Organisms Commons^™

Bacterial Association Networks From Healthy And Cancer-Associated Gut Microbiomes, Mark Loftus

Electronic Theses and Dissertations, 2020-2023

The human gastrointestinal tract is colonized by a diverse community of symbiotic microorganisms, mainly bacteria, that are known to play essential roles in maintaining the health of their human host. Disruption of this bacterial community has been associated with numerous diseases, including Colorectal Cancer (CRC). CRC is one of the leading causes of cancer-related deaths worldwide. As such, focus has been placed on the modulation of the bacterial community within the cancer-associated gut microbiome as the next step in possible CRC treatment and prevention strategies. To use the bacterial community for these purposes, a better understanding of the associations that …

Advancing Cyanobacteria Biomass Estimation From Hyperspectral Observations: Demonstrations With Hico And Prisma Imagery, Ryan E. O'Shea, Nima Pahlevan, Brandon Smith, Mariano Bresciani, Todd Egerton, Claudia Giardino, Lin Li, Tim Moore, Antonio Ruiz-Verdu, Steve Ruberg, Stefan G.H. Simis, Richard Stumpf, Diana Vaičiūtė

Biological Sciences Faculty Publications

Retrieval of the phycocyanin concentration (PC), a characteristic pigment of, and proxy for, cyanobacteria biomass, from hyperspectral satellite remote sensing measurements is challenging due to uncertainties in the remote sensing reflectance (∆R_rs) resulting from atmospheric correction and instrument radiometric noise. Although several individual algorithms have been proven to capture local variations in cyanobacteria biomass in specific regions, their performance has not been assessed on hyperspectral images from satellite sensors. Our work leverages a machine-learning model, Mixture Density Networks (MDNs), trained on a large (N = 939) dataset of collocated in situ chlorophyll-a concentrations (Chla), …

Comparisons Of Oral, Intestinal, And Pancreatic Bacterial Microbiomes In Patients With Pancreatic Cancer And Other Gastrointestinal Diseases, Mei Chung, Naisi Zhao, Richard Meier, Devin C. Koestler, Guojun Wu, Erika De Castillo, Bruce J. Paster, Kevin Charpentier, Jacques Izard, Karl T. Kelsey, Dominique S. Michaud

Department of Food Science and Technology: Faculty Publications

Background: Oral microbiota is believed to play important roles in systemic diseases, including cancer. Methods: We collected oral samples (tongue, buccal, supragingival, and saliva) and pancreatic tissue or intestinal samples from 52 subjects, and characterized 16S rRNA genes using high-throughput DNA sequencing.

Results: Bray–Curtis plot showed clear separations between bacterial communities in the oral cavity and those in intestinal and pancreatic tissue samples. PERMANOVA tests indicated that bacterial communities from buccal samples were similar to supragingival and saliva samples, and pancreatic duct samples were similar to pancreatic tumor samples, but all other samples were significantly different from each …

Utilizing The Coughing Rat Model Of Pertussis To Improve Vaccine Efficacy, Jesse M. Hall

Graduate Theses, Dissertations, and Problem Reports (ETD)

Pertussis, also known as whooping cough, is a respiratory disease caused by the highly contagious, Gram-negative pathogen Bordetella pertussis (Bp). Infection occurs through inhalation of aerosolized droplets containing Bp, which then colonizes ciliated epithelial cells of the respiratory tract. Here, Bp expresses toxins and virulence factors that lead to leukocyte recruitment, paroxysmal cough, and impairment of host innate responses. Currently, in developed countries, acellular pertussis vaccines (aP; DTaP; Tdap) are used to prevent Bp infection and whooping cough disease. However, we currently realize that the aP vaccine efficacy quickly wanes resulting in a reemergence of pertussis. Recent …

Dendrimer-Based Antibiotics For The Treatment Of Bacterial Biofilm In Cystic Fibrosis (Cf), Younan Ma

Theses and Dissertations

Pseudomonas aeruginosa (PA) is the predominant pathogen in chronic lung infections of cystic fibrosis (CF) patients. The most important mechanism of adaptation of PA to host defense and antibiotic treatment is the formation of biofilms within the mucus layer covering the lung bronchi. The effectiveness of antibiotics such as aminoglycosides is significantly attenuated by their limited penetration through thick mucus and embedded biofilm matrix in patients’ lung. Inhaled tobramycin (Tobra), which is the most commonly used antibiotics in the treatment of PA infections for CF patients, is usually found to be in very high concentration in patients’ lung, and yet …

A Microbiome Analysis Of The Relationship Among Crayfish Ectosymbionts And Their Environment, John Hoverson

Senior Honors Theses

The purpose of this project was to determine if there are differences present between the α-diversities of the crayfish microbiome and its surrounding water and sediment. Furthermore, this project sought to discover if these differences hold when microbiomes are evaluated between crayfish of first and second stream orders. Finally, this project sought to determine if the presence of branchiobdellidan ectosymbionts on the crayfish caused further differences in the crayfish microbiome. While the hypothesized patterns between crayfish, ectosymbionts, and stream order were not found to exist, a significantly different microbiome was observed between water, sediment, and crayfish, and the α-diversity of …

Increasing Antibiotic Resistance In Shigella Bacteria In The United States, William J. Pharr

The Corinthian

Shigella bacteria cause half a million infections, 6,000 hospitalizations, and 70 deaths annually in the United States. These bacteria are of particular concern due to their high survivability, low infectious dose, and high adaptability. Cases of shigellosis from Shigella sonnei are becoming a more prevalent issue in the U.S. as the bacteria continues to develop higher resistance to today’s strongest antibiotics. Much of this resistance is connected to the exchange of genes between strains of Shigella due to insertion sequences (IS), intercontinental travel, and men who have sex with men (MSM). As a result of increased resistance, the use of …

Author Correction: Roadmap For Naming Uncultivated Archaea And Bacteria (Nature Microbiology, (2020), 5, 8, (987-994), 10.1038/S41564-020-0733-X), Alison E. Murray, John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, Peter Kämpfer, Konstantinos T. Konstantinidis, Christopher E. Lane, R. Thane Papke, Donovan H. Parks, Ramon Rossello-Mora, Matthew B. Stott, Iain C. Sutcliffe, J. Cameron Thrash, Stephanus N. Venter, William B. Whitman, Silvia G. Acinas, Rudolf I. Amann, Karthik Anantharaman, Jean Armengaud, Brett J. Baker, Roman A. Barco, Helge B. Bode, Eric S. Boyd, Carrie L. Brady, Paul Carini, Patrick S.G. Chain, Daniel R. Colman, Kristen M. Deangelis, Maria Asuncion De Los Rios, Paulina Estrada-De Los Santos

Life Sciences Faculty Research

No abstract provided.

Investigating Microbial And Host Factors That Modulate Severity Of Clostridioides Difficile Associated Disease, Armando Lerma

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Clostridioides difficile is recognized as one of the most important pathogens in hospital and community healthcare settings. The clinical outcome of infection of toxigenic C. difficile infection (CDI) ranges from asymptomatic colonization to fulminant pseudomembranous colitis and death. In recent studies, it has been suggested that a high proportion of nosocomial CDI cases are transmitted from asymptomatic carriers which might be acting as infection reservoirs. Understanding what causes the different responses to infection could lead to the development of novel prevention and treatment strategies. Although several explanations have been proposed to explain variations in susceptibility, understanding of the exact mechanisms …

Response Of Extensively Drug Resistant Salmonella Typhi To Treatment With Meropenem And Azithromycin, In Pakistan, Sonia Qureshi, Abdullah B. Naveed, Mohammad Tahir Yousafzai, Khalil Ahmad, Sarwat Ansari, Heeramani Lohana, Aiman Mukhtar, Farah Naz Qamar

Department of Paediatrics and Child Health

Introduction: Salmonella Typhi is one of the leading health problems in Pakistan. With the emergence of extensively drug resistant (XDR) Salmonella Typhi, treatment options are limited. Here we report the clinical manifestations and the response to treatment of patients with XDR Typhoid fever. The patients were treated with either Meropenem or Azithromycin or a combination of both.
Methods: We reviewed the records of culture confirmed XDR typhoid who visited Aga Khan University Hospital (AKUH), Karachi and Aga Khan Secondary Care Hospital, Hyderabad from April 2017 to June 2018. Symptoms developed during disease, unplanned treatment extension and complications developed while on …

Vitamin D In Covid-19 Pneumonia: High Yield With Low Risk, Shahan Waheed, Emaduddin Siddiqui

Department of Emergency Medicine

No abstract provided.

The Inhibitory Effects Of An Antimicrobial Gel On The Staphylococcus Species, Mara Trinkle

Undergraduate Honors Theses

The prevalence of antibiotic resistant bacteria has made the choices for topical treatments for patients who experience burns wounds extremely limited. The Staphylococcus genus is naturally occurring in and on the human body but can become harmful once it enters the bloodstream. A novel antimicrobial gel has been shown by our laboratory to inhibit both the planktonic growth and biofilm formation of Staphylococcus aureus in previous studies. The antimicrobial gel is made of seven natural compounds including antioxidants (vitamin C and E). We wanted to examine the effects of the antimicrobial gel on numerous other Staphylococcal species because it is …

Plasmodium Impairs Antibacterial Innate Immunity To Systemic Infections In Part Through Hemozoin-Bound Bioactive Molecules., Christopher Lynn Harding

Electronic Theses and Dissertations

Despite efforts to decrease the global health burden of malaria, infections with Plasmodium species continue to cause over 200 million episodes of malaria each year which resulted in 405,000 deaths in 2018 [1]. One complication of malaria is increased susceptibility to invasive bacterial infections. Plasmodium infections impair host immunity to non-Typhoid Salmonella (NTS) through activities of heme oxygenase I (HO-I) )-induced release of immature granulocytes and myeloid cell-derived IL-10. Yet, it is not known if these mechanisms are specific to NTS. We show here, that Plasmodium yoelii 17XNL (Py) infected mice had impaired clearance of systemic Listeria monocytogenes (Lm) during …

Utility Of Molecular Tools For The Identification And Characterization Of Infectious Agents, Shih Keng Loong

Student Works (2020-2029)

Molecular tools involving nucleic acid sequence-based detection offer rapid, sensitive and specific identification of bacterial infections, all together instrumental in timely patient management and infection control. Analyses of DNA sequences played a pivotal role in the discovery of novel or uncommon bacterial pathogens. This method can be applied to detect and identify rare and potentially pathogenic bacterial infectious diseases emerging from the interactions between human, animal and the environment. In this study, the 16S rDNA sequencing demonstrated superior utility against the conventional phenotypic identification systems for the identification of rare pathogenic bacteria. Its inability to differentiate between certain bacterial species …

A Race Against Time: Reduced Azithromycin Susceptibility In Salmonella Enterica Serovar Typhi In Pakistan, Junaid Iqbal, Irum Fatima Dehraj, Megan E. Carey, Zoe A. Dyson, Denise Garrett, Jessica C. Seidman, Furqan Kabir, Senjuti Saha, Stephen Baker, Farah Naz Qamar

Department of Paediatrics and Child Health

Antimicrobial resistance is an ongoing issue in the treatment of typhoid fever. Resistance to first-line antimicrobials and extensively drug resistant (XDR) Salmonella Typhi isolates in Pakistan have left azithromycin as the only remaining effective oral treatment. Here, we report the emergence of organisms with a single point mutation in acrB gene, implicated in azithromycin resistance, in a S. Typhi isolate from Pakistan. The isolation of this organism is worrisome and highlights the significance of the introduction of typhoid conjugate vaccine in South Asia.
Importance: The emergence of XDR Salmonella Typhi in Pakistan has left azithromycin as the only viable oral …

Genomic Diversity Of Bacteriophages Infecting Microbacterium Spp, Deborah Jacobs-Sera, Lawrence A. Abad, Richard M. Alvey, Kirk R. Anders, Haley G. Aull, Suparna S. Bhalla, Lawrence S. Blumer, David W. Bollivar, J. Alfred Bonilla, Kristen A. Butela, Roy J. Coomans, Steven G. Cresawn, Tom D'Elia, Arturo Diaz, Ashley M. Divens, Nicholas P. Edgington, Gregory D. Frederick, Maria D. Gainey, Rebecca A. Garlena, Kenneth W. Grant, Susan M.R. Gurney, Heather L. Hendrickson, Lee E. Hughes, Margaret A. Kenna, Karen K. Klyczek, Hari Kotturi, Travis Mavrich, Angela L. Mckinney, Evan C. Merkhofer, Jordan Moberg Parker, Sally D. Molloy

Life Sciences Faculty Research

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, …

Fecal Microbiota Transplantation And Gut Microbiome Effects On Psychiatric Illnesses, Mona Seresht

Physician Assistant Studies | Student Authored Articles

Despite the medical advances that have been made in regards to mental health, psychiatric medications, and alternative therapies, many patients continue to suffer day in and day out, unable to live the type of life they desire. Many times, the medication route includes many episodes of trial and error, side effects, and no significant improvement in actual symptoms. Therapy, although effective, typically necessitates a supplemental medication for the best results. Fecal microbiota transplantation (FMT) is a method where feces from a healthy donor is transferred to an affected patient, typically via colonoscopy. Theoretically, this alters the gut microbiome in a …

Multicenter Clinical Evaluation Of The Revogene Strep A Molecular Assay For Detection Of Streptococcus Pyogenes From Throat Swab Specimens, Dithi Banerjee, Jeff Michael, B. Schmitt, H. Salimnia, N. Mhaissen, D. M. Goldfarb, P. Lachance, M. L. Faron, T. Aufderheide, N. Ledeboer, A. Weissfeld, Rangaraj Selvarangan

Manuscripts, Articles, Book Chapters and Other Papers

Copyright © 2020 Banerjee et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license Group A streptococcus (GAS) species cause bacterial pharyngitis in both adults and children. Early and accurate diagnosis of GAS is important for appropriate antibiotic therapy to prevent GAS sequalae. The Revogene Strep A molecular assay (Meridian Bioscience Canada Inc, Quebec City, QC, Canada) is an automated real-time PCR assay for GAS detection from throat swab specimens within approximately 70 min. This multicenter prospective study evaluated the performance of the Revogene Strep A molecular assay compared to that …

Identifying Determinants Of Target Specificity In Two Related Bacterial Peptide Toxins, Andrew D. Holmes

Honors Thesis

Toxin-antitoxin (TA) systems were originally identified as two-component systems ensuring the stable inheritance of plasmids in bacterial populations. Recently, they have been identified on bacterial chromosomes where their functions remain mostly undefined. The par locus of E. faecalis plasmid pAD1 (par_pAD1) was the first TA system defined in a Gram-positive bacterium and a homolog encoded on the E. faecalis chromosome (par_EF0409) was later described. Related loci numbering in the hundreds have been identified throughout Gram-positive bacteria based on homology to the toxin of the system, Fst, and similarities in genetic organization and regulation. Despite …

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, …

Hexadecane Petroleum, And Biofuel Utilization In Marine Bacteria Isolated From Ballast Tanks, Alex Yashchenko

Graduate Theses

This study characterized the growth of bacteria isolated from ballast tank fluids in hexadecane, petroleum, plant, and algae-derived fuels. The study was performed to explore the capacity of ballast tank isolates to survive and grow within fuels that may be stored within ballast tanks. Results of the hexadecane analysis indicated that most isolates had higher viable cell counts in media supplemented with hexadecane. Members of Alteromonas, Pseudoalteromonas, and a single Brevundimonas species had viable cell counts that were one or several orders ofmagnitude greater than that of controls. Results offuel analysis indicated higher viable cell counts in pure JP-5 and …

Fatty Acid Mediated Alterations In Biofilm Formation With Vibrio Cholerae, Isabel Gray

Honors Theses

Vibrio cholerae is a Gram-negative bacterium known as a waterborne pathogen. It is often found in marine conditions and can infect humans through ingestion. V. cholerae is responsible for cholera, a disease characterized by profuse diarrhea, vomiting, and other dehydration symptoms. Ultimately, severe cases can cause extreme electrolyte imbalances, shock, and acute renal failure which lead to death in a short period of time. Annually, V. cholerae causes approximately 3 million cases of cholera and 100,000 deaths worldwide. V. cholerae can persist in motile and biofilm lifestyles under aquatic and host conditions, a unique biphasic lifestyle that contributes to Vibrio’s …

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 …

The Effect Of Alcaligenes Faecalis On Inhibition Of Candida Albicans Biofilm And Planktonic Growth, Nausheen A. Siddiqui

Undergraduate Honors Theses

Candida albicans is a fungal microorganism found on the human body and in the environment. An opportunistic pathogen causing local and systemic infection, this fungus is one of the leading causes of nosocomial infections. More alarming is its growing resistance against the limited number of antifungals we have for treatment Candida infections. An area of current research, termed polymicrobial interactions, focuses on how different microorganisms interact with each other for limited space, nutrients, and survival. The current study focuses on attempting to inhibit planktonic and biofilm growth stages by using the benign bacterium Alcaligenes faecalis, previously shown in our …

Bacterial Load In Virtual Reality Headsets, Benjamin Creel

Honors Theses

Virtual reality technology is a rapidly growing field of computer science. Virtual reality utilizes headsets which cover the user’s eyes, nose, and forehead. In this study, I analyzed the potential for these headsets to become contaminated with bacteria. The nosepieces and foreheads of two HTC Vive VR headsets of the Department of Computer Science of the University of Mississippi were sampled over the course of a seven-week Immersive Media (CSCI 447) course. Serial dilutions were performed, and samples were plated on various culture media. Following incubation, counts of bacteria were determined. DNA was extracted from bacterial growth on plates from …

Epidemiologic Survey Of Legionella Urine Antigen Testing Within A Large Wisconsin-Based Health Care System, Caroline P. Toberna, Hannah M. William, Jessica J. F. Kram, Kayla Heslin, Dennis J. Baumgardner

Journal of Patient-Centered Research and Reviews

Purpose: Legionella pneumophila pneumonia is a life-threatening, environmentally acquired infection identifiable via Legionella urine antigen tests (LUAT). We aimed to identify cumulative incidence, demographic distribution, and undetected disease outbreaks of Legionella pneumonia via positive LUAT in a single eastern Wisconsin health system, with a focus on urban Milwaukee County.

Methods: A multilevel descriptive ecologic study was conducted utilizing electronic medical record data from a large integrated health care system of patients who underwent LUAT from 2013 to 2017. A random sample inclusive of all positive tests was reviewed to investigate geodemographic differences among patients testing positive versus negative. Statistical comparisons …

Biological Sex Influences Susceptibility To Acinetobacter Baumannii Pneumonia In Mice, Sílvia Pires, Adeline Peignier, Jeremy Seto, Davida S. Smyth, Dane Parker

Publications and Research

Acinetobacter baumannii (A. baumannii) is an extremely versatile multidrug-resistant pathogen with a very high mortality rate; therefore, it has become crucial to understand the host response during its infection. Given the importance of mice for modeling infection and their role in preclinical drug development, equal emphasis should be placed on the use of both sexes. Through our studies using a murine model of acute pneumonia with A. baumannii, we observed that female mice were more susceptible to infection. Likewise, treatment of male mice with estradiol increased their susceptibility to infection. Analysis of the airway compartment revealed enhanced inflammation and reduced …

Impacts On Fitness Associated With Acquisition Of Gut Microbiota In Drosophila, Corinne Topolski

Honors Projects

Drosophila melanogaster is a model organism that has been studied to demonstrate the role of gut microbiota in fitness. It has already been established the gut microbiota is extremely important for the health of the organism, but the source of the microbiota has not been studied as thoroughly. In order to test if the source of microbiota affects the fitness of the individual, adult male and female flies were placed onto plates to defecate after being raised on standard food and food with carbenicillin. Stock eggs were washed in either water or a bleach solution, then placed on the defecation …

Detection And Quantification Of Bacterial Species Important To Mental And Physical Health, David G. Leonard

Theses and Dissertations

The human gut microbiome contains an abundance of microorganisms which could influence mental health as well as physical health. These microorganisms produce chemicals which affect the brain and the body in various ways. Probiotic bacteria and yeasts have been studied to determine effects they have on mice, rats, and humans to illustrate the importance these microorganisms on health. Studies have shown that adding beneficial microorganisms to the human diet can have positive effects on mental and physical health, to include lessening symptoms of depression and anxiety, lessen gastrointestinal inflammation, displacing pathogens, and improving immunomodulatory response. A quantitative way to identify …