Microbiology Commons^™

Exploring Competitive Dynamics Between Pseudomonas Baetica And Salmonella In A Polymicrobial System, Braxton E.M. Stout

Electronic Theses and Dissertations

The global rise in antimicrobial resistance has catalyzed a greater focus on polymicrobial research aimed at characterizing microbial interactions and uncovering new therapeutic strategies. Though it has long been of interest, environmental soil-derived bacteria remain largely under-represented in research and thus uncharacterized in this field. This project aimed to identify soil microbes that display inhibitory mechanisms to potential nosocomial pathogens. Soil sample S1S3-2 displayed inhibitory phenotypes toward numerous bacteria and was identified as Pseudomonas baetica. In both planktonic and biofilm growth, P. baetica was able to inhibit Salmonella arizonae through a contact-dependent and temperature-dependent manner. Screening of a transposon insertion …

The Role Of Seed Mix Characteristics And Soil Amendments During Post-Agricultural Prairie Restoration, Valerie N. Thurston, Michaela J. Woods, Madelaine Gregory, Mary C. Lloyd, Ryan W. Mcewan

Biology Faculty Publications

Introduction: Prairie restoration on degraded lands may be influenced by seed mix characteristics, including species richness and legume establishment. Soil amendments may facilitate restoration; however, the practical usefulness of techniques such as applications of whole soil and leaf mulch remains relatively unclear.

Objectives: We assessed whether increasing species richness and legume content in seed mixes enhances prairie restoration success and examined how soil amendments interact with seed mix composition to influence cover, species richness, diversity, and legume establishment.

Methods: We conducted a field experiment on a 12-ha post-agricultural site in Ohio, U.S.A. Twenty 50 × 50 m plots received one …

Hydrogels For Local Drug Delivery In Biofilm-Associated Periprosthetic Joint Infection: Current Progress And Future Directions, Karolina Kraus, Pawel Mikziński, Bindu Subhadra, Emil Paluch

Faculty Publications - Biological Sciences

Periprosthetic joint infection (PJI) remains one of the most serious complications of arthroplasty, largely due to the formation of microbial biofilms on implant surfaces. Biofilm-associated infections exhibit increased tolerance to antimicrobial therapy and host immune responses, making eradication difficult and often requiring repeated surgical interventions. Consequently, there is a growing need for effective local therapeutic strategies capable of delivering high concentrations of antimicrobial agents directly to the site of infection while minimizing systemic toxicity. Hydrogels have emerged as promising drug delivery platforms for the management of biofilm-associated PJI. Their biocompatibility, injectability, high water content, and tunable physicochemical properties enable controlled …

Sporicidal Activity Mechanism Of Lactic Acid And Peracetic Acid On Bovine Pathogenic Bacillus Cereus Spores, Xin Zhang, Yunjiao Chen, Jingjing Zhao, Haiying Zheng, Lanlan Liu, Wei Liu, Mingshan Fu, Weijuan Jia, Zelin Jia, Jiayu Cui, Yuhang Zhang, Huisheng Xiong, Yujie Ma, Xueli Wang, Haifeng Wang

The Thai Journal of Veterinary Medicine

In recent years, the pathogenicity of Bacillus cereus (B. cereus) has increased significantly, its host adaptability has continued to expand, and the infection spectrum has also expanded. At the same time, food contamination by B. cereus is also common. Therefore, it is of practical significance to select green, safe and effective inhibitors. Lactic acid (LA) and peroxyacetic acid (PAA) possess good antibacterial properties, making them environmentally friendly, safe, and non-toxic. The purpose of this experiment was to preliminarily explore the inhibition mechanism of LA and PAA on B. cereus spores. The effects of LA and PAA on B. …

Developing Field And Spaceflight Microscopy, Nikki Johnston

Dissertations and Theses

Designing for spaceflight favors the reduction of unnecessary features and cost-cutting, whether thisbe computation, hardware, or procedure. Resources are spent toward fortification and mission success over convenience. Such design goals paired with the relatively smaller budgets of academia lead us to do as much as we can in-house and use open-source as much as we can without compromising mission success. We also believe that thoroughly testing technology in extreme environments on earth is necessary for the success of a flight instrument. We focus on microscopy for life detection. I have spent my time here learning methods of hand-building microscopes to …

Host-Pathogen Dynamics Underpinning Staphylococcus Aureus Growth During Intracellular Osteoclast Infection, Luke D. O'Connor

WUSM Theses and Dissertations – All Programs

Bone infection is most commonly caused by the gram-positive bacterium Staphylococcus aureus. It has myriad ways in which it can circumvent or subvert killing by the host or antibiotics. Intracellular infection is one such niche that is protective from immune and antibiotic attack. In 2019, Krauss and colleagues discovered that infected osteoclasts (OCs) allow S. aureus to replicate intracellularly. There they found that the ability of S. aureus to grow inside the cell was tied to OC differentiation. The magnitude of overnight bacterial expansion positively correlated with OC maturity and duration cultured with the osteoclastogenic factor RANK ligand (RANKL). Bacterial …

Antimicrobial Responses Of Staphylococcus Aureus In Simulated Spaceflight Conditions, Mikayla Dutkiewicz, Yegor Bushnev

Discovery Day - Daytona Beach

Microbial persistence in confined environments, such as spacecraft, can pose challenges to astronaut health and habitat maintenance. This project investigates Staphylococcus aureus, a Gram-positive bacterium commonly associated with human microbiota and opportunistic infections, in spaceflight-relevant environmental conditions. Further, this project will assess the influence of the antimicrobial/antioxidant compound quercetin to assess its effects on bacterial growth and virulence under standard Earth gravity and simulated International Space Station (ISS) conditions. This approach will assess whether spaceflight-relevant stressors, including microgravity and radiation, alter treatment efficacy by influencing microbial physiology and antimicrobial susceptibility. Data collection and analysis are ongoing, and results are expected …

Observing Antibiotic Resistance In Bacterial Co-Cultures Under Simulated Microgravity, Tyler Jenkins, Marina Vaden

Discovery Day - Daytona Beach

Bacteria grow in complex natural environments with multiple factors affecting their growth, metabolism, and physiology. While astronauts are still preparing to travel to Mars, scientists must learn how to simulate a more realistic Martian environment. While a small volume of publications investigates the independent effects of microgravity or Martian regolith on microorganisms (Liao et al., 2025; Allen et al., 2022; Naz et al., 2023; Duri et al., 2025), to our knowledge no current experiments exist on the joint effects of microgravity and Martian simulant on a co-culture. This experiment aims to investigate the effect of a microgravity analog on the …

Investigation Of Biofilm Formation And Osmotic Stress Tolerance Of Nonmotile Escherichia Coli In Simulated Microgravity, Tyler Jenkins

Discovery Day - Daytona Beach

Simulated microgravity presents multiple physiological stressors for astronauts, including bone demineralization, muscle loss, and weakening of the immune system. Bacteria serve as viable model organisms to study physiological changes because of their abundance in the human digestive system and skin. Motility in bacteria plays a significant role in cell survival, but few studies have been conducted on microgravity’s effect on motility phenotypes. While motile strains like Escherichia coli K12 have been studied extensively under microgravity conditions, the effects of simulated microgravity on non-motile strains are largely unknown. To better understand this relationship, the nonmotile E. coli MG1655 strain was inoculated …

Evaluation Of Antimicrobial Resistance In Pathogens Relevant To Long-Duration Space Missions, Natalie Brattain, Yegor Bushnev, Mikayla M. Dutkiewicz

Discovery Day - Daytona Beach

Antimicrobial resistance is a growing global concern that necessitates the development of effective strategies for selecting appropriate antibiotics, especially in the context of future long-duration space missions, where infection control and treatment options are limited. This study employs the Kirby–Bauer disk diffusion assay to evaluate the antimicrobial susceptibility of Pseudomonas aeruginosa and other clinically and spaceflight-relevant bacterial pathogens such as Klebsiella pneumoniae, Staphylococcus aureus, and Streptococcus pneumoniae. These pathogens will be tested with commonly used antibiotics and potential natural compounds.   The pathogens will be cultured and isolated onto Mueller–Hinton agar plates. Antibiotic disks, along with various flavonoids disks, such as …

From Dust To Growth: Microbial Pathways To Extraterrestrial Farming, Stefani Capasso Villanueva, Nupur Kulkarni

Discovery Day - Daytona Beach

From Dust to Growth: Microbial Pathways to Extraterrestrial Farming addresses the fundamental challenge of sustaining long-term human habitation on other planets. In the era of the Artemis missions, establishing a cost-effective, bioregenerative food source is critical to reducing logistical dependency on Earth, and mitigating the physiological stressors faced by spacecrew through improved nutrition. This study initially investigated the viability of cultivating Mizuna, a proven ISS model organism, in a substrate of Martian regolith simulant amended with organic compost. Following iterative trials, it was found that the plant survival rate was extremely low, even after varying percentages of compost and simulant. …

Effects Of Microgravity And Gamma Radiation On Biofilm Growth, Anya Pavlidis, Kaitlyn Mills Mills, Eva Mcclory, Grant Erlinder, Allen Qiu

Discovery Day - Daytona Beach

Biofilms are collections of bacteria that commonly grow on a variety of surfaces. They are resistant to environmental impacts as bacteria fortify themselves to a surface. Biofilms are commonly found on Earth, but more problematically are also found on spacecraft. On the ISS biofilms have developed in spaces like the workout area, food spaces, and most concerning in the Water Recovery System (WRS). Biofilms tend to react differently to attempted cleaning methods in space than they do on Earth and can be located in extremely difficult to reach places.   This study aims to explore the effects of gamma radiation on …

Escherichia Coli Concentrations In Sand And Water At Tributary-Influenced Lake Michigan Beaches, Josie Elaine Kuhlman

Masters Theses

Contamination of public recreational water and sand is a human health concern, creating a management challenge for public health officials. Past research has shown that Escherichia coli can persist in sediment and can be washed into recreational water. Currently, beach monitoring practices only utilize E. coli concentrations in water samples to determine beach safety and do not consider potential exposure to sediment/sand concentrations. In this study, I investigated the relationship between E. coli concentrations in water and sand samples, which will aid public health officials in making more informed decisions about beach closures. I utilized culture-based measurements of E. coli …

Function And Regulation Of Long Polar Fimbriae During Enterohemorrhagic Escherichia Coli Infection, Walter J. Galdamez

Dissertations and Theses (Open Access)

Enterohemorrhagic Escherichia coli (EHEC) is a foodborne pathogen that causes severe gastrointestinal disease and hemolytic uremic syndrome. EHEC employs multiple virulence factors to colonize the host intestine, including the locus of enterocyte effacement (LEE) encoded type III secretion system, intimin, and flagella, yet the role of long polar fimbriae (Lpf) in adhesions and infection remains less well understood. Long polar fimbriae can mediate bacterial attachment to host cells in vitro, yet the regulation and function of its two fimbrial operons, lpf1 and lpf2 in vivo remain poorly understood. Preliminary RNA-seq data from zebrafish infected with EHEC reveal that expression of …

Defining The Role Of Spxa1 And Spxa2 In Group A Streptococcus (Gas), Gretchen Anne Morrison

Dissertations and Theses (Open Access)

Group A Streptococcus (GAS) is a human-restricted pathogen whose global incidence has surged in the post-COVID era. The ability of GAS to shift from a colonizing to invasive phenotype depends on coordinated virulence gene regulation in response to host-imposed stressors. The paralogous global transcriptional regulators, SpxA1 and SpxA2, have emerged as central mediators of these adaptive responses; however, the mechanisms by which these regulators influence both global gene regulation in direct response to external stresses and the host response as a result of regulatory changes remain incompletely understood. Using an integrated multi-omic approach, we define the distinct yet interconnected regulatory …

Mutational Analysis Of Domain Functions In The Yeast Decapping Enzyme Dcp2, Jellisa Ewan, Ambro Van Hoof

Dissertations and Theses (Open Access)

In yeast, the major mRNA decay pathway involves deadenylation of the 3’ poly-A tail, followed by decapping of the 5’ m7Gppp cap and subsequent 5’ to 3’ degradation or 3’ to 5’ degradation. This is carried out by Pan2/Pan3 and Ccr4/Not deadenylases, the decapping enzyme Dcp2, and Xrn1 and  RNA exosome exoribonucleases, respectively. The eukaryotic mRNA decapping enzyme complex, Dcp1/Dcp2, is essential in yeast, and deletion of either gene is lethal. However, the deadenylases that act upstream and the 5’ exoribonuclease that act downstream of the decapping step are not, even though they are all highly conserved with no known …

Tissue-Specific And Sex-Dependent Microbiome Structure In East African Cattle Ticks (Amblyomma Gemma And Rhipicephalus Pulchellus) And Their Bovine Hosts, Dennis Getange, Samson Mukaratirwa, Rua Khogali, Epaphrus Yuko, James Kabii, Joel L. Bargul, Jandouwe Villinger

All Peer-Reviewed Publications

Ticks and their vertebrate hosts share intimate ecological interactions that shape microbial community composition, with implications for tick fitness and pathogen transmission. However, the extent and specificity of tick–host microbial interactions remain poorly understood, particularly in East African tick species. Here, we characterised microbial communities across multiple tissue types from two economically important tick species (Amblyomma gemma and Rhipicephalus pulchellus) and their shared bovine host using 16S rRNA V1-V2 gene sequencing. We profiled haemolymph, midgut, salivary glands, and gonads from individual ticks (25 Am. gemma and 8 Rh. pulchellus), alongside 12 bovine blood samples. Microbiota were dominated by Proteobacteria, Firmicutes, …

Bridging The Gap In Science Research: Preparing Students For College- Level Research In The Sciences, Victoria Helwig, Yaoguang Li

UConn Library Presentations

Many first-year students enter college unprepared to fully engage with scientific literature and academic library resources. Drawing on experiences from academic librarians working with STEM students, this session explores common gaps in science research skills, including navigating databases, identifying scholarly sources, and understanding the structure of scientific literature. Participants will be introduced to practical strategies and classroom-ready activities to better prepare students for college-level research. Discussion questions: What science research skills do students struggle with most when entering college? How can high school instruction better support these skills? Where can librarians and educators collaborate to support student success?

Analysis Of The Atypical Temperature Dependence And Conformational Changes During Turnover Of A Lactobacillus Chlorogenic Acid Esterase, Nathaniel Carl, Yianni Tsigaris, Dan Ji, Nora K. Anpree, Kellie K. Omori, Cedric P. Owens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Many bacterial chlorogenic acid esterases (ChlEs) exhibit atypical temperature behavior, featuring activities that barely change with temperature and activity maxima that fall below the thermal denaturation point. This work focuses on a ChlE from Lactobacillus helveticus (Lh–ChlE), which has a flat temperature dependence. First, it was determined that conformational changes during Lh–ChlE turnover are not rate-limiting and that the overall rate depends on the chemical step at all temperatures. Next, Lh–ChlE’s temperature dependence was investigated using a conformational equilibrium model that assumes the existence of a temperature-dependent equilibrium between an active and an inactive conformation and an activation heat capacity …

De Novo Pyrimidine Synthesis Controls Germinal Center B Cell And Plasma Cell Fates And Systemic Autoimmunity, Julia L. Weber, Tien Bui, Keomonyroth Nuon, Adam J. Fike, Sophia M. Crocker, Kristen N. Bricker, Anju Maharjan, Wujuan Zhang, Aaron R. Goldman, Sathi Babu Chodisetti, Ziaur S. M. Rahman

Department of Microbiology and Immunology Faculty Papers

Whether and how pyrimidine metabolites promote systemic autoimmunity is unknown. Here, metabolomics and 15N-amide glutamine tracing show enhanced flux through de novo pyrimidine synthesis in systemic lupus erythematosus (SLE)-prone B cells. Temporal inhibition of pyrimidine synthesis dampens SLE-prone but not foreign antigen-specific germinal center (GC), plasma cell (PC), and antibody responses. Uridine monophosphate synthase (UMPS) conditional deletion, however, reveals a B cell-intrinsic requirement of de novo pyrimidine synthesis in foreign antigen-driven and SLE-prone GC, PC, and antibody responses and kidney immune complex deposition. Metabolomics, mitochondrial stress test, metabolic flow cytometry, glycolytic rate assay, and RNA sequencing highlight the importance of …

Systemic Infection Of Beauveria Bassiana In A Stranded Endangered Green Turtle Chelonia Mydas: A Case Report, Ming-An Tsai, I-Chun Chen, Tsung-Hsien Li

The Thai Journal of Veterinary Medicine

The green turtle (Chelonia mydas) is the most frequently encountered marine turtle species in Taiwan. This study describes the postmortem findings of a juvenile green turtle with injuries to the right foreflipper that was rescued off the Taiwan coast and died after 3 months in rehabilitation. Necropsy revealed large, yellow, multifocal caseous lesions involving the right foreflipper, spleen, liver, kidneys, and lungs. Fungal infection of Beauveria bassiana was confirmed by culture, morphological and molecular characterization, phylogenetic analysis, and histopathological examination. This report provides evidence that B. bassiana is associated with a systemic fungal infection which can be fatal …

In Vivo Expression Profiling Of Listeria Monocytogenes Internalins (Inlf, Inlp, Inlj) And Their Corresponding Host Receptors (Vim, Afdn, Muc2) Using A Rabbit Ligated Intestinal Loop Model, Nawar Al-Janabi, Nadhim Mushtaq Hashim Al-Bderee, Zahraa M. Madania, Mohanad Jawad Kadhim

Karbala International Journal of Modern Science

Listeria monocytogenes is a Gram-positive pathogen that causes severe infections, particularly in immunocompromised individuals. Internalin genes are important virulence factors that facilitate the bacterium's invasion of host cells. This research aimed to quantify in vivo expression of selected internalin genes (inlF, inlP, and inlJ) and their corresponding host receptors (VIM, AFDN, and MUC2) during L. monocytogenes infection. To achieve this aim, a rabbit ligated intestinal loop model was constructed comprising two intestinal loops. The first loop was injected with 1 mL of L. monocytogenes (1 × 10⁷ CFU/mL), while the second loop was injected with 1 mL of PBS as …

Pharky, Phedro, Phractured, And Stagephright: Complete Genome Sequences Of Four Ek2 Cluster Microbacterium Phages, Susan M. R. Gurney, Medha Gupta, Deeksha Reddy, Gloria Zacharias, Aleda S. Jomy, Carly J. Smith, Matthew T. Mcdonald, Brett M. Condon

Student Papers, Posters & Projects

We report the complete genome sequence of four Microbacterium phages, Pharky, Phedro, Phractured, and StagePhright, isolated using the bacterial host Microbacterium foliorum from soil samples collected in Philadelphia. All four phages are genetically very similar and contain a gene of unknown function, which is uncommon in the EK2 cluster.

Homocysteine Thiolactone From Translation Proofreading Is An Endogenous Ligand For Cell-Cell Signaling By The Receptor Sdia, Lorenzo Eugenio Leiva, Roberto A. Zúñiga, Gregory J. Phillips, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Several widespread mechanisms enable cellular communication and coordinate the behavior of bacterial populations. The modules responsible for cellular communication are often found in matching pairs: an enzyme that synthesizes a signal molecule and a specific receptor that decodes it. A notable exception is Escherichia coli SdiA, a homolog of known N-acyl-homoserine lactone (AHL) receptors, for which no corresponding AHL synthase exists. SdiA is an orphan receptor that enables cross-talk by sensing AHLs from other bacterial species. In this work, we investigated whether homocysteine thiolactone (HTL), an AHL-like molecule arising from a proofreading reaction of methionyl tRNA synthetase (MetRS) to correct …

Understanding The Effects Of Simulated Microgravity On Staphylococcus Epidermidis And Escherichia Coli In Co-Culture, Emma Costa, Mitchell K. Villafania, Makaila Olson, Kareigh N. Gammon, Hugo Castillo

Beyond: Undergraduate Research Journal

With the popularity of space travel increasing, it is important to understand the effects of microgravity on microbial communities as alterations on bacterial interactions can occur. Staphylococcus epidermidis and Escherichia coli are bacteria that are commonly found within human microbiomes. S. epidermidis is a cocci-shaped gram-positive bacterium that is part of the human skin microbiome. However, it can gather on sites of open skin and enter the body leading to an infection. E. coli is a rod-shaped gram-negative bacterium that can be found in the human gut microbiome. The pathogenic strains of E. coli have the potential to cause harmful …

Effectiveness Of Organic Amendments In Enriching Nitrogen In Compost Produced From Organic Fractions Of Market Waste Generated In Dar Es Salaam, Tanzania, Amani Bilula, Ally Mahadhy, Anthony Manoni Mshandete, Amelia Kivaisi

Tanzania Journal of Science

Low nitrogen (N) content remains a key limitation of compost derived from urban organic waste. This study evaluated the effectiveness of selected plant-based organic amendments in enhancing nitrogen content and improving compost quality. Four plant- based organic amendments, Leucaena leucocephala (BN01), Commelina benghalensis (BN02), Morus alba (BN03), and Helianthus annuus (sunflower) cake (BN04), were incorporated into market waste compost at ratios of 1:0.06:0.04, 1:0.06:0.25, and 1:0.06:0.5 (organic waste: sawdust: amendment). Composting was conducted using a 4 × 3 factorial design with three replicates per treatment (n = 36). Temperature, moisture, and pH were monitored throughout the composting period. Total nitrogen, …

Birds Of A Tether Flock Together: Examining Centromere Tethering And Chromosome Segregation In Caulobacter Crescentus, Jake Dwyer, Simon Kruczak, Rodrigo Arana-Garrido, Paola Mera

MICRO-CCS student projects

Introduction:

Chromosome segregation is essential for all domains of life. Caulobacter crescentus is a key model for studying this process. It divides asymmetrically into two morphologically distinct cells. Proteins can be seen directly with fluorescent tags.

Research done on Caulobacter can apply to many different bacteria. The ParABS system is integral to chromosome segregation in Caulobacter.

ParS – DNA sequence on the chromosome

ParB – CTP-binding protein that specifically recognizes parS

ParA – ATP-binding protein that non-specifically binds DNA and provides the force for segregation.

PopZ – Polar tethering protein via interactions with ParB.

TipN - Polar protein that …

Has Plant Domestication Compromised Plant Defensive Chemistry? Aphid Induced Stress In Tomatoes, Nhi Do, Satinderpal Kaur, Minxing Zhu, Esther N. Ngumbi

MICRO-CCS student projects

Tomato plants have natural defensive mechanisms.

Direct: Phenolics are secondary metabolites that can protect the plant by intoxicating the herbivores and/or producing strong repulsive odors.

Indirect: VOCs, Volatile Organic Chemicals, are gas phase signals that attract the predators of the attacking herbivore to the plant.

Domestication of plants may chemically alter these defenses by prioritizing fruit production over defensive traits.

We hypothesize that wild/ancient tomato plants would have a greater quantity of volatiles and increased concentration of leaf total phenolics compared to cultivated tomatoes during aphid herbivory.

How Does High-Oil Sorghum Change Potential Extracellular Enzyme Activity Across Soil Depth Profiles Under Drought Conditions?, Krystal Monique Role, Rounak Patra, Wendy Yang

MICRO-CCS student projects

Transgenic oil sorghum reallocates photosynthate-carbon (C) into vegetative lipids, accumulating nonstructural lipids in both shoot and root tissues. Altered plant C allocation and root lipid accumulation may shift root exudate chemistry, belowground C inputs, and microbial nutrient demand throughout the soil profile. While aboveground productivity in high-oil sorghum is well-characterized, its belowground impacts on soil microbial enzyme activity and exchangeable cation dynamics, especially across soil horizons under drought stress remain unknown.

Project objective was to find out how transgenic high oil sorghum (Tx-HO1) influences CNP acquiring extracellular enzyme activities and soil exchangeable cation dynamics across soil horizons under drought and …

Investigation Of Biological Denitrification Inhibition By Specific Anthocyanins, Kristin Palazzo, Holly Anderson, Aislinn Geedey, Angela Kent

MICRO-CCS student projects

Nitrogen fertilizers are applied to corn fields to support high crop yields, but some nitrogen is lost through microbial denitrification, producing nitrous oxide (N2O), a potent greenhouse gas. Some plants produce certain flavonoids that can suppress microbial denitrification, a trait known as biological denitrification inhibition (BDI). Maize produces flavonoids in the form of anthocyanins, including cyanidin-3-glucoside (C3G), the major anthocyanin produced by maize.

The goals of this project were to determine whether C3G:

is produced in maize roots

inhibits microbial denitrification