Microbiology Commons^™

Closing The Gaps: Reforming Maryland Controls On Veterinary Antimicrobial Distribution, Samantha Capaldo, Kerry Mcclaughry

Journal of Food Law & Policy

Antimicrobials have been used in livestock and other food animals in the United States (“U.S.”) since the late 1940s. An antimicrobial is “[a]ny natural, synthetic, or semisynthetic substance that can eradicate or prevent the growth of microbes,” including “[a]ntibacterial, antifungal, antiparasitic, and antiviral medications.” Antimicrobial use in food animals is subject to a complex statutory and regulatory framework at both the state and federal levels. Antimicrobial use in food animals has been widely criticized for contributing to antimicrobial-resistant bacterial infections in humans. In response to this criticism, the U.S. Food and Drug Administration (“FDA”) and several states, including Maryland, have …

Dried Water Treatment Residuals Might Be An Option To Reduce Soluble Reactive Phosphorus Release From Soils, Katie B. Mckay

Biological and Agricultural Engineering Undergraduate Honors Theses

Nonpoint source pollution from agricultural landscapes contributes to freshwater eutrophication, with legacy phosphorus (P) in soils potentially driving soluble reactive phosphorus (SRP) losses to surface waters. The objectives of this study were to evaluate SRP adsorption by dried water treatment residuals (WTRs) produced by Beaver Water District, quantify reductions in soil SRP release across increasing WTR application rates, and compare dried WTR performance to prior WTR studies.

Dried WTRs (~98% solids) were assessed using batch sorption experiments and soil core incubations. Phosphorus sorption was measured by mixing WTRs with CaCl₂ solutions containing increasing SRP concentrations and fitting results to …

Advancing The Virus Diagnostic Toolkit: Development Of Accurate And Reliable Artificial Virus-Mimicking Positive Controls And Crispr-Based Detection, Habeeb Yinka Atanda

Graduate Theses and Dissertations

Accurate and reliable detection of plant viruses is critical for protecting berries and other economically important crops. Yet diagnostic programs face persistent challenges with positive control availability, biosafety concerns, and specificity limitations. This thesis advances the diagnostic toolkit for berry viruses through three complementary innovations that address fundamental gaps in current detection methodologies. First, this research developed and validated virus-mimicking artificial positive controls (ViMAPCs) for diverse viruses affecting berry crops for endpoint PCR applications. ViMAPCs incorporate size differentiation, which enables immediate visual gel band discrimination between control and natural infection signals. Amplification efficiency analysis demonstrated close correspondence with true-positive controls …

Evaluation Of Tracheal And Cecal Microbial Composition In Heat Stressed Broilers Supplemented With Phytogenic Additives, Andressa Silveira Stein

Graduate Theses and Dissertations

The rise in global temperatures has become a concern due to its significant impact on the agricultural sector, including poultry production. Heat stress caused by high temperatures directly affects animal welfare, health and productivity, leading to major losses in the poultry sector. In broilers, heat stress affects feed consumption, weight gain, mortality and may also lead to changes in the microbiome, which can increase the predisposition to disease and impact the overall performance of these animals. The aim of this thesis was to reproduce field conditions, simulating an increase in temperature, and to evaluate possible changes in the respiratory and …

In Vitro Assessment Of The Antihistomonal Activity Of Methyl Jasmonate And Jasmonic Acid, Mckayla B. Williams

Poultry Science Undergraduate Honors Theses

Histomonas meleagridis is a protozoan parasite and the causative agent of histomonosis in gallinaceous birds. There are currently no approved prevention or treatment options available for histomonosis control in the United States. Mortality in affected turkey flocks can exceed 80% which highlights the urgent need for research investigating novel strategies to mitigate histomonosis in the field. The objective of this study was to evaluate the in vitro antihistomonal and antibacterial effects of of methyl jasmonate (MeJA) and jasmonic acid (JA), two plant-derived compounds, in a xenic culture of H. meleagridis. Assays were conducted using cultured H. meleagridis (PHL strain) treated …

Phosphatase Activity And Structure Of The Spoiie Protein In Clostridioides Difficile, Kathryn Wootten

Biological Sciences Undergraduate Honors Theses

Clostridioides difficile is a major cause of severe gastrointestinal infections and diseases, particularly in healthcare settings. Because of its ability to produce infectious endospores by sporulation, the protein SpoIIE, which is known to play a role in the regulation of this process, is being explored as a potential therapeutic target. In order to gain better insight into the structure and function of this protein, a concentrated and purified sample of the protein must be obtained. The goal of this study was to determine the conditions that would yield the highest amount of SpoIIE. The density of the cultures of bacteria …

Identifying Microbial Complexities And Control Strategies At Pre-Harvest Poultry Production, Tolulope Tiwa Ogundipe

Graduate Theses and Dissertations

While significant progress has been made in post-harvest control of Salmonella in the poultry industry, the development of effective pre-harvest intervention strategies remains critical for reducing foodborne pathogens. Environmental reservoirs such as poultry litter and drinking water systems (DWS) are potential harborage sites for Salmonella and other microbial communities. Understanding the microbiota of these environments, including biofilms within water lines, is essential to identifying factors contributing to Salmonella colonization and improving pre-harvest control approaches. This study aimed to evaluate the incidence and quantity of Salmonella in poultry litter and water lines, characterize the microbial populations in these environments, and assess …

Bacterial Chondronecrosis With Osteomyelitis In Broilers: Etiology And Selected Mitigation Measures, Khawla Saud Alharbi

Graduate Theses and Dissertations

Bacterial chondronecrosis with osteomyelitis (BCO) is the predominant cause of lameness in broiler chickens. It mainly impacts broiler production and animal welfare, causing substantial financial losses accounting for 1- 2% due to bird condemnations at the marketing age. Remediating BCO lameness disease demands investigating its causes using appropriate models and evaluating preventive measures, such as enhancing epithelial tissue health and tight junction integrity in the digestive and respiratory tract, strengthening immune functions, and improving bone strength. Therefore, the objectives of this dissertation were to 1) study predisposing factors for BCO lameness by investigating the effects of deoxynivalenol (DON) and fumonisin …

Characterization Of Streptococcus Gallolyticus: An Emerging Pathogen Causing Turkey Streptococcosis, Latasha S. Gray

Graduate Theses and Dissertations

During the past five years, there has been an increased occurrence of Streptococcus gallolyticus in young turkey poults. This emerging pathogen previously affected turkey flocks without any indication of disease prior to acute mortality. However, recently there has been two cases of neurological presentation associated with S. gallolyticus subsp. pasteurianus that are unique to traditional disease presentation in turkey poults. The objectives of the present dissertation were to compile data associated with the two neurological cases and compare different S. gallolyticus strains as well as pathogenic Enterococcus cecorum to the neurological strains. The two neurological cases occurred between July and …

Bactericidal Mechanism Of Peracetic Acid Against Salmonella Mediated By Reactive Oxygen Species, Mohammed Khalid Wheib Al-Doury

Graduate Theses and Dissertations

Peracetic acid (PAA) is extensively used as a bactericidal agent in poultry processing to reduce foodborne pathogens, including Salmonella enterica serotype Typhimurium (S. Typhimurium). Despite its widespread application, the exact mechanisms underlying its bactericidal effects, particularly the role of reactive oxygen species (ROS), remain incompletely understood. This dissertation examines the role of ROS in PAA-mediated bacterial killing and explores both genetic and metabolic factors that influence bacterial susceptibility to PAA. Findings from these studies have implications for enhancing the efficacy of PAA, thereby improving food safety practices in the industry.

The first study investigates ROS as a central component …

Natural Panola Mountain Ehrlichia Infections In Cattle In A Longitudinal Study Of Angus Beef Calves, Cierra Briggs, Drew Casey, Anna Grace Deakins, Jeremy G. Powell, Kelly Loftin, Emily G. Mcdermott

Entomology and Plant Pathology Faculty Publications and Presentations

Panola Mountain Ehrlichia (PME) is an emerging zoonotic pathogen, transmitted by Amblyomma americanum ticks in the southeastern United States. It is closely related to Ehrlichia ruminantium, the causative agent of heartwater disease. Heartwater disease is an often-fatal illness of ruminant livestock present in Africa and the Caribbean. The taxonomic relationship between PME and E. ruminantium has raised concerns about the pathogenicity of PME in livestock. To determine whether cattle could be naturally infected with PME in an endemic area, we conducted a one-year longitudinal study of Angus-breed beef calves in Fayetteville, Arkansas. One hundred seventy-seven calves born between September …

Multiomics Of Yaks Reveals Significant Contribution Of Microbiome Into Host Metabolism, Shuli Yang, Jeiyi Zheng, Huaming Mao, Paramintra Vinitchaikul, Dongwang Wu, Jianmin Chai

Animal Science Faculty Publications and Presentations

An intensive feeding system might improve the production cycle of yaks. However, how intensive feeding system contributes to yak growth is unclear. Here, multi-omics, including rumen metagenomics, rumen and plasma metabolomics, were performed to classify the regulatory mechanisms of intensive feeding system on yaks. Increased growth performance were observed. Rumen metagenomics revealed that Clostridium, Methanobrevibacter, Piromyces and Anaeromyces increased in the intensively fed yaks, contributing to amino acid and carbohydrate metabolism. The grazing yaks had more cellulolytic microbes. These microbiomes were correlated with the pathways of "Alanine aspartate and glutamate metabolism" and "Pyruvate metabolism". Intensive feeding increased methane degradation functions, …

Draft Genome Sequence Of Ruoffia Tabacinasalis Isolated From A Bovine Nasal Swab: A Novel Member Of The Bovine Nasal Microbiota, Samantha Howe, Xiaoyuan Wei, Jasna Kovac, Jiangchao Zhao

Animal Science Faculty Publications and Presentations

We report the isolation and draft genome sequence of Ruoffia tabacinasalis, a novel member of the bovine nasal microbiota. The genome, which is estimated to be 90.5% complete, is composed of one contig comprising 2,363,349 bp with a GC content of 36.66%.

Tulane Virus Persistence And Microbial Stability In 3d Food Ink Under Various Storage Conditions: A Pre- And Post-Printing Analysis, Allyson N. Hamilton, Kristen E. Gibson

Food Science Faculty Publications and Presentations

3D food printers facilitate novel customization of the physicochemical properties of food. This study aimed to investigate the impact of storage conditions on the inactivation of the human norovirus surrogate, Tulane virus (TuV), within 3D printed foods. TuV-inoculated protein cookie food ink (∽ 4 log PFU/g) was distributed into 18 3D food printer capsules (50 g each); half immediately underwent extrusion. Storage of the capsules and printed food products at 20 °C (0, 6, 12, and 24 h), 4 °C (0, 1, 3, and 5d), and − 18 °C (0, 1, 3, and 5d) was completed before analysis for TuV …

Phylogenomic Analyses Of Three Distinct Lineages Uniting Staphylococcus Cohnii Snd Staphylococcus Urealyticus From Diverse Hosts, L. Caroline House, Amer Hasan, Andi Asnayanti, Adnan A. Alrubaye, Jeff Pummill, Douglas Rhoads

Poultry Science Faculty Publications and Presentations

We sequenced and assembled genomes for 17 isolates of Staphylococcus cohnii isolated from osteomyelitis lesions in young broilers from two separate experiments where we induced lameness using a hybrid wire-litter flooring system. Whole genome comparisons using three different methods support a close relationship of genomes from both S. cohnii and Staphylococcus urealyticus. The data support three different lineages, which we designated as Lineage 1, Lineage 2, and Lineage 3, uniting these two species within an evolving complex. We present evidence for horizontal transfer between lineages of genomic regions from 50–440 kbp. The transfer of a 186 kbp region from …

The Impact Of Reactive Oxygen Species On Bactericidal Activity And Drug Resistance In Salmonella Typhimurium Upon Chlorine And Eugenol Exposure, Mohammed Aljuwayd

Graduate Theses and Dissertations

Salmonella Typhimurium (S.T) is a foodborne pathogenic bacterium which causes salmonellosis in human beings. Chicken is the most common source of S.T contamination. In chapter I, I discuss the growth of the poultry industry, the role chickens play as Salmonella reservoirs, the spread of drug-resistant strains caused by chicken husbandry and antibiotic use, and how eugenol can be used in poultry feed to decrease Salmonella infections and improve intestinal health. In chapter Ⅱ, I summarize the role of reactive oxygen species (ROS) in bactericidal activity. In chapter Ⅲ, I describe the killing mechanism of sodium hypochlorite (NaOCl) and identify the …

Evaluating The Impact Of The Poultrystar®Bro Probiotic On The Incidence Of Bacterial Chondronecrosis With Osteomyelitis Using The Aerosol Transmission Challenge Model, Ruvindu Perera, Khawla Alharbi, Amer Hasan, Andi Asnayanti, Anh Dang Trieu Do, Abdulkarim Shwani, Raj Murugesan, Shelby Ramirez, Michael Kidd, Adnan A. Alrubaye

Poultry Science Faculty Publications and Presentations

Bacterial chondronecrosis with osteomyelitis (BCO) lameness is a major welfare issue for broiler production worldwide affecting approximately 1.5% of broilers over 42 days old. Excessive body weight gain causes mechanical stress on long bones, leading to micro-fractures. This condition induces a bacterial infection of fractures, resulting in bone necrosis and eventual BCO lameness. Increasing gut integrity and supporting Calcium metabolism contribute to the optimal bone structure and subsequently reduce BCO lameness. Probiotics thus provide an excellent strategy for alleviating BCO due to the improvement of intestinal integrity and barrier function. Accordingly, the present study investigated the lameness reduction through the …

Isolation Of Naegleria Lustrarea N. Sp. (Excavata, Discoba, Heterolobosea) From The Feces Of Ambystoma Annulatum (Ringed Salamander) In Northwest Arkansas, Brian M. Becker, Idan Banson, James M. Walker, Anant Deshwal, Matthew W. Brown, Jeffrey D. Silberman

Biological Sciences Faculty Publications and Presentations

The salamander, Ambystoma annulatum, is considered a “species of special concern” in the state of Arkansas, USA, due to its limited geographic range, specialized habitat requirements and low population size. Although metazoan parasites have been documented in this salamander species, neither its native protists nor microbiome have yet been evaluated. This is likely due to the elusive nature and under-sampling of the animal. Here, we initiate the cataloguing of microbial associates with the identification of a new heterlobosean species, Naegleria lustrarea n. sp. (Excavata, Discoba, Heterolobosea), isolated from feces of an adult A. annulatum.

Editorial: The Gut-Skin Axis: Interaction Of Gut Microbiome And Skin Diseases, Jianmin Chai, Feilong Deng, Ying Li, Xiaoyuan Wei, Jiangchao Zhao

Animal Science Faculty Publications and Presentations

Editorial on the Research Topic: The gut-skin axis: interaction of gut microbiome and skin diseases

Hydroponic Nutrient Solution Temperature Impacts Tulane Virus Persistence Over Time, Gayatri R. Dhulappanavar, Kristen E. Gibson

Food Science Faculty Publications and Presentations

Controlled environment agriculture (CEA), or indoor agriculture, encompasses non-traditional farming methods that occur inside climate-controlled structures (e.g., greenhouses, warehouses, high tunnels) allowing for year-round production of fresh produce such as leaf lettuce. However, recent outbreaks and recalls associated with hydroponically grown lettuce contaminated with human pathogens have raised concerns. Few studies exist on the food safety risks during hydroponic cultivation of leaf lettuce; thus, it is important to identify contributing risk factors and potential mitigation strategies to prevent foodborne transmission via hydroponically grown produce. In this study, the concentration of infectious Tulane virus (TV), a human norovirus surrogate, in hydroponic …

Recombinant Bile Salt Hydrolase Enhances The Inhibition Efficiency Of Taurodeoxycholic Acid Against Clostridium Perfringens Virulence, Tahrir Alenezi, Bilal Alrubaye, Ying Fu, Janashrit Shrestha, Samar Algehani, Hong Wang, Rohana Liyanage, Xiaolun Sun

Chemistry & Biochemistry Faculty Publications and Presentations

Clostridium perfringens is the main pathogen of chicken necrotic enteritis (NE) causing huge economic losses in the poultry industry. Although dietary secondary bile acid deoxycholic acid (DCA) reduced chicken NE, the accumulation of conjugated tauro-DCA (TDCA) raised concerns regarding DCA efficacy. In this study, we aimed to deconjugate TDCA by bile salt hydrolase (BSH) to increase DCA efficacy against the NE pathogen C. perfringens. Assays were conducted to evaluate the inhibition of C. perfringens growth, hydrogen sulfide (H₂S) production, and virulence gene expression by TDCA and DCA. BSH activity and sequence alignment were conducted to select the …

Survival Of Methanogens Desiccated On Mars Soil Simulants: Implications For Life On Mars, Lanee Knight

Biological Sciences Undergraduate Honors Theses

Because of Mars’s chemical features, it can be studied in the search for life and is a significant figure in the study of astrobiology (McKay, 2010). Dr. Kral’s laboratory studies methanogens, microorganisms in the domain Archaea, as possible life forms on Mars. Since some methanogens can withstand harsh environmental conditions and emit methane as a waste product, the growth of these microorganisms can be used as an indicator of potential life in the Mars subsurface (Kral et al., 1998). In this research, four methanogens, Methanothermobacter wolfeii, Methanobacterium formicicum, Methanosarcina barkeri, and Methanococcus maripaludi were desiccated in the …

Growth Of Methanogens On Kaolinite, A Clay That Has Been Identified On Mars, Hailey Littrell

Biological Sciences Undergraduate Honors Theses

Methanogens have been studied as a model for life on Mars for 28 years now in the Kral lab. The discovery of methane in the Martian atmosphere by ground-based and orbital observations as well as Curiosity Rover (Formisano, V. et al., Krasnopolsky, V.A. et al., Mumma, M.J. et al.) has added relevance to these types of studies. Methanogens were chosen due to their ability to live in harsh environments, very similar to the Martian terrain. In addition to methane in the atmosphere, phyllosilicate clays have also been identified. One of those clays is kaolinite. Kaolinite has been found to not …

A Meta-Analysis For Laboratory Diagnostics For Coccidioidomycosis, Mary C. Cowen

Biological Sciences Undergraduate Honors Theses

Coccidioidomycosis, commonly referred to as Valley Fever, is a fungal infection found in arid regions of the southwestern United States and Mexico. Infection occurs through inhalation of airborne spores from Coccidioides species, Coccidioides immitis and/or Coccidioides posadasii, and proceeds in both pulmonary and disseminated fashions. Approximately 60% of patients with coccidioidomycosis remain asymptomatic, while 40% will experience symptoms. Within the literature, there are no papers that summarize sensitivity and specificity values between different tests; therefore, this paper presents sensitivity and specificity results across different tests and companies (Meridian, IMMY, and MiraVista).

The Effect Of Microbial Bile Acid Metabolism On Clostridium Perfringens Virulence, Tahrir Jatli Alenezi

Graduate Theses and Dissertations

Clostridium perfringens is a predominant intestinal pathogen affecting both humans and animals, including chickens resulting in significant economic losses. In chapter I, I have overviewed the dynamics of the intestinal immune system, the composition of the intestinal microbiome, and how the microbiome influences inflammation in the development of Clostridium infection. The intricate interplay between immunity, microbiota, and their metabolites is likely critical in the pathogenesis of C. perfringens and uncovering these interactions may unveil new avenues for prevention and treatment. The objective of this chapter is to provide updated insights into the role of host-microbe interactions and their potential therapeutic …

Bootstrapping For Estimating The Conservative Kill Ratio Of The Surrogate To The Pathogen For Use In Thermal Process Validation At The Industrial Scale, Arshpreet Kaur Khattra, Surabhi Wason, Kevin Thompson, Andy Mauromostakos, Jeyamkondan Subbiah, Jennifer C. Acuff

Food Science Faculty Publications and Presentations

A surrogate is commonly used for process validations. The industry often uses the target log cycle reduction for the test (LCR_Test) microorganism (surrogate) to be equal to the desired log cycle reduction for the target (LCR_Target) microorganism (pathogen). When the surrogate is too conservative with far greater resistance than the pathogen, the food may be overprocessed with quality and cost consequences. In aseptic processing, the Institute for Thermal Processing Specialists recommends using relative resistance (D_Target)/(D_Test) to calculate LCR_Test (product of LCR_Target and relative resistance). This method uses the mean values …

Exploring The Intestinal Microbial Community Of Lantang Pigs Through Metagenome-Assembled Genomes And Carbohydrate Degradation Genes, Jianbo Yang, Ying Fan, Rui Jin, Yunjuan Peng, Jianmin Chai, Xiaoyuan Wei, Yunxiang Zhao, Feilong Deng, Jiangchao Zhao, Ying Li

Animal Science Faculty Publications and Presentations

High-fiber, low-cost agricultural byproducts offer a sustainable alternative for mitigating the competition for crops between humans and livestock. Pigs predominantly utilize dietary fibers through the process of microbial fermentation within the gut. This study explored the gut microbiota and the capacity for carbohydrate degradation in 30 individual Lantang pigs, a breed indigenous to China. Through metagenomic analysis, a total of 671 metagenome-assembled genomes (MAGs) were assembled and assigned into 14 bacterial and 1 archaeal phylum, including 97 species from uncultured microbes. The phylum with the highest abundance were identified as Bacillota_A, Bacteroidota, and Bacillota. Remarkably, the investigation revealed nearly 10,000 …

Clostridium Butyricum And Carbohydrate Active Enzymes Contribute To The Reduced Fat Deposition In Pigs, Lingyan Ma, Shiyu Tao, Tongxing Song, Wentao Lyu, Ying Li, Wen Wang, Qicheng Shen, Yan Ni, Jiang Zhu, Jiangchao Zhao, Hua Yang, Yingping Xiao

Animal Science Faculty Publications and Presentations

Pig gastrointestinal tracts harbor a heterogeneous and dynamic ecosystem populated with trillions of microbes, enhancing the ability of the host to harvest energy from dietary carbohydrates and contributing to host adipogenesis and fatness. However, the microbial community structure and related mechanisms responsible for the differences between the fatty phenotypes and the lean phenotypes of the pigs remained to be comprehensively elucidated. Herein, we first found significant differences in microbial composition and potential functional capacity among different gut locations in Jinhua pigs with distinct fatness phenotypes. Second, we identified that Jinhua pigs with lower fatness exhibited higher levels of short-chain fatty …

Molecular Genomic Analyses Of Enterococcus Cecorum From Sepsis Outbreaks In Broilers, Douglas D. Rhoads, Jeff Pummill, Adnan Ali Khalaf Alrubaye

Poultry Science Faculty Publications and Presentations

Extensive genomic analyses of Enterococcus cecorum isolates from sepsis outbreaks in broilers suggest a polyphyletic origin, likely arising from core genome mutations rather than gene acquisition. This species is a normal intestinal flora of avian species with particular isolates associated with osteomyelitis. More recently, this species has been associated with sepsis outbreaks affecting broilers during the first 3 weeks post-hatch. Understanding the genetic and management basis of this new phenotype is critical for developing strategies to mitigate this emerging problem. Phylogenomic analyses of 227 genomes suggest that sepsis isolates are polyphyletic and closely related to both commensal and osteomyelitis isolate …

Us Public Opinion About The Safety Of Gene Editing In The Agriculture And Medical Fields And The Amount Of Evidence Needed To Improve Opinions, Brandon R. Mcfadden, Joy N. Rumble, Kathryn A. Stofer, Kevin M. Folta

Agricultural Economics and Agribusiness Faculty Publications and Presentations

Introduction: Implementation of gene editing in agriculture and medicine hinges on public acceptance. The objectives of this study were to explore U.S. public opinion about gene editing in agricultural and medical fields and to provide more insight into the relationship between opinions about the safety of gene editing and the potential impact of evidence to improve opinions about safety.

Methods: Data were from two samples of U.S. respondents: 1,442 respondents in 2021 and 3,125 respondents in 2022. Survey respondents provided their opinions about the safety of gene editing in the agricultural and medical fields and answered questions about the number …