Microbiology Commons^™

Microbial Stimulation Of Oxytocin Release From The Intestinal Epithelium Via Secretin Signaling, Heather A Danhof, Jihwan Lee, Aanchal Thapa, Robert A Britton, Sara C Di Rienzi

Faculty, Staff and Students Publications

Intestinal microbes impact the health of the intestine and organs distal to the gut. Limosilactobacillus reuteri is a human intestinal microbe that promotes normal gut transit, the anti-inflammatory immune system, wound healing, normal social behavior in mice, and prevents bone reabsorption. Oxytocin impacts these functions and oxytocin signaling is required for L. reuteri-mediated wound healing and social behavior; however, the events in the gut leading to oxytocin stimulation and beneficial effects are unknown. Here we report evolutionarily conserved oxytocin production in the intestinal epithelium through analysis of single-cell RNA-Seq datasets and imaging of human and mouse intestinal tissues. Moreover, …

Development Of Novel Methods To Study Host-Microbe Interactions In The Larval Zebrafish Gastrointestinal Tract, Anh K. Trinh Nguyen

Dissertations and Theses (Open Access)

The dynamic nature and inaccessible location of the intestine pose significant challenges to the study of intestinal physiology and pathology. Zebrafish larvae, possessing optical transparency and genetic tractability, offer an accessible and clinically relevant model for investigating dynamic events in the intestine via time-lapse imaging. In the first part of this work, I discuss our efforts to optimize the parameters of a foodborne infection assay using paramecia as a vehicle. This method provides an effective, high-throughput alternative to infection via immersion or oral gavage, and replicates the most common route of transmission of gastrointestinal (GI) infection in humans. The foodborne …

The Developmental Process For Adenoviral Vectored Canine Influenza Vaccines, Nicholas Jeanjaquet

School of Biological Sciences: Dissertations, Theses, and Student Research

Canine Influenza Virus (CIV) is a recently emerged branch of Influenza A virus that is highly infectious in dogs. The first strain was isolated in 2003, and it has quickly become endemic in areas with dense dog populations, most notably in Asia. The proximity of dogs to humans, along with their potential to serve as mixing vessels for reassortment, raises concern for possible zoonotic transmission and a potential human pandemic. Available vaccines are not frequently updated and struggle to prevent the spread of currently circulating strains. This highlights the need for a new and more effective vaccine. We outline the …

Lactic Acid Bacterial Surface Display Of Scytovirin Inhibitors For Anti-Ebolavirus Infection, Joshua Wiggins, Ngan Nguyen, Wenzhong Wei, Leah Liu Wang, Haley Hollingsead Olson, Shi-Hua Xiang

Nebraska Center for Virology: Faculty Publications

Scytovirin (SVN) is a lectin from cyanobacteria which has a strong inhibitory activity against Ebola virus infection. We engineered scytovirin as the inhibitor for surface display of lactic acid bacteria to block Ebola virus infection. Two different bacterial strains (Lactobacillus casei and Lactococcus lactis) were successfully engineered for scytovirin expression on the bacterial surface. These bacteria were found to be effective at neutralizing pseudotyped Ebolavirus in a cell-based assay. This approach can be utilized for prophylactic prevention, as well as for treatment. Since lactic acid bacteria can colonize the human body, a long-term efficacy could be achieved. Furthermore, …

Distinct Transcriptomic Profiles In Children Prior To The Appearance Of Type 1 Diabetes-Linked Islet Autoantibodies And Following Enterovirus Infection, Jake Lin, Elaheh Moradi, Karoliina Salenius, Suvi Lehtipuro, Tomi Häkkinen, Jutta E Laiho, Sami Oikarinen, Sofia Randelin, Hemang M Parikh, Jeffrey P Krischer, Jorma Toppari, Åke Lernmark, Joseph F Petrosino, Nadim J Ajami, Jin-Xiong She, William A Hagopian, Marian J Rewers, Richard E Lloyd, Kirsi J Rautajoki, Heikki Hyöty, Matti Nykter, Teddy Study Group

Faculty, Staff and Students Publications

Although the genetic basis and pathogenesis of type 1 diabetes have been studied extensively, how host responses to environmental factors might contribute to autoantibody development remains largely unknown. Here, we use longitudinal blood transcriptome sequencing data to characterize host responses in children within 12 months prior to the appearance of type 1 diabetes-linked islet autoantibodies, as well as matched control children. We report that children who present with insulin-specific autoantibodies first have distinct transcriptional profiles from those who develop GADA autoantibodies first. In particular, gene dosage-driven expression of GSTM1 is associated with GADA autoantibody positivity. Moreover, compared with controls, we …

Vaginal Microbial Dynamics And Pathogen Colonization In A Humanized Microbiota Mouse Model, Marlyd E Mejia, Vicki Mercado-Evans, Jacob J Zulk, Samantha Ottinger, Korinna Ruiz, Mallory B Ballard, Stephanie W Fowler, Robert A Britton, Kathryn A Patras

Faculty, Staff and Students Publications

Vaginal microbial composition is associated with differential risk of urogenital infection. Although Lactobacillus spp. are thought to confer protection against infection, the lack of in vivo models resembling the human vaginal microbiota remains a prominent barrier to mechanistic discovery. Using 16S rRNA amplicon sequencing of C57BL/6J female mice, we found that vaginal microbial composition varies within and between colonies across three vivaria. Noting vaginal microbial plasticity in conventional mice, we assessed the vaginal microbiome of humanized microbiota mice (

A Novel Subcluster Of Closely Related Bacillus Phages With Distinct Tail Fiber/Lysin Gene Combinations, Rachel E. Loney, Veronique A. Delesalle, Brianne E. Chaudhry, Megan Czerpak, Alexandra A. Guffey, Leo Goubet-Mccall, Michael Mccarty, Madison S. Strine, Natalie T. Tanke, Albert C. Vill, Gregory P. Krukonis

Biology Faculty Publications

Bacteriophages (phages) are the most numerous entities on Earth, but we have only scratched the surface of describing phage diversity. We isolated seven Bacillus subtilis phages from desert soil in the southwest United States and then sequenced and characterized their genomes. Comparative analyses revealed high nucleotide and amino acid similarity between these seven phages, which constitute a novel subcluster. Interestingly, the tail fiber and lysin genes of these phages seem to come from different origins and carry out slightly different functions. These genes were likely acquired by this subcluster of phages via horizontal gene transfer. In conjunction with host range …

Investigating The Role Of The Metabolite Je As An Inflammatory Modulator, Rim Ahmed Noufal

Master's Theses

Innate immunity represents the first line of defense against pathogens that invade our bodies. It greatly relies on a family of abundant receptors called pathogen recognition receptors (PRRs). These are germ-line encoded proteins abundant in immune cells like macrophages, dendritic cells, and natural killer cells. PRRs encompass five categories, one of which includes toll-like receptors (TLRs). TLRs could either be located on the surface of the cells or intracellularly. The mechanism by which TLRs act is through recognizing a myriad of foreign structures derived from microbes, such as proteins, lipids, and carbohydrates as well as their genetic material. Generally, these …

Investigations Of Emerging Zoonotic And Vector-Borne Viruses At The Juncture Of Environmental, Human, And Animal Health, Erik A. Turner

LSU Doctoral Dissertations

Reemerging and emerging zoonotic viruses are some of the most important public and One Health threats facing the world. Understanding the transmission dynamics of these viruses is vital to reducing the disease burden, and one of the key aspects to these transmission systems is the environmental vertex of the One Health triangle. SARS-CoV-2 has only recently emerged as a global public health threat, and within 4 years, over 700 million cases have been reported. As a novel pathogen, many aspects of transmission, including environmental fomite transmission and disinfection, were initially a glaring gap in knowledge. Additionally, while chikungunya virus (CHIKV) …

Mimicking Biofilms: Photosynthetic Assessments Of C. Reinhardtii In 3 Physical Forms, John Michael Roesgen

Biology ETDs

Oxygenic photosynthesis supports the majority of life on Earth through the capture of energy from sunlight and the assimilation of CO₂ into basic building blocks of cells. Microalgae are fast growing and account for about half of global photosynthesis. In addition, they can be cultivated and their metabolism can be redirected to generate additional useful products ranging from biofuels to pharmaceuticals. However, the efficiency of metabolite production is severely impacted by the slow diffusion of CO₂ through water and the high energetic costs of harvesting microalgae from liquid cultures. Microalgae grow in open water, but they also form …

Dietary L-Tryptophan Consumption Determines The Number Of Colonic Regulatory T Cells And Susceptibility To Colitis Via Gpr15, Nguyen Van, Karen Zhang, Rachel Wigmore, Anne Kennedy, Carolina Dasilva, Jialing Huang, Manju Ambelil, Jose Villagomez, Gerald O'Connor, Randy Longman, Miao Cao, Adam Snook, Michael Platten, Gerard Kasenty, Luis Sigal, George C Prendergast, Sangwon Kim

Department of Microbiology and Immunology Faculty Papers

Environmental factors are the major contributor to the onset of immunological disorders such as ulcerative colitis. However, their identities remain unclear. Here, we discover that the amount of consumed L-Tryptophan (L-Trp), a ubiquitous dietary component, determines the transcription level of the colonic T cell homing receptor, GPR15, hence affecting the number of colonic FOXP3⁺ regulatory T (Treg) cells and local immune homeostasis. Ingested L-Trp is converted by host IDO1/2 enzymes, but not by gut microbiota, to compounds that induce GPR15 transcription preferentially in Treg cells via the aryl hydrocarbon receptor. Consequently, two weeks of dietary L-Trp supplementation nearly double …

Distinguishing Community Assembly Through Functional Redundancy Models., Sandra A. Tsiorintsoa, Sharon Bewick, Matthew Macauley

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Comparative Analysis Of Swine Antibody Responses Following Vaccination With Live-Attenuated And Killed African Swine Fever Virus Vaccines, Hung Q. Luong, Huong T. L. Lai, Lam Q. Truong, The N. Nguyen, Hanh D. Vu, Hoa T. Nguyen, Lan T. Nguyen, Trang H. Pham, David Scott Mcvey, Hiep Vu

Nebraska Center for Virology: Faculty Publications

African swine fever virus (ASFV) is circulating in many swine-producing countries, causing significant economic losses. It is observed that pigs experimentally vaccinated with a live-attenuated virus (LAV) but not a killed virus (KV) vaccine develop solid homologous protective immunity. The objective of this study was to comparatively analyze antibody profiles between pigs vaccinated with an LAV vaccine and those vaccinated with a KV vaccine to identify potential markers of vaccineinduced protection. Thirty ASFV seronegative pigs were divided into three groups: Group 1 received a single dose of an experimental LAV, Group 2 received two doses of an experimental KV vaccine, …

A Novel Application Of Spinning Disk Technology To Collect Plasma From Whole Blood Prior To Quantifying Plasma Rna, Naomi Rapier-Sharman, Mae-Lynn L. Hutchinson, Carlos M. Moreno, Abraham Quaye, Brian D. Poole, K. Scott Weber, William G. Pitt, Brett E. Pickett

Faculty Publications

The spinning disk technology has previously been utilized to isolate bacterial components from blood in hours instead of days. We hypothesized that this platform could be applied as an alternative approach to isolating plasma RNA from a whole blood sample. We consequently tested the efficacy of the spinning disk technology to extract plasma from whole blood upstream of RNA isolation and analysis. To do so, we collected plasma using either the spinning disk or the typical two-spin centrifuge method. We found that the spinning disk method results in significantly more hemolysis during collection than the conventional two-spin centrifuge method. However, …

Integrated Periphyton Biofilters In Marine Recirculating Aquaculture Systems, Adam N. Bell

USF Tampa Graduate Theses and Dissertations

Marine aquaculture is a growing industry that has the potential to reduce eutrophication, overfishing, and loss of biodiversity. Recirculating aquaculture systems (RAS) are a type of aquaculture system that decreases discharge, raises biological control, and conserves water; however, RAS are challenged due to high energy cost, low biodiversity, water quality control, and waste nutrients. Periphyton biofilters are a new technology that allows for feed production, water quality control, microbial diversity, and resource recovery in marine aquaculture systems. The overarching question that this dissertation investigates is, how can periphyton biofilters be integrated into RAS to address the challenges of modern sustainable …

Towards Better Detection And Treatment Of Mycobacterial Disease., Laura O'Connell

ORBioM (Open Research BioSciences Meeting)

Background

Mycobacterial disease is a major cause of fatality, with 1.5 million deaths per 10 million infections annually. Due to the emergence of multi- and extensively-drug resistant clinical isolates, mycobacteriophage (MP) are being investigated as an alternative to antibiotics.

Objectives

The objectives of this study were: to characterise an emerging cohort of MP, to determine suitable in vivo modes of delivery for MP including encapsulation, to examine the application of a MP-based viability assay, and to examine the functionality of MP in raw milk.

Methods

The fast-growing Mycobacterium smegmatis was used as a host in all assays to demonstrate phage …

Investigating The Ability Of Saltwater Isolates To Inhibit Biofilm Formation By Clinically Significant Pathogens, Monica Murphy

ORBioM (Open Research BioSciences Meeting)

Background

Nosocomial pathogens are responsible for chronic and persistent infections partly due to their ability to form protective biofilms which enhance their antibiotic tolerance. Biofilm disruption combats antimicrobial resistance as dispersed cells regain antibiotic susceptibility. The goal of this study was to evaluate the antibiofilm potential of isolates from marine environments against a pathogen panel consisting of MRSA and clinical Staphylococcus aureus strains, Acinetobacter baumannii and Escherichia coli pathogens.

Method

A large bank of saltwater bacterial isolates was cultured in glucose-supplemented trypticase soy broth (TSBg) and resulting colonies were screened against the pathogen panel. Isolates of interest were further examined …

Short Chain Fatty Acid Combination Treatment Protects Against 6-Ohda And Wt Α-Synuclein Induced Decreases In Neurite Growth In In Vitro Models Of Parkinson’S Disease., Alex Morris

ORBioM (Open Research BioSciences Meeting)

Background

Parkinson’s disease (PD) is a neurodegenerative disorder characterized by dopaminergic neuron degeneration. This degeneration is partly driven by over expression of α-synuclein (α-syn) and development of α-syn aggregates known as Lewy bodies throughout the substantia nigra. As well as motor dysfunction, PD presents with several chronic gastrointestinal comorbidities, which cause a decline of gut microbial diversity and microbially derived short chain fatty acids (SCFAs). Recent in vivo studies have shown SCFAs to be neuroprotective in various degenerative disease states, suggesting that SCFAs may protect against dopaminergic degeneration.

Methods

Human neuroblastoma SH-SY5Y cells were used as a model of human …

Urobiome Screening For Antimicrobial Peptides Against Uropathogenic Escherichia Coli, Jennifer Jones

ORBioM (Open Research BioSciences Meeting)

BACKGROUND: Urinary tract infections (UTIs) are one of the most common bacterial infections worldwide. As global incidences of UTIs caused by multidrug resistant bacteria continue to increase, so too does the demand for novel antimicrobial therapies.

Due to its relatively understudied nature, the urinary microbiome represents a niche with an untapped source of potentially novel antimicrobials (e.g., bacteriocins). Improvements to bacterial culturing and sequencing techniques have highlighted these potential alternative treatments and control strategies to target antibiotic resistant uropathogenic E. coli (UPEC).

METHODS: Expanded quantitative urine culture (EQUC) was used to culture bacterial isolates from mid-stream urine samples. Urinary isolates …

Examining The Absorbance Maximum, Protein Concentration And Antimicrobial Activity Of Seaweed Extracts, Claudia Kenneally

ORBioM (Open Research BioSciences Meeting)

Background

The emergence of antimicrobial resistance (AMR) has highlighted the need for novel antimicrobials. Antimicrobial compounds can be isolated from various marine sources, including seaweed, which contain pigments and proteins. This study focuses on screening seaweeds for potential antimicrobial compounds.

Methods

Four seaweed types (A, B, C, D) were collected from beaches in Cork, Ireland, and extracts of each were prepared using both methanol (-M) and water (-H₂O). The absorbance maximum (λ_max)of seaweed extracts was determined from 220 – 800 nm to investigate potential pigment interference at 600 nm. The bicinchoninic acid (BCA) assay was preformed …

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 …

Development Of A Protocol For The Extraction Of Genomic Material From Fecal Matter For Metagenome And Virome Sequencing, Keith Coughlan

ORBioM (Open Research BioSciences Meeting)

With the advent of increasingly more accurate and reliable sequencing methods, the requirement for extraction methods yielding large volumes of high-quality genomic material has become progressively more significant. While the analysis of genomic material through bioinformatics can offer some methods of “cleaning” and standardizing data, it is essential that the “wet lab” aspects of data produce abundant amounts of high-quality genetic material. Therefore, the purpose of this project is to develop an optimized method of DNA extraction for fecal material sequencing in microbiome and virome investigations. The samples used for the optimized protocol are infant fecal samples collected and stored …

Mycobacteriophage: A Demonstration Of The Reduction Of M. Smegmatis In Various Matrices., Laura O'Connell

ORBioM (Open Research BioSciences Meeting)

Background

Mycobacterial disease is a major cause of fatality worldwide, with approximately 1.5 million deaths for every 10 million infections. These infections are difficult to treat due to the intrinsic resistance of its mycolic acid rich cell wall to many antibiotics. There is potential for mycobacteriophage (MP) to be used therapeutically for multidrug- and extensively-drug resistant infections. Mycobacterium smegmatis mc² 155 is a useful substitute for slow-growing pathogenic mycobacteria, as it propagates quickly under lab conditions. This feature of M. smegmatis increases the pace of analysis, by ensuring the quick isolation and characterisation of MP and acting as a …

Bioengineered Nisin A Derivatives Display Enhanced Activity Against Clinical Neonatal Pathogens, Anna Desmond

ORBioM (Open Research BioSciences Meeting)

Neonatal infection is a significant cause of mortality and morbidity in infants. Globally, neonatal pathogens are increasingly becoming multi-drug resistant, indicating the need to discover novel alternative treatment strategies. Nisin is an antimicrobial peptide that exhibits broad-spectrum activity against Gram-positive and Gram-negative bacteria including a wide variety of clinical pathogens. Nisin can be used in combination with antibiotics to improve their efficacy. This study examined the activity of nisin and bioengineered derivatives against multi-drug resistant Streptococcus agalactiae and Staphylococcus capitis isolates and investigated the potential synergy between nisin peptides and selected antibiotics. Whole genome sequence analysis of the strains revealed …

In Vitro Antimicrobial Activity Of Cell-Free Supernatants From Asymptomatic Bacteriuria (Abu) Isolates Against Multi-Drug Resistant Uropathogenic Escherichia Coli (Upec), Ciara Kenneally

ORBioM (Open Research BioSciences Meeting)

Background

Multi-drug resistant uropathogenic Escherichia coli (UPEC) cause > 80% of community acquired urinary tract infections (UTIs) and > 40% of nosocomial UTIs. Preliminary evidence suggests a beneficial role for UPEC’s commensal counterparts, asymptomatic bacteriuria (ABU), in establishing bacterial interference against UPEC. The aim of this study was to analyse the antimicrobial activity of cell free supernatants (CFS) from ABU isolates against UPEC.

Methods

In vitro antagonistic effects of nine uncharacterised ABU isolates were compared against the inhibitory affect induced by the prototype ABU isolate, E. coli 83972. Turbidimetric growth assays were performed using the CFS of the ABU isolates against eight …

Investigating The Thermotolerance Of Cronobacter Sakazakii In Powdered Infant Formula, Fiona Ryan O'Connor

ORBioM (Open Research BioSciences Meeting)

Background

The powdered infant formula (PIF) sector is a growing global market, with Ireland at the forefront of the European exports market; reaching €1.5bn and accounting for 35% of all dairy exports in 2015. However, a major concern associated with PIF is the risk of contamination with the neonatal pathogen Cronobacter sakazakii. Although PIF undergoes thermal treatment during manufacture, it is possible that re-contamination of the product may occur via later processing measures. We investigated the resistance of C. sakazakii to thermal inactivation following inoculation in commercial PIF as a potential treatment for contaminated powder.

Method

Five strains of C. …

The Pseudomonas Syringae Pv. Tomato Dc3000 Effector Hopd1 Interferes With Cellular Dynamics Associated With The Function Of The Plant Immune Protein Atnhr2b, Luis Francisco Marin-Ponce, Catalina Rodriguez-Puerto, Perla Rocha-Loyola, Clemencia M. Rojas

Entomology and Plant Pathology Faculty Publications and Presentations

The plant pathogenic bacterium Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) causes disease in tomato, in the model plant Arabidopsis thaliana, and conditionally in Nicotiana benthamiana. The pathogenicity of Pst DC3000 is mostly due to bacterial virulence proteins, known as effectors, that are translocated into the plant cytoplasm through the type III secretion system (T3SS). Bacterial type III secreted effectors (T3SEs) target plants physiological processes and suppress defense responses to enable and support bacterial proliferation. The Pst DC3000 T3SE HopD1 interferes with plant defense responses by targeting the transcription factor NTL9. This work shows that HopD1 also targets the …

Tracing Evolution Of Gene Transfer Agents Using Comparative Genomics, Roman Kogay

Dartmouth College Ph.D Dissertations

The accumulating evidence suggest that viruses and their components can be domesticated by their hosts, equipping them with convenient molecular toolkits for various functions. One of such domesticated system is Gene Transfer Agents (GTAs) that are produced by some bacteria and archaea. GTAs morphologically resemble small phage-like particles and contain random fragments of their host genome. They are produced only by a small fraction of the microbial population and are released through a lysis of the host cell. Bioinformatic analyses suggest that GTAs are especially abundant in the taxonomic class of Alphaproteobacteria, where they are vertically inherited and evolve …

Cell Surface And Plasma Biomarkers Of Kaposi Sarcoma, Sara R. Privatt

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Kaposi sarcoma-associated herpesvirus is the etiological agent of several pathologies including Kaposi sarcoma, primary effusion lymphoma, and multicentric Castleman’s disease. Here, we investigated both the tumor microenvironment (TME) in KS lesions as well as plasma from KSHV-infected individuals and how metabolic dysfunction and dysregulated cytokines might have a systemic effect on KS tumorigenesis. Based on previously published KS tumor transcriptomics, one aspect of our investigation involved characterizing cell surface glycoproteins with potential to serve as therapeutic targets against KSHV-infected cells or KS tumors or as biomarkers for disease. Expression patterns of such markers may also suggest the cellular origin of …

Connecting The Nebraska Water Quality Index To The Aquatic Microbial Community Of The North Platte River Basin, Nebraska, Paula R. Guastello

School of Natural Resources: Dissertations, Theses, and Student Research

The Nebraska Water Quality Index, under development by the Nebraska Department of Environment and Energy, summarizes in a single value eight environmental parameters that have been monitored in Nebraska for nearly 20 years. Water quality parameters including those used in the Nebraska Water Quality Index have been shown in previous studies to impact bacterial growth. As such, this index has the potential to correlate with the freshwater microbial community. Here, I relate the Nebraska Water Quality Index to microbial community composition and structure using 16S rRNA gene amplicon sequence data collected from the North Platte River Basin, Nebraska. This index …