation of glycogen and spores, which are both associated with starvation. To test this hypothesis, we grew the wild type (WT) Streptomyces sp. SFB5A and bld4 in broth cultures containing 3HB. We compared 3HB consumption, glycogen accumulation, PHA depolymerase synthesis, protein accumulation, and spore …

Development Of An Attenuated Zika Virus By Editing The 5’ Untranslated Region, E. Ashley Thompson

Master's Theses

Zika Virus (ZIKV) is a mosquito-transmitted flavivirus that usually causes no symptoms to mild febrile in humans, and it has been regarded as an insignificant pathogen to public health. However, recent outbreaks of ZIKV infection have revealed that ZIKV can cause severe neurological effects in adults, such as Guillain-Barre Syndrome (GBS), and in infants whose mothers acquired the virus during pregnancy, causing Congenital Zika Syndrome (CZS). Currently, no approved vaccine is available and there is a critical need to develop an effective and safe vaccine. While most vaccine developmental strategies target the viral prM-E protein of ZIKV, we aimed to …

The Effects Of Farnesol, A Quorum Sensing Molecule From Candida Albicans, On Alcaligenes Faecalis, Savannah Hutson

Undergraduate Honors Theses

Quorum sensing molecules have become a recent focus of study to learn if and how they can be used, both on their own and in conjecture with current antimicrobial methods, as a means of bacterial control. One such quorum sensing molecule is the sesquiterpene alcohol, Farnesol, which is synthesized and released by the fungus, Candida albicans. In most in-vivo cases, our laboratory has shown that Alcaligenes faecalis overtakes C. albicans, preventing its growth. However, as a way to counteract this inhibitory effect, Farnesol may be one way that Candida has found to fight back. In this study, we …

A Study Of The Polymicrobial Inhibitory Interactions Between Alcaligenes Faecalis And Staphylococcus Aureus, Blakeley Griffin

Undergraduate Honors Theses

Members of the Staphylococcus genus are found as a part of normal microflora in humans and can commonly be found on the skin or in the nasal cavity. However, these microorganisms can cause serious and life-threatening opportunistic infections when there is a break in the physical barrier of skin. These infections have become difficult to treat as resistant strains emerge, particularly Methicillin Resistant Staphylococcus aureus (MRSA). MRSA has become a commonly acquired nosocomial infection which is difficult to treat with conventional antibiotics of the blactam class. Even Vancomycin, a last resort antibiotic, has been ineffective on some infections. Furthermore, …

Gut Pathophysiology In Mouse Models Of Social Behavior Deficits, Kyla Scott

Undergraduate Honors Theses

Autism spectrum disorders (ASD) encompass neurodevelopment disorders characterized by atypical patterns of development that impact multiple areas of functioning beginning in early childhood. The etiology of ASD is unknown and there are currently no preventative treatment options. Gastrointestinal symptoms are commonly associated comorbidities. The microbiota-gut-brain axis is a multidirectional communication chain that connects the central and enteric nervous system that relates brain function to peripheral intestinal functions. Changes within this axis have been postulated in ASD. For example, the “leaky gut theory” proposes that chronic inflammation is linked to alterations in the bacterial profiles of the gut microbiome and subsequent …

The Effects Of Storage Temperature On The Bovine Nasal Microbiome, Hunter Usdrowski

Animal Science Undergraduate Honors Theses

Bovine respiratory disease (BRD) is one of the largest economic burdens facing United States beef producer’s modern day. The complexity in the onset and development of this multifactorial disease necessitates further insights into its functions to alleviate the tremendous consequences it generates for producers. The respiratory microbiome and their metabolomics play an important role to maintain health and predict BRD. However, due to low biomass, new technology is needed to increase the microbial concentration for omics (e.g. metatranscriptomics) research. In this study, a novel self-enrichment storage technique on the bovine nasal microbiome was performed and compared to a traditional nasal …

Surface Runoff Alters Cave Microbial Community Structure And Function, Madison Davis, Maria A. Messina, Giuseppe Nicolosi, Salvatore Petralia, Melvin D. Baker, Christiana K. S. Mayne, Chelsea M. Dinon, Christina J. Moss, Bogdan P. Onac, James R. Garey

Molecular Biosciences Faculty Publications

Caves formed by sulfuric acid dissolution have been identified worldwide. These caves can host diverse microbial communities that are responsible for speleogenesis and speleothem formation. It is not well understood how microbial communities change in response to surface water entering caves. Illumina 16S rRNA sequencing and bioinformatic tools were used to determine the impact of surface water on the microbial community diversity and function within a spring pool found deep in the Monte Conca Cave system in Sicily, Italy. Sulfur oxidizers comprised more than 90% of the microbial community during the dry season and were replaced by potential anthropogenic contaminants …

A Putative Cystathionine Beta-Synthase Homolog Of Mycolicibacterium Smegmatis Is Involved In De Novo Cysteine Biosynthesis, Saroj Kumar Mahato

Graduate Theses and Dissertations

Mycobacteria include serious pathogens of humans and animals. Mycolicibacterium smegmatis is a non-pathogenic model that is widely used to study core mycobacterial metabolism. This thesis explores mycobacterial pathways of cysteine biosynthesis by generating and study of genetic mutants of M. smegmatis. Published in vitro biochemical studies had revealed three independent routes to cysteine synthesis in mycobacteria involving separate homologs of cysteine synthase, namely CysK1, CysK2, and CysM. However, in vivo data were lacking. The M. smegmatis genome encodes only a CysM homolog and lacks orthologs for CysK1 or CysK2. The gene that codes for CysM is a part of an …

The Release, Transport, And Utilization Of Phosphorus From Bed-Sediments: A Study Of A Eutrophic Littoral Cove On Beaver Lake In Northwest Arkansas, James A. Mccarty

Graduate Theses and Dissertations

Eutrophication of surface waters not only impacts the environment but also water treatment processes, the most significant of which is from the effects of algae. During peak algal growth in many southern U.S. reservoirs, inflows that bring nutrients are at an annual minimum, and phosphorus released from bed-sediments is trapped in the hypolimnion. Littoral areas, described as the most productive zone of the lake, may be a possible source of phosphorus that fuels algal growth in the reservoir. I studied an isolated shallow cove in the War Eagle Creek arm of Beaver Lake in Northwest Arkansas to measure, quantify, and …

Reversible Inhibition Of Mycobacterial Dnab Protein Splicing By Zinc, Gabrielle Hardison

Honors College Theses

Inteins are emerging as post-translational regulatory elements, undergoing conditional protein splicing in response to a variety of environmental cues. Inteins are seamlessly removed by self-splicing from exteins, or flanking portions of the host protein, which they interrupt. DnaB of Mycobacterium smegmatis, a helicase essential for replication, harbors two inteins known as DnaBi1 and DnaBi2, each with discrete structural characteristics and insertion positions. DnaBi1 was used here to design a reporter system which links splicing with resistance to the antibiotic kanamycin. We built a construct that strictly requires catalytically active DnaBi1 for survival in the presence of kanamycin and used …

Effects Of Light, Nutrients, And Salts On Microbial Biofilm Productivity And Detrital Processing In Aquatic Mesocosms, Bethanie Brooke Howard-Parker

Graduate Theses and Dissertations

Anthropogenic activities associated with urbanization, agriculture, and resource extraction continue to increase to support increasing needs of the growing population. These activities increase the amounts of pollutants entering freshwater streams and put aquatic ecosystems at structural and functional risk. Aquatic microbes play an important role in detrital processing in streams as a key linkage in moving carbon from detrital stocks into aquatic food webs. My research investigates the effects of light, nutrients, and salts on detrital microbes and decomposition in freshwaters using a mesocosm approach. In chapter one, I modified a current priming effect (PE) hypothesis model to include light …

A Comparative Taxonomic And Diversity Study Of Litter-Associated Fungi In Northwest Arkansas Forests, Rajaa Abdulrazzaq Abbas Al Aanbagi

Graduate Theses and Dissertations

Fungi are taxonomically the most species-rich group of organisms on the earth, ecologically occupy distinctive niches and interact with diverse other organisms throughout their biogeographic distributions and functionally play key roles through their various lifestyles. Plant litter, in particular, is a keystone component in ecosystems and provides heterogeneous microhabitats for the often overlooked litter-decomposing fungi and other organisms on the floor of temperate deciduous forests. Litter fungi involve indirect interactions with the plant, soil and whole food web network. However, the community structure and functions of litter-associated fungi as well as patterns of species richness distributed across various litter microhabitats …

Elucidating The Molecular Pathways Involved In The Fitness And Water Stress Response Of Pseudomonas Synxantha 2-79 In The Plant Rhizosphere, Clint Henry D. Pablo

Master's Theses

Pseudomonas synxantha 2-79 is a biocontrol agent that represents beneficial indigenous rhizobacteria that are broadly distributed in the Pacific Northwest, USA and flourish in the rhizosphere of commercially grown wheat under surprisingly arid conditions. The molecular adaptation of 2-79-like bacteria to plants growing in dry soils is poorly understood. We hypothesized that the ability of 2-79 to colonize and persist in the rhizosphere of water-stressed plants is underpinned by the formation of hydrating biofilms and the utilization of root exudates that contain plant-derived osmoprotectants called quaternary ammonium compounds (QACs). We tested this hypothesis by identifying waters stress response pathways in …

Second Messenger Cyclic-Di-Gmp Regulation In Acinetobacter Baumannii, Justin Deal

Undergraduate Honors Theses

Over time, “superbugs,” or bacteria that have become resistant to antibiotics, have become a great concern in modern medicine. Viable alternates are currently being looked into as effective and safe ways to prevent or treat infections caused by these superbugs. One such method is through the utilization of the second messenger molecule cyclic-di-GMP (c-di-GMP) that has been shown to regulate phenotypes within other bacteria that may control surface colonization in Acinetobacter baumannii. Through a series of experiments, the active enzymes that create c-di-GMP - diguanylate cyclases - and break down c-di- GMP - phosphodiesterases - have been inactivated in …

Characterization Of The Broad-Spectrum Inhibitory Capability Of Alcaligenes Faecalis And A. Viscolactis Against Potential Pathogenic Microorganisms, Andrew Fuqua

Undergraduate Honors Theses

The recent rise of multidrug resistant microorganisms has grown from an isolated concern to a massive public health crisis. It has become imperative that scientists look for new ways to combat this issue. Due to the selective pressures of competition, bacteria and other microbes possess a host of defenses and weapons designed to exploit vulnerabilities in other microorganisms. Consequently, the study of these systems and microbial interactions has much to reveal in the search for novel antimicrobial treatments. Previous research from our laboratory has discovered that both Alcaligenes faecalis and Alcaligenes viscolactis, two rarely studied and generally non-virulent bacteria, …

Synergistic Inhibition Of Resistant Enterobacteriaceae Using A Possible Klebsiella Secreted Bacteriocin With Broad-Spectrum Antibiotic, Andrew Robbins

Undergraduate Honors Theses

Due to the increasing prevalence of multi-drug resistant (MDR) bacteria, it is now important to begin the search for novel means of defending against such resistant infections. Enterobacteriaceae is a clinically relevant family of bacteria that has shown extensive resistance to many antibiotics, especially after biofilm formation. Inhibitory poly-microbial interactions within this family have been observed. It is known that Citrobacter freundii (CF) growth is significantly inhibited by Klebsiella pneumoniae (KP) through a secreted protein. In this study, the potential KP bacteriocin was screened for its inhibitory effects on CF at various phases of biofilm development. The suspected KP bacteriocin …

Regulation Of Weak Acid-Dependent Cell Death By The Msaabcr Operon During Biofilm Formation Of Staphylococcus Aureus, Sarah-Elizabeth M. Polley

Honors Theses

Staphylococcus aureus is a dangerous human pathogen and a leading cause of both nosocomial and community-associated infections. Infection by S. aureus is a growing health concern due to the emergence of antibiotic resistance and the capability to form robust biofilms. Major constituents of the biofilm extracellular matrix are demonstrated to be released via controlled autolysis of a subpopulation of the biofilm. As indicated in past studies, the programmed cell death (PCD) of S. aureus grown in a biofilm microenvironment is potentiated by the buildup of acetate, a byproduct of glucose metabolism, which causes cytoplasmic acidification. Furthermore, it has been shown …

The Effects Of Light On The Bacterial Biomass Of Decomposing Leaf Litter In Freshwater, Savannah L. Underwood

Honors Theses

Recent evidence has suggested that the presence of light (and in conjuction, periphytic algae) stimulates the growth and production of bacteria on decaying plant litter. However, the current method of measuring bacterial biomass, flow cytometry, drastically underestimates the bacterial biomass levels associated with litter samples. To determine and correct for this underestimation, the present study determined conversion factors using direct counting methods via epifluorescence microscopy. These conversion factors were then applied to flow cytometry counts for seven different studies. The studies analyzed the effects of light and other covarying factors on the bacterial biomass associated with various samples of leaf …

Assessing The Influence Of Riparian Invasion By The Shrub Lonicera Maackii On Terrestrial Subsidies To Headwater Streams, Erin C. Rowekamp, Julia I. Chapman, Ryan Mcewan

Biology Faculty Publications

Invasion of Amur honeysuckle (Lonicera maackii) into riparian areas of headwater streams creates strong potential for alterations of terrestrial subsidies that may drive bottom-up effects on aquatic biota. In this study, we analyzed effects of L. maackii on terrestrial subsidies in stream sites that represented a gradient of invasion intensity in temperate deciduous forests of southwestern Ohio (USA). Leaf litter biomass, terrestrial and aquatic fine woody debris (0.5–9.9 cm diameter) volume and count, and terrestrial and aquatic coarse woody debris (>9.9 cm diameter) volume were analyzed. Based on previous research, we hypothesized that sites with a higher …

Phospholipid Remodeling Via Exogenous Polyunsaturated Fatty Acid Uptake Modulates Stress Resistance In Vibrio Cholerae, William Strike

Honors Theses

Antibiotic-resistant pathogens represent an escalating threat to public health worldwide, substantially increasing the burden of healthcare and community-acquired infections. Several factors contribute to the emergence and spread of this threat, including but not limited to improper antibiotic use and prescriptions in health-care settings and the community, increasing global travel and migration from countries that have higher levels of antibiotic-resistant pathogens, and a lack of new antibiotics under development. According to the World Health Organization, rising rates of resistance among Gram-negative bacteria (such as Vibrio cholerae) are of particular concern. These bacteria have evolved a number of endogenous membrane remodeling strategies …

Development Of In Vitro Models To Study The Rapid Extraintestinal Dissemination Of Salmonella., Adarsh Gopinath

Electronic Theses and Dissertations

Salmonella appears in the bloodstream of mice in as little as 15 minutes after oral inoculation and establishes persistent colonies in the spleen and liver. While its pathway to blood is undetermined, this phenomenon is dependent on the activity of Salmonella pathogenicity island 2 (SPI-2) coded type III secretion system (T3SS) and CD18+ phagocytes. We hypothesize that dendritic cells associated with the basal face of the gut epithelium, that are naturally migratory and known to sample for luminal antigens directly transport Salmonella to the bloodstream. This process comprises of at least two phases, dissociation and reverse transmigration. We define dissociation …

Draft Genome Sequences Of Two Extensively Drug-Resistant Strains Of Acinetobacter Baumannii Isolated From Clinical Samples In Pakistan, Sara Lomonaco, Matthew A. Crawford, Christine Lascols, Debra J. Fisher, Kevin Anderson, David R. Hodge, Segaran P. Pillai, Stephen A. Morse, Erum Khan, Molly A. Hughes, Marc W. Allard, Shashi K. Sharma

Department of Pathology and Laboratory Medicine

Infections in immunocompromised patients that are caused by extensively drug-resistant (XDR) Acinetobacter baumannii strains have been increasingly reported worldwide. In particular, carbapenem-resistant A. baumannii strains are a prominent cause of health care-associated infections. Here, we report draft genome assemblies for two clinical XDR A. baumannii isolates obtained from hospitalized patients in Pakistan.

Soil Microbial Diversity And Litter Decomposition Increase With Time Since Land Use Disturbance In Tropical Montane Forests Of Malaysian Borneo, Renee Sniegocki

Graduate Theses and Dissertations

Logging and forest conversion are occurring at alarming rates in the tropical forests of Southeast Asia. These disturbances alter soil chemistry, microbial diversity, and disrupt carbon cycling through shifts in litter decomposition. Direct links between microbial diversity and soil properties such as pH are well established; however, the indirect impacts of logging and forest conversion on microbial diversity and litter decomposition are poorly understood. We used surface (5 cm) soil to assess soil physicochemical properties, next-generation DNA sequencing to assess soil microbial diversity, and standardized litterbags to assess litter decomposition stabilization at five sites along a land use disturbance gradient …

Tobacco Enhances Bacterial-Induced Periodontal Bone Loss In Mice., Mina Iskander

Electronic Theses and Dissertations

Background: Tobacco smoking is the leading environmental risk factor for periodontal diseases. Delineation of the mechanisms underlying tobacco-induced or exacerbated periodontitis is hampered by the lack of an appropriate and reliable animal model. Hypothesis: We hypothesized that Porphyromonas-gingivalis-infected, cigarette smoke-exposed mice would represent reproducible models of acute (ligature model) and chronic (oral gavage model) tobacco-enhanced periodontitis that reflect multiple aspects of the disease noted in human smokers. Methods: In a chronic oral gavage disease model, Balb/c mice (6-8 weeks, 4 groups of n = 6 per group) were exposed to smoke produced by a Teague-10 smoking machine from 1R6F research …

Toxicity Analysis Of 2’-Deoxyguanosine-N2-6-Aminopyrene And 2’-Deoxyguanosine-N2-8-Aminopyrene In Escherichia Coli, Emily Janeiro

Honors Scholar Theses

Cancer is a disease that stems from genomic errors that are not corrected properly by cellular repair mechanisms. Errors are more likely to form when organisms are subjected to DNA damage by mutagenic compounds. 1-Nitropyrene, a nitrated polycyclic aromatic hydrocarbon (nitro-PAH), has been shown to be a potent mutagen that causes cancer. Nitro-PAHs can arise from diesel exhaust products in the environment. Out of all nitro-PAHs, 1-nitropyrene is found in largest quantities in the environment. This poses a great need to study its effects biochemically in order to address its toxicity in DNA. Other nitropyrene derivatives, including 1,6-dinitropyrene and 1,8-dinitropyrene, …

Identification And Analysis Of Feather Degrading Bacteria: A Search For Keratinase Genes, Nehal Navali

Honors Scholar Theses

Over two million tons of feather waste is generated annually by the poultry industry, the majority of which goes into landfills due to the difficulty of degrading its major component keratin. Although a portion of feather waste is eliminated via incineration or chemical treatment, the use of Feather Degrading Bacteria (FDB) has been proposed as a cheap and eco-friendly alternative. FDBs have been consistently isolated from the feather microbiome of birds and contain genes coding for the specialized protein keratinase which is able to degrade feathers. By doing so, feather waste, which is rich in nutrients, can be repurposed as …

Antibiotic Resistant Bacteria, Antibiotic Resistance Genes And Potential Drivers In The Aquatic Environments, Shuo Shen

Dissertations

As antibiotic resistance genes in aquatic environment have been increasing across the world, affecting water quality and public health, many studies documented concentrations of antibiotic resistance genes and some studies discussed their potential drivers. However, systematic and quantitative reviews that link antibiotic resistance genes (ARGs) to anthropogenic and environmental factors are limited. Nevertheless, this information will be important for developing regulation policy on controlling antibiotic use and therefore reducing potential risks to antibiotic resistance. I conducted meta-analysis of ARGs concentration at a global scale using Bayesian inference to explore climatic and socio-economic factors as drivers. I found local-scale climatic variables …