Microbiology Commons^™

Surveillance And Comparative Genomics Of Bacteria From Hospital And Human Reservoirs, Emily E. Benedict

WUSM Theses and Dissertations – All Programs

Bacteria are diverse and adaptable and, consequently, present in a wide variety of environments. They are capable of growing under intense pressures, including those brought on by the human immune system and disinfection strategies. To survive these pressures, bacteria develop resistances. Antimicrobial resistance, which occurs when a microbe is no longer responsive to the antibiotic intended to control it, is one such adaptation that presents an especially serious threat, as it limits treatment options for infections caused by antimicrobial resistant microbes. Similarly, the ability of bacteria to survive in environments subjected to heavy disinfection efforts, such as intensive care units …

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 …

Antibiotic Resistance Genes In Diabetic Foot Ulcer Microbiomes: Molecular Mechanisms And Clinical Management Strategies, Fitra Adi Prayogo

Chulalongkorn Medical Journal

Background: Diabetic foot ulcers (DFUs) affect 19-34% of diabetic patients lifetime, representing a major global health burden with over 18 million cases annually. The polymicrobial nature of DFU infections, combined with emerging antibiotic resistance genes, poses unprecedented clinical management challenges. Methicillin-resistant Staphylococcus aureus (MRSA) prevalence reaches 84% and extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae exceeds 50% in some regions, creating urgent therapeutic concerns.

Objective(s): This comprehensive review examines current understanding of microbial communities in diabetic foot ulcers and their associated resistome, analyzing molecular mechanisms underlying antibiotic resistance and clinical implications to identify evidence-based management strategies.

Methods: A narrative review approach was …

Bioactive Potential Of Microbial Isolates From Yoluja Cave And Jepirramüin Rock Shelter, Cabo De La Vela (Colombia), Juan Sebastián López Caro, Virginia Patricia Roa Angulo, Alex Alberto González Vargas

International Journal of Speleology

Subterranean environments harbor diverse microbial communities with significant potential for the production of bioactive compounds. This study evaluated the antimicrobial and antioxidant potential of microbial isolates obtained from Yoluja Cave and the Jepirramüin rock shelter, located in the coastal region of La Guajira, Colombia. Field sampling was conducted during three campaigns in July, September, and November 2025, including soil and surface samples collected along environmental gradients within each site. Microorganisms were isolated using selective culture media and identified through morphological and biochemical characterization. Selected strains were subjected to liquid fermentation and organic solvent extraction to obtain crude metabolites. Analysis of …

The Relationship Between Light Intensity And Tall Goldenrod Productivity Across Greencastle Fields, Erniya Jean Jacques '29, Rose Keith

Annual Student Research Poster Session

This study investigates the effects of environmental conditions, specifically light availability and climate variation, on the growth and productivity of Solidago altissima (tall goldenrod) across four field sites in Greencastle, Indiana (including sites associated with DePauw University, such as Prindle, Ullem, QA, and NP). By sampling 160 specimens across contrasting light environments (sunny vs. shaded plots) and comparing data between 2024 and 2026, the project evaluates key physical traits including plant height, biomass, and light intensity (μmol). Findings indicate a trade-off in energy allocation: plants in shaded conditions invest more energy into height growth to capture limited sunlight, whereas individuals …

Building Genetic And Culturing Tools For The Understudied Soil Bacterium E. Flagellatus, Aaron Butler, Brenda Pratte, Lon Chubiz

Undergraduate Research Symposium

Soil bacteria play essential roles in nutrient cycling, yet many abundant groups remain poorly characterized due to challenges in cultivation and genetic manipulation. One such organism is Edaphobacter flagellatus, a member of the Acidobacteriota frequently detected in soil environments but lacking well-developed experimental tools. To address this limitation, our laboratory has generated a genome-wide mutant library using the Tn5 transposon, enabling random disruption of genes across the population.

This project aims to establish culture conditions necessary to support the use of this library for functional genomic studies. In particular, defined minimal media can impose selective pressures that reveal …

A Single-Step Plate Method For The Screening Of Xyl-A Mutant Libraries Based On Gene Expression, Bilqees Fatima, Muhammad Mohsin Javed

Journal of Bioresource Management

A single-step plate method is described for the screening of transformants of cloned gene xyl-A encoding xylose isomerase. It is rapid, inexpensive, easy to perform, and more specific, as the selection is based on xyl-A expression level. The crucial composition of the plate medium comprised agar, buffer, nutrients, co-factor, substrate, inducer, antibiotic, and an indicator, i.e., 2, 3, 5-triphenyl tetrazolium chloride (TTC). Transformed cells of E. coli BL21 (DE3) with a plasmid (pET21(a)⁺+xyl-A), were exclusively capable of growing, isomerizing the substrate, and producing deep-red formazan by reducing TTC, whereas the untransformed cells and cells containing a …

Novel Chitosan-Pyrazole Derivatives: Synthesis, Characterization, And Antimicrobial Potential Assessment, Samar A. Salim, Elrefaie S. Kenawy, Mohamed G. Altamami, Ahmed A. Safaan, Manar M. Emara, Elbadawy A. Kamoun, Atif A. Elgharably

Nanotechnology Research Centre

Double novel chitosan Schiff-base series (I and II) based on heterocyclic moieties were synthesized to improve the pristine antibacterial capabilities of chitosan. Series (I) chitosan Schiff bases were prepared by reacting chitosan with six derivatives of 4-formyl-1H-pyrazole in an acidic medium, whereas series (II) was prepared by reacting chitosan with six derivatives of 1-(4-vinylbenzyl)-3-aryl-1H-pyrazole-4-carbaldehyde in an acidic medium. The chemical configurations of the twelve manufactured Schiff bases were verified using FTIR analysis & TGA measurements. We assessed the antimicrobial efficacy of chitosan and its Schiff base derivatives against four standard bacterial species, Staphylococcus aureus, Enterococcus faecalis, Pseudomonas aeruginosa, and Escherichia …

Temporal Variation In Picophytoplankton Pigment Phenotypes Of Two Urban Rivers, Kylee M. Lamberson, Camille E. Wendlandt, Kristin E. Forgrave, Anne W. Thompson

International Journal of Undergraduate Research and Creative Activities

Picophytoplankton are a group of photosynthetic, unicellular organisms, making them key primary producers in aquatic ecosystems. These cells numerically dominate in oceans and lakes where picophytoplankton communities contain phenotypic subpopulations that correspond to biogeographic patterns. In rivers, however, such community dynamics are less studied. We examined the phenotypic subpopulations of picophytoplankton in two converging urban river environments of Portland, Oregon (USA): the Columbia and the Willamette Rivers. From September 2022 through July 2023, we took roughly bi-weekly surface water samples and used multi-laser flow cytometry to distinguish between photosynthetic cells based on their size and pigment fluorescence. We discovered seven …

Comparison Of Preenrichment And Screening Methods For The Detection Of Salmonella Enterica Serovar Agona In Meat Analog Products, Kylie Sacapano, Amanda Tabb, Biola Fatusin, Samantha M. Covaia, Isha Shingre, Lieuchi Phan, Kyson Chou, Jamie Du, Beilei Ge, Donna Williams-Hill, Rosalee S. Hellberg

Food Science Faculty Articles and Research

With the growing demand and variety of meat analogs on the commercial market, there is a need to revisit testing methods for foodborne pathogens in these products. The U.S. Food and Drug Administration (FDA) regulatory methods for Salmonella enterica detection in meat analogs follow the Bacteriological Analytical Manual and are relatively time-consuming. Therefore, this study aimed to compare preenrichment and screening methods for the detection of Salmonella in meat analogs by evaluating current FDA reference methods alongside alternative preenrichment broths and rapid molecular screening techniques. Meat analog samples were inoculated with S. enterica serovar Agona at three levels: (1) uninoculated …

Amorphous Calcium Phosphate Maintains Casein Microarchitecture While Modulating Bacterial Growth Kinetics, Vuk Uskoković, Michael Ibba, Lorenzo Eugenio Leiva

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Casein, the primary source of protein in ruminant milk, represents a family of proteins that self-assemble into globules composed of finer spherical subunits and stabilized by calcium phosphate (CP) nanoparticles. These globules act as holdase-type chaperones for unfolded or partially folded proteins, preventing their aggregation. Simultaneously, by integrating CP nanoparticles, they enable the bioavailability of calcium and phosphate beyond their solubility limits, thereby enhancing the nutritional value of milk. Using a range of physicochemical and biological characterization techniques, including scanning and transmission electron microscopy, organic and inorganic elemental analyses, SDS-PAGE, and vibrational, UV/Vis and NMR spectroscopies, it is demonstrated that …

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 …