Microbiology Commons^™

Cyclic Di-Gmp Regulates Motility, Biofilm Formation, And Desiccation Tolerance In Acinetobacter Baumannii, Garrett Reynolds

Electronic Theses and Dissertations

Acinetobacter baumannii is an increasingly multidrug-resistant pathogen contributing to hospital-acquired infections necessitating the discovery of novel treatments. A bacterial second messenger, cyclic diguanosine monophosphate (cyclic di-GMP), can regulate various persistence factors that are potentially advantageous for survival in hospital environments. Cyclic di-GMP–modulating enzymes and cyclic di-GMP–binding effectors predictively are encoded in the Acinetobacter baumannii genome. I hypothesized that cyclic di-GMP controls motility, biofilm formation, and desiccation tolerance in Acinetobacter baumannii. Disrupting cyclic di-GMP–modulating enzymes or cyclic di-GMP–binding effectors should alter the regulatory effectiveness of these phenotypes. I tested the multidrug-resistant isolate Acinetobacter baumannii strain AB5075 and identified several transposon …

Defining The Importance Of The Hnrnp I Interaction To The Sindbis Virus Subgenomic Viral Rna Using An Innovative Tethering Approach., Claire Westcott

Electronic Theses and Dissertations

Old World alphaviruses cause significant outbreaks of illness and debilitating multi-joint arthritis for prolonged periods. Currently, there are no FDA approved vaccines or antiviral therapies; and thus, there is a critical need to identify and characterize the molecular biology of alphaviruses. Alphaviruses rely on the host cell machinery to complete the viral lifecycle and are dependent on interactions with host RNA binding proteins. Accordingly, several host heterogenous nuclear ribonucleoprotein proteins (hnRNPs) have been found to bind to the Sindbis virus (SINV) RNAs. Disrupting the interaction sites in the viral RNAs of these RNA:Protein interactions results in decreased viral titers in …

The Effects Of Short Chain Fatty Acids On Clostridioides Difficile Growth, Sporulation, And Toxin Production, Michelle Baldassare

All Theses

Short chain fatty acids (SCFAs) are products of bacterial fermentation that help maintain important gut functions such as the intestinal barrier, signaling, and immune homeostasis. The main SCFAs acetate, propionate, and butyrate have demonstrated beneficial effects for the host, including importance in combatting infections caused by pathogens such as Clostridioides difficile. C. difficile infection (CDI) is a public health concern and causes 30,000 deaths each year mainly due to the overuse of antibiotics. Despite the potential role of SCFAs in mitigating C. difficile infection, their direct effect on C. difficile remains unclear. Through a set of in-vitro experiments, we …

Microbial, Chemical, And Functional Components In Kefir, Natto, And Feed Ingredients, Dana Mccurdy

All Dissertations

Kefir grains were purchased from online, home kitchen vendors in the United States (n = 22), inoculated into UHT milk, and incubated at 25°C for 22 hours. Results indicated lactobacilli, lactococci and yeast in all samples. Six out of 11 samples contained coliform, and all samples contained pseudomonal and staphylococcal species. Using targeted genome sequencing (16S) of kefir grain samples 1, 2, and 3 revealed that lactobacilli were the predominant genera of bacteria. ITS sequencing revealed different fungal species in each grain. Results indicated potential presence of menaquinone-4 and menaquinone-7 by UPLC-MS/MS analysis.

The fermentation of whole and ground soybeans, …

Habitability, And Evolution Of Microorganisms Under Extreme Conditions, Azarin Yazdani

Graduate Theses and Dissertations

The choice of a solvent determines the possible biochemistry of life. Life on Earth is based on carbon biochemistry and has evolved in an environment with water as a solvent. As a polar solvent abundant on Earth, water has unique physical properties, including a large range of liquidity and low viscosity, making it a very good solvent for terrestrial life. Liquids other than water are abundant in the universe, and the chemical nature of these liquids might lead to different chemistries of life. In the first chapter, we review the main characteristics of a good solvent, and then we use …

Genomic Analysis And Characterization Of Surface Properties Of Naphthalene Degrading Acinetobacter Isolates, Gunn Emilie Berge

Graduate Theses and Dissertations (2019 - present)

No abstract provided.

Allelopathic Effect Of Cereal Straw Extracts On Growth Of Raphidocelis Subcapitata And Microcystis Aeruginosa, Holly Wren

Graduate Theses and Dissertations

Harmful algal blooms are increasing in size, duration, and intensity around the globe. For several decades, cereal straws have been recognized as a viable algal control method, though the mechanisms by which cereal straws inhibit algae remain a topic of research. The objectives of this study were to evaluate the effectiveness of decomposing cereal straw extract, particularly rice (Oryza sativa) and barley (Hordeum vulgare) straw extract, to inhibit the green alga Raphidocelis subcapitata or cyanobacteria Microcystis aeruginosa in bioassays and to determine if the effectiveness of decomposing rice straw extract is altered by the presence of natural organic matter or …

Chondronecrosis With Osteomyelitis In Broilers: Bacterial Species Involvement And Influence Of Probiotics And Synbiotics, Amer Abdullah Hasan

Graduate Theses and Dissertations

Since 1945, the market for broiler production has evolved from a collection of smallholder poultry farms into an industry worth billions of dollars. Poultry production has not gone without challenges. Lameness in young broilers is presently a serious issue in the poultry industry for reasons of animal health and welfare, as well as significant lost production and revenue. Bacterial chondronecrosis with osteomyelitis (BCO) is a major form of lameness in broilers. This dissertation contains information about (i) the influence of Staphylococcus agnetis, Staphylococcus saprophyticus, Staphylococcus epidermidis and Enterococcus faecalis on inducing BCO lameness, (ii) evaluation of of probiotics for reducing …

Bacterial Chondronecrosis With Osteomyelitis In Broilers: Genomics, Phylogenomics, And Methods To Detect Specific Pathogens During Outbreaks., Abdulkarim Abdulaziz A. Shwani

Graduate Theses and Dissertations

Lameness is a major issue in animal welfare and the broiler industry. Bacterial chondronecrosis with osteomyelitis (BCO) is one of the main causes of lameness. Many staphylococcal species, including Staphylococcus agnetis isolate 908, have been isolated from the bones and blood of lame broilers at the University of Arkansas. Staphylococcus agnetis is a coagulase-variable, Gram-positive bacterial species that has been previously associated with subclinical or mild clinical cases of mastitis in dairy cattle. The annotated complete genome of hypervirulent strain 908 was published at NCBI. In this study, it has been compared to nine genomes we assembled for hypervirulent isolates …

Sorption Of Cellulases In Biofilm Enhances Cellulose Degradation By Bacillus Subtilis, Yijie Deng, Shiao Y. Wang

Faculty Publications

Biofilm commonly forms on the surfaces of cellulosic biomass but its roles in cellulose degradation remain largely unexplored. We used Bacillus subtilis to study possible mechanisms and the contributions of two major biofilm components, extracellular polysaccharides (EPS) and TasA protein, to submerged biofilm formation on cellulose and its degradation. We found that biofilm produced by B. subtilis is able to absorb exogenous cellulase added to the culture medium and also retain self-produced cellulase within the biofilm matrix. The bacteria that produced more biofilm degraded more cellulose compared to strains that produced less biofilm. Knockout strains that lacked both EPS and …

Salivary Biomarker Evaluation Of Chronic Pancreatitis Patients Reveals Alterations In Human Proteins, Cytokines, Prostaglandin E2 Levels, And Bacterial Diversity, Richard T Waldron, Elaina K Jones, Vincent I Anani, Jolaine M Hines, Jing Zhao, Aurelia Lugea, Marcio A Diniz, Sungjin Kim, Aida Habtezion, Kristi L Hoffman, Joseph F Petrosino, William E Fisher, Liang Li, Ryan J Lennon, Ravinder Jit Singh, Santhi Swaroop Vege, Stephen J Pandol, Mark D Topazian

Faculty, Staff and Students Publications

OBJECTIVES: Chronic pancreatitis (CP) is a chronic fibroinflammatory condition of the pancreas difficult to diagnose in early stages. Novel biomarkers useful to facilitate early diagnosis or treatment responses may be found in biofluids. Although saliva can be easily and noninvasively collected from patients, useful salivary biomarkers from CP patients have not yet been identified.

METHODS: Here, we analyzed the proteome by quantitative proteomics, cytokine/chemokine levels by Luminex analysis, prostaglandin E2 (PGE2) levels by a mass spectrometry-based assay, and bacterial species diversity by 16S ribosomal ribonucleic acid sequencing in saliva samples from confirmed CP patients and healthy controls.

RESULTS: Our results …

An Overview Of The Extracurricular Polysaccaride Production Of Probiotic Lactic Acid Bacteria, Olujimi Babajide Olowokere

Theses (2016-Present)

The study focuses on a comprehensive review of lactic acid bacteria and their production of extracellular polysaccharide substrates (EPS). Two important factors are addressed in the work; and these are 1) identification of LAB stains found in the commercially sold daily milk, 2) significant factors impacting polysaccharide production. Motivation behind these focus points is to allow further inquiries and studies on exploring these strains of bacteria for human wellness promotion. With microbial EPS production being a recent interest of study among healthcare and food industries sectors, new species of bacteria are extensively exploited for further investigation to improve human health, …

Genomic And Functional Characterization Of Vancomycin-Resistant Enterococci-Specific Bacteriophages In The Galleria Mellonella Wax Moth Larvae Model, Lynn El Haddad, Georgios Angelidakis, Justin R Clark, Jesus F Mendoza, Austen L Terwilliger, Christopher P Chaftari, Mark Duna, Serena T Yusuf, Cynthia P Harb, Mark Stibich, Anthony Maresso, Roy F Chemaly

Faculty, Staff and Students Publications

Phages are naturally occurring viruses that selectively kill bacterial species without disturbing the individual’s normal flora, averting the collateral damage of antimicrobial usage. The safety and the effectiveness of phages have been mainly confirmed in the food industry as well as in animal models. In this study, we report on the successful isolation of phages specific to Vancomycin-resistant Enterococci, including Enterococcus faecium (VREfm) and Enterococcus faecalis from sewage samples, and demonstrate their efficacy and safety for VREfm infection in the greater wax moth Galleria mellonella model. No virulence-associated genes, antibiotic resistance genes or integrases were detected in …

Identification Of Microorganisms From The Depths Of Wind Cave, Abbie Bangs, Justin Peters Ph.D., Joshua Sebree Ph.D.

Summer Undergraduate Research Program (SURP) Symposium

During 2022, samples were collected at Wind Cave National Park on three different trips. As the team goes deeper and deeper into the cave, the goal is to actively trace the types of microorganisms (fungi, bacteria, and archaea) throughout the cave. The process to obtain species level identification of these samples utilizes PCR amplification of different sections of their genomic DNA followed by sequencing analysis. An initial phylogenetic tree showing relatedness of the identified microorganisms is presented.

Exploring Microbes At Wind Cave As An Analog For Exobiological Environments Off Earth, Abby K. Sliwiniski, Emma W. Pellegrino, Nicole Geerdes, Marek K. Sliwinski

Summer Undergraduate Research Program (SURP) Symposium

Subterranean environments on Earth serve as an analog for the study of microbes on other planets. This has become an active area of research with the discovery of exoplanets. To learn about the microbial species living in Wind Cave, we are comparing methods to sample environmental DNA because most microbes cannot be cultivated using standard laboratory methods. We are then probing the environmental DNA with broad primers that are designed to amplify most life and narrower primers such as those specific to the domain Archaea. Of the methods compared, the Qiagen DNeasy Powerbiofilm kit produced the purest template as measured …

Arsr Family Regulator Msmeg_6762 Mediates The Programmed Cell Death By Regulating The Expression Of Hnh Nuclease In Mycobacteria, Xiangke Duan, Xue Huang, Junqi Xu, Xue Li, Jingjing Niu, Xiaoli Du, Xiaoyu Wang, Jiang Li, Michael Kelly, Jiaohan Guo, Ke Zhang, Yu Huang, Biao Kan, Jianping Xie

Biology Student Work

Programmed cell death (PCD) is the result of an intracellular program and is accomplished by a regulated process in both prokaryotic and eukaryotic organisms. Here, we report a programed cell death process in Mycobacterium smegmatis, an Actinobacteria species which involves a transcription factor and a DNase of the HNH family. We found that over-expression of an ArsR family member of the transcription factor, MSMEG_6762, leads to cell death. Transcriptome analysis revealed an increase in the genes’ transcripts involved in DNA repair and homologous recombination, and in three members of HNH family DNases. Knockout of one of the DNase genes, MSMEG_1275, …

Growth Outcomes Of Pseudomonas Aeruginosa Inhibitor Of Vertebrate Lysozyme Knockouts In Conditions Mimicking The Cystic Fibrosis Lung Environment, Amani Gaddy

Master of Science in Chemical Sciences Theses

Pseudomonas aeruginosa (PA) is a Gram-negative bacterium, often found in cystic fibrosis (CF) patients and can lead to the decline of lung functioning and premature death in 80% of infected patients when microcolonies form within the mucin of the lung. Due to its major capacity for antibiotic resistance, an alternative strategy towards defending against the bacterial invasion of PA is by the antibacterial activity of our own innate immune system with use of elements such as lysozyme. Pseudomonas aeruginosa inhibitor of vertebrate lysozyme class 1 (Ivyp1) is a periplasmic protein produced by gram-negative bacteria that inhibits the enzymatic activity of …

Using Dietary Additives To Improve Palatability Of Diets Containing Single‐Cell Protein From Methanotrophic Bacteria In Yellowtail Kingfish (Seriola Lalandi) Diets, Luke Pilmer, Lindsey Woolley, Alan J. Lymbery, Michael Salini, Gavin Partridge

Fisheries Research Articles

Single-cell protein (SCP) derived from methanotrophic bacteria has significant potential as a fishmeal alternative in aquafeeds. However, SCP has known palatability issues, to overcome these issues tuna hydrolysate and garlic powder were tested as palatability enhancers against basal diets without these additives. This study tested the inclusion of SCP at four dietary levels of 0%, 10%, 20% and 30%, representing 0%, 25%, 50% and 75% fishmeal replacement in juvenile yellowtail kingfish (Seriola lalandi) (YTK) diets. YTK were fed these diets in triplicate over 35 days. Compared with the control diet, fish fed the SCP10% diet ate less feed, …

Analysis Of Geographic Variability Of Fecal Microbiomes Of Fratercula Arctica And Cross-Comparison Of Fecal Microbiomes Of Different Avian Feeding Types, Eric Jose Ramon Martinez

LSU Master's Theses

Gastrointestinal (gut) microbiota have a multitude of effects on their host, from aiding in digestion, to facilitating nutrient uptake, detoxification, and interactions with the immune system. Multiple factors have been identified that influence the composition of vertebrate microbiomes; these include host genetics, environmental conditions, diet and age, sex, and geography. However, broad inferences about wild avian gut microbial diversity and function under natural conditions are limited. Most knowledge on avian microbiomes is derived from studies on domestic poultry. Information on non-model taxa may provide important contextual information about vertebrate host-microbiome interactions and aid in future management of vulnerable species. Here, …

Tissue Decay Tested In Modern Metasequoia Leaves: Implications For Early Diagenesis Of Leaves In Fossil Lagerstätten, Caitlyn R. Witkowski, Qin Leng, Christopher W. Reid, Liang Feng, Hong Yang

Science and Technology Department Faculty Journal Articles

Sedimentary deposits yielding extraordinarily-preserved fossils (known as Lagerstätten) may provide significant insights into the physiology and environments of ancient plants, particularly when the fossils represent their original characteristics with limited diagenetic modifications. To better understand molecular, isotopic, and morphological changes during the early stages of diagenesis, degradation experiments were conducted in two time series: 1) a laboratory decay series using fungi on leaves over the course of a month and 2) a natural decay series with leaves collected from different stages of leaf senescence and early diagenesis. Both experiments used modern leaves of the dawn redwood Metasequoia glyptostroboides …