Microbiology Commons^™

Recovering Plasmid-Id Barcoded Strains Of Sinorhizobium Meliloti From A Native Soil Microbiome, Kenny Sacks, Hannah Murray, Katy Heath

MICRO-CCS student projects

Introduction

Legume-Rhizobia Mutualism: Nitrogen is an essential nutrient for plant growth. Plants can’t produce nitrogenous compounds. Rhizobia fix atmospheric nitrogen gas into bioavailable forms. Rhizobia form a nutrient exchange mutualism with leguminous plants.

Project description

Can our bacteria persist within the rhizosphere and into the nodule when faced with native microbial competitors? The Medicago-Sinorhizobium mutualism is used as a model system. Survival of strains post competition is difficult to measure due to identical 16S rRNA sequences and similar marker genes. Plasmid-ID barcoding sequences may provide a way of testing strains against a community.

Soil Microbiome Effect On Seedling Diseases And High Throughput Isolate Identification, Annalaysia Smith, Mara Krone, Santiago Mideros

MICRO-CCS student projects

The soil microbiome has a substantial effect on disease suppression. Organic farming is a practice used to create a more diverse microbiome which can create disease suppression. Different agricultural practices such as fertilization and rotation system are known to affect the microbiome (Schlatter et al 2017). Therefore, it is important to study the effects of different microbiomes on disease suppression. Furthermore, methods are necessary for quantifying the effect of disease suppression on specific pathogen populations. To do this, it is important to properly identify the pathogens.

Objectives:

1. Test if different nitrogen treatments cause variations in organic soils disease suppression. …

Effects Of Varying Ph Levels On Prophenoloxidase Activity And Hemocyte Recruitment In Daphnia Dentifera, Yusra Siddiqi, Carla Caceres

MICRO-CCS student projects

Anthropogenic activities and natural processes are responsible for changing the pH of freshwaters which can impact aquatic life. D. dentifera is a keystone species found in midwestern lakes that is susceptible to a parasitic yeast called Australozyma monospora. A. monospora spores puncture the Daphnia gut into the hemolymph and begin using the host’s resources. Invertebrate immunity is under researched.

Research objective: How will different pH impact prophenoloxidase (proPO) activity and hemocyte recruitment in Daphnia dentifera?

Screening A Random Hile Mutant Library To Characterize Hild Regulation In Salmonella, Danista Kannah, Gracious Donkor, James M. Slauch

MICRO-CCS student projects

Salmonella is a leading cause of gastrointestinal diseases globally. It utilizes a type three secretion system (T3SS) encoded on Salmonella Pathogenicity Island 1 (SPI1) to invade host intestinal epithelial cells during infection.

HilE directly regulates HilD via a direct protein-protein interaction. The Slauch lab identified two HilD variants, A141V and A141T, which are blind to HilE. These variants activate hilA expression even in the presence of HilE, indicating that the binding of HilE to these mutants is compromised.

Hypothesis: Performing random mutagenesis of hilE could lead to changes at the protein level which could compensate for the loss of interaction …

Fungal Diversity In Lespedeza Cuneata Roots, Gwendolyn Happ, Sophia Mcdade, Anthony Yannarell

MICRO-CCS student projects

Background

• Plants form a relationship with fungi that can be beneficial or harmful
• Fungi may grow on the plant surface, within plant tissues, or around roots
• Plants release compounds that invite fungi to their roots and chemicals  that can diminish unwanted fungi

Why Lespedeza cuneata? 

• Invasive that competes with native plants and damages biodiversity within plant and animal communities
• Alters soil microbiome
• Expansive seed bank and deep root system
• Understanding its microbiome can help in understanding invasive species success and ecology

Efficacy And Evolutionary Dynamics Of 222 Nm Far-Uvc Against Vibrio Cholerae, Kadicha Madakimova, Angus Wu, Nkrumah Grant

MICRO-CCS student projects

The Far-UVC light at 222 nm wavelength (UV222) is one of the emerging methods of disinfection of bacteria in public spaces such as hospitals and labs.

• Does not penetrate human skin and does not cause harm to eyes making it a safer alternative to conventional UV systems.

• Primarily targets proteins preventing regrowth and repair pathways.

However, the potential for bacterial adaptation following sublethal UV222 exposure remains largely unknown.

Central question: How does QS transcriptional state influence the efficacy and resistance profile of V. cholerae to UV222 nm irradiation?

Hypothesis: Qurom-sensing transcriptional state determines V. cholerae susceptibility to UV222 nm UV …

A Tale Of Two Symbionts: Comparative Cellular Localization Of Two Manipulative Rickettsiella Strains In A Spider, Kaitlyn Costanza, Thea Bliss, Matthew Doremus

MICRO-CCS student projects

Many arthropods harbor maternally transmitted endosymbionts that manipulate host reproduction to increase their transmission. One such manipulation is cytoplasmic incompatibility (CI), in which embryos produced by infected males and uninfected females fail to develop.

Rickettsiella has recently been discovered to cause CI in Mermessus fradeorum. Two geographically distinct Rickettsiella strains infect this spider: R1 causes strong CI, whereas R2 causes weaker CI.

Hypothesis: H1: Both Rickettsiella strains will localize within or near developing sperm cells in the testes. H2: The stronger R1 strain will exhibit more consistent localization within infected adult reproductive tissues than the weaker R2 strain.

The Deep Darkness Microbiome: Functional And Taxonomic Diversity In An Oligotrophic Temperate Cave, Philips O. Akinwole, Nina G. Shaffer '25, Emma E.C. Jacobs '25, Zoe Green '27, Thi Doan '27, Crimson Hickman '28, Kaija M. Carr '25, Kenneth L. Brown

Biology Faculty publications

Many subterranean ecosystems are chronically energy limited, yet the mechanisms governing microbial community assembly and metabolic function under extreme carbon scarcity remain poorly resolved. We combined 16S rRNA gene sequencing with community-level physiological profiling (CLPP) to examine how physicochemical gradients regulate microbial diversity and carbon-use strategies across a surface-subsurface transition into the Deep Darkness zone of Indiana Caverns. Progressive isolation from surface inputs resulted in sharp declines in microbial biomass, total organic carbon, and nitrogen, accompanied by increased water content and C:N ratios, indicating strong attenuation of allochthonous organic matter and intensified resource filtering. Microbial communities spanned 42 bacterial phyla, …

Endophytic Actinobacteria: Deciphering Therapeutic And Industrial Potential, And Prospects Of Genome Mining In Novel Products Discovery, Yusra Waheed, Rabia Shahdin, Imran Sajid

Journal of Bioresource Management

Endophytic actinobacteria are a diverse group of Gram-positive bacteria with high G+C content, which inhabit plants’ internal tissues, and represent a significant yet underexplored reservoir of bioactive secondary metabolites. In host plants, a remarkable repertoire of metabolites, including broad-spectrum antibiotics, anticancer, antiviral, antifungal, antioxidant, and immunomodulatory compounds, is synthesized by these microbial allies, carrying significant medicinal and agricultural potential. These endophytes, in contrast to their soil relatives, have developed unique biosynthetic gene clusters (BGCs) strongly influenced by plant-associated factors, leading to the production of structurally novel metabolites. In recent years, the advances in genome mining, metagenomics, and metabolomics have accelerated …

Mobile Genetic Elements Shape Microbial Diversity And Functions In Thawing Permafrost Soils, Jiarong Guo, Samuel T. N. Aroney, Guillermo Domínguez-Huerta, Derek Smith, Dean Vik, Carlos Owusu-Ansah, Akbar Adjie Pratama, Sergei Solonenko, Funing Tian, Cristina Howard-Varona, Zhi-Ping Zhong, Aminata Fofana, Garrett J. Smith, Suzanne B. Hodgkins, Dylan Cronin, Isogenie Field Teams 2010–2017, 2019, Emerge Coordinators, Ben J. Woodcroft, Gene W. Tyson, Virginia I. Rich, Matthew B. Sullivan, Simon Roux, Sarah C. Bagby, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Ecosystems are shaped by communities of microorganisms whose niches and impacts depend on functional profiles influenced by gene gains and losses. Culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, but quantitative understanding of these dynamics in natural systems remains limited. Here we develop and apply a systematic, meta-omic framework to investigate MGEs in a complex natural system using an 8-year soil time series collected at Stordalen Mire, in Sweden’s thawing permafrost margin. In this climate-critical peatland, we identify ~2.1 million MGE recombinases across 89 microbial phyla and assess ecological distributions, affected functions, past mobility and current …

Biofilm Formation By Histophilus Somni On 3d Bovine Respiratory Tissue Cultures, Bindu Subhadra, Neeti Gandhi, Dianjun Cao, Yue-Jia Lee, Padmavathy Rajagopalan, Thomas J. Inzana

Faculty Publications - Biological Sciences

The development of bacterial biofilms following infection involves bacterial attachment to tissues and maturation of the biofilm matrix (BM). However, studying the development of bacterial biofilms in vivo is difficult to follow. An established example of biofilm formation during host infection is bovine respiratory disease (BRD) due to Histophilus somni. To more accurately investigate in vivo biofilm development, three-dimensional bovine airway organoids comprised of bovine turbinate epithelial (BE) and pulmonary artery endothelial (BAE) cells embedded in type I collagen were developed. Cell-free concentrated culture supernatant (CCS) from biofilm-grown H. somni suppressed proliferation of epithelial cells more than endothelial cells, affected …

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 …

Promiscuous Mutualisms: John Dupré And The Centrality Of Symbiosis In The Living World, Thomas Pradeu

Presidential Fellows Articles and Research

My goal in this chapter is to show that symbiosis, especially symbiotic interactions between ‘macrobes’ (non-microbial organisms) and microbes, is a central topic in John Dupré’s work. This topic is undeniably one of the topics by which Dupré has gained wide recognition among practicing scientists, in addition to his recognition within the philosophical community. I spell out why symbiosis has turned out to be a sort of ideal trope for Dupré, as it encapsulates many of his main personal themes—from promiscuous realism to process ontology. I then show that immunology offers one interesting and complementary entry point into microbial symbiosis …

Describing Propagation Of Carbapenem-Resistant Acinetobacter Baumannii Through Comparative Genomics And Phenotypic Analysis Of Modern-Day Clinical Isolates, Emma Graffice

ETDs from 2020-2029

Understanding the genomic structure of bacterial populations is essential for tracking antimicrobial resistance and informing public health strategies to prevent spread of multidrug resistant organisms. In this study, we investigated the diversity and distribution of carbapenem-resistant Acinetobacter baumannii (CRAb) lineages across a major healthcare system in the U.S. Deep South through both retrospective and prospective isolate collection. Our analysis revealed a heterogeneous population composed of multiple genotypically and phenotypically distinct lineages. To improve the resolution of lineage classification, we applied average nucleotide identity (ANI) as a high-resolution metric for comparative genomics. A ≥99% ANI threshold effectively delineated lineages, outperforming traditional …

Jnk Signaling Impacts Car-T Cell Effector Function, Charles Kuhlmann

ETDs from 2020-2029

The potent cytotoxic activity of T cells serves as a natural defense against cancers. Chimeric antigen receptor (CAR) T cell therapy represents a strategy for harnessing T cells against advanced tumors. CAR-T cell therapy has seen striking success against hematologic malignancies, prompting its application to new diseases. Ovarian cancer is a highly lethal disease characterized by frequent recurrence and aggressive nature, prompting the investigation of CAR-T cell therapy as a salvage regimen. However, like in other solid tumors, the early performance of CAR-T cell therapy in ovarian cancer is poor. While many strategies exist for improving the longevity of CAR-T …

Dual-Action Antibacterial Agents Targeting Biofilm Reduction And Membrane Disruption In Staphylococcus Aureus, Rahmat Folashade Zakariyah, Waliyullahi Akorede Husain, Elohor Precious Samuel, Wonder Olanipekun Oloruntoba, Fatmah Opeyemi Saka, Khalid Ayinde Oyelami, Mariam Temitope Baker

Al-Bahir

Antimicrobial resistance in Staphylococcus aureus is a serious global health problem as the organism rapidly develops resistance against widely used antibiotics. This study sought to investigate the antibacterial and antibiofilm properties of γ-Tocopherol, a natural compound from Ocimum gratissimum, as well as its synergism with 5-hydroxymethylfurfural (5-HMF) against S. aureus. The antibacterial activities and minimum inhibitory concentrations of the compounds were determined using agar diffusion and microbroth dilution methods, respectively. Biofilm reduction was evaluated using 2,3,5-triphenyltetrazolium chloride (TTC) assay and membrane integrity was evaluated using the crystal violet microtiter plate assay and the ion leakage assay. The results …

Hiv-1 Tat-Driven Glutamate Dysregulation: Implications For Cognitive Impairment In Hand, Brenna Duffy, Michael Nonnemacher, Sandhya Kortagere

Kimmel Cancer Center Faculty Papers

PURPOSE OF REVIEW: HIV-1-associated neurocognitive disorders (HAND) manifest in 15% to 50% of people with HIV, impairing learning and memory and executive function. The chronic generation of HIV-1 Transactivator of transcription (Tat) likely contributes to HAND via direct neuronal toxicity and glial-mediated toxicity. This review summarizes our current understanding of how chronic Tat generation from microglia and astrocytes promote glutamate excitotoxicity.

RECENT FINDINGS: In recent years, the indirect effects of Tat through the activation of glial cells have gained significant interest. This review highlights microglia and astrocytes as HIV-1 reservoirs that release Tat protein in the central nervous system. Specific …

Discovery Of Bmi-Associated Gut Microbiome Signatures In The Awi-Gen 2 Cohort, Meriem Yagoubi

Theses and Dissertations

Obesity is increasing across sub-Saharan Africa amid rapid dietary, environmental, and urbanization transitions, yet the gut microbiome features associated with adiposity in African populations remain under-characterized. This study investigated whether species-level gut microbiome composition is associated with body mass index (BMI) in the AWI-Gen 2 cohort, and whether BMI-associated microbial signals remain detectable after accounting for the dominant geographic structure of the microbiome. Gut microbiome community structure and diversity were characterized across 1,665 participants, and differential abundance analysis was used to identify taxa associated with BMI after controlling for study site. Machine learning models were then trained to assess how …

Marine Heatwaves And Fish Reproduction: Endocrine Responses In The Eurythermal Sheepshead Minnow (Cyprinodon Variegatus), Isabel Villafuerte

Master's Theses

Marine heatwaves associated with climate change are increasing in frequency and severity, posing significant threats to fish populations in shallow habitats such as estuaries and salt marshes. Because temperature is a primary regulator of fish reproduction, understanding how heatwaves affect reproductive physiology is critical for anticipating the biological consequences of ongoing climate change for coastal fishes. Here we examined how simulated heatwave conditions affect the reproductive hypothalamic-pituitary-gonadal (HPG) endocrine axis in the estuarine sheepshead minnow (Cyprinodon variegatus), a eurythermal fish well suited to studying thermal stress responses in estuarine environments. Adult sheepshead minnows acclimated to a daily oscillating …

Mapping The Tar Vrna Interaction With Hiv-1 Integrase, Jian Sun, Rahul Yadav, Tolga Catmakas, Luke Fisher, Nicholas C. Fitzkee, Jacques J. Kessl

Faculty Publications

A series of critical interactions within the viral core between viral RNA (vRNA) and HIV-1 Integrase (IN) has previously been reported. In these studies, contact points between vRNA and IN were identified using RNA-seq and MS-based protein foot-printing approaches. Several IN amino acids located in its C-terminal domain (CTD) were found to be essential for vRNA binding, and their alanine substitution severely impacted the correct morphogenesis of the mature viral core. Here, we have used the TAR element to extend these studies by performing a comprehensive mapping of the interaction by deploying RNA crosslinking and NMR methodologies. Together, these approaches …

Microbial Literacy, Equity, And Sustainability At Cal Poly: A Policy Framework With University Housing As A Pilot Case, Joseph B. Fewel

Biological Sciences

Microorganisms play a fundamental role in human health, environmental systems, and the functioning of built environments, yet they remain largely absent from sustainability and public policy discussions. This project proposes a framework for integrating microbial literacy, equity, and health into institutional decision-making, using California Polytechnic State University (Cal Poly) as a case study and university housing as a pilot site for implementation. Drawing on interdisciplinary literature in microbiology, public health, environmental justice, and sustainability, as well as policy analysis and stakeholder interviews, this project examines how campus systems, including housing, ventilation, sanitation, food systems, and waste management, shape microbial exposure …

Synergies Of Microecology And Macroecology Elicit Insights For Creation Care, David Warners, John T. Wertz

University Faculty Publications and Creative Works

This article reports on a collection of microecological and macroecological insights that emerged from extended conversations between Calvin University professors David Warners, a botanist concentrating in restoration ecology, and John Wertz, a micro-biologist specializing in microbial ecology. Classic descriptions of ecology identify biological interactions as happening at the ecosystem, community, or population level. And yet, ecological interactions are very much occurring at the microbial level as well. Furthermore, microbial-level interactions frequently influence the quality and character of macroecological relationships and vice versa. Allowing ecological principles to be applied across all life forms broadens our comprehension of interactions that are happening …

Protein Glycosylation In Natural And Synthetic Minimal Genome Mycoplasmas, John Sanford

ETDs from 2020-2029

Mycoplasmas are cell wall-less bacterial symbionts with remarkably streamlined genomes. Mycoplasmas offer two intriguing model organisms for studying concepts of minimal life. Mycoplasma genitalium has streamlined its genome to 580-kbp while maintaining virulence to suit its niche of parasitizing the human urogenital tract. The J. Craig Venter Institute has synthesized and transplanted a 543-kbp genome into a recipient cell, resulting in a non-pathogenic organism termed JCVI-syn3A. The conservation of a biological process in M. genitalium and JCVI-syn3A strongly implies an essential function in mycoplasmas, and potentially all life. Despite common thought of mycoplasmas being the simplest cells, much of their …

Exploring The Durability Of Marine Picocyanobacterial Microcolonies, Erik Swanson

University Honors Theses

Picocyanobacteria of the genus Synechococcus are widespread aquatic photoautotrophs that play essential roles in primary production and carbon cycling. Some Synechococcus strains form multicellular microcolonies, but the mechanisms of cell-to-cell attachments and structural durability of these microcolonies remain poorly understood. This research investigated the physical durability of microcolonies in two marine Synechococcus strains (CC9605 and CC9311) using physical disruption treatments. Cultures were subjected to vortexing and sonication treatments, and populations of single cells and microcolonies were quantified using flow cytometry based on differences in measures of size. Results indicated that strain CC9605 showed no significant treatment effect, whereas CC9311 displayed …

Developing A High-Resolution Off-Axis Common-Mode Digital Holographic Microscope, Lucy Cook

University Honors Theses

Off-axis digital holographic microscopy (DHM) is a powerful tool for 3D, non-invasive live-cell tracking without moving parts. However, traditional setups face an inherent dilemma: split-path interferometers offer high spatial resolution but poor temporal stability, while more stable common-mode configurations are historically limited to lower numerical aperture (NA) regimes. This thesis bridges that gap by scaling a common-mode DHM architecture into a high-resolution benchtop instrument featuring NA = 0.65 objectives, paired with a high-power 520 nm laser source to combat transmission losses and sustain imaging frame rates across an expanded optical footprint. We map the multi-variable design space required to satisfy …

Immunomodulatory And Signaling Molecules From Plant-Associated Bacteria: Toll-Like Receptor 4 Agonist Adjuvants And Diketopiperazine-Mediated Communication, Marian Romaine

Dissertations, Theses, and Capstone Projects

Medicinal plants and their associated microbiomes constitute a rich source of bioactive natural products with applications in immunotherapy and microbial ecology. Herbal formulations have long been valued for safe immune enhancement, while bacterial signaling molecules govern community behaviors critical to pathogenesis, symbiosis, and environmental processes. Bacterial lipopolysaccharides (LPS) from plant-associated Gram-negative bacteria have emerged as potent TLR4 agonists, yet their endotoxic potential limits direct use, and diketopiperazines (DKPs) serve as versatile quorum-sensing mediators capable of modulating biofilms in mixed microbial systems.

The work in this thesis comprises two independent but complementary research strands. The first strand pursued the engineering of …

Evaluating Soil Health And Crop Yield In Louisiana Agricultural Systems: Impacts Of Best Management Practices And Prediction Models, Hector J. Mendoza Lagos

LSU Doctoral Dissertations

The adoption of conservation management practices is critical for improving soil health, enhancing nutrient use efficiency, and sustaining crop productivity in row crop systems in Louisiana. This study evaluated the role of conservation agronomic practices, soil biochemical indicators, and machine learning predictive models to improve soil nutrient dynamics, soil health indicators, microbial communities (MC), and crop productivity on a corn (Zea mays L.) research plot scale and in a commercial forty-hectare cotton (Gassypium hirsutum L.)-corn-soybean (Glycine max L.) rotation system in northeast Louisiana. The objectives of the study were to evaluate soil nutrient dynamics and MCs under …

Examining The Ligands, Location, And Function Of Toll-Like Receptor 10, Kiefer Keanu Tam

Master's Theses

Toll-like receptors are a class of innate immune pattern recognition receptors that detect pathogen-associated molecular patterns and regulate downstream inflammatory responses. Toll-like receptor 10 remains the only human TLR whose ligand specificity, cellular localization, and immunological function are not fully defined. Emerging evidence suggests that TLR10 may play an anti-inflammatory role and can heterodimerize with TLR2 to modulate immune signaling. Previous studies from our laboratory demonstrated that stimulation with heat-killed Mycobacterium tuberculosis promotes TLR2-TLR10 heterodimerization and trafficking to the cell surface. In this study, we expanded our ligand panel to include additional gram-positive bacteria, particularly anti-inflammatory probiotic species, to further …

Assessment Of The Bioremediation Potentials Of Biosurfactant-Producing Bacterial Strains Recovered From Spent Engine Oil-Contaminated Environments In Southwest Nigeria, Nafisa Mohammed Babayola, Nasiru Bright Lecky, Chinweizu Obioma Onumaegbu, Olufunmiso Olusola Olajuyigbe, Martins Ajibade Adefisoye

Journal of Environmental Science and Sustainable Development

Environmental pollution from hydrocarbons and their derivatives is predominantly of anthropogenic origin, occurring mainly during mining, transportation, and storage. This often in an annual release of substantial amounts of pollutants into the environment. The effective restoration of petroleum-contaminated environments requires a series of interventions to remediate soil to its natural state. This study aimed to isolate and characterize biosurfactant-producing bacterial strains with potential bioremediation capabilities to assess the potential application for remediating soils polluted with spent engine oil in the Remo district, Ogun State. Bacterial isolates were recovered from soil samples collected from spent engine oil contaminated sites, using standard …

Urobiome Composition Varies With Vesicoureteral Reflux Grade And History Of Febrile Urinary Tract Infection, Theresa C. Barrett, Kelvin Li, Adam Fitch, Asha Patel, Bhanu Sharma, Jacqueline Holden, Kermina Abdelsayed, Nina N. Kowalewski, Sridhar Narla, Daniel Bushnell, Barbara A. Methé, Catherine S. Forster

Department of Medicine Faculty Papers

Vesicoureteral reflux (VUR) is a risk factor for urinary tract infection (UTI). However, data describing the urobiome in children with VUR are limited. Here, we characterized the urobiome in children with and without VUR to better understand its potential role in VUR pathogenesis. Catheterized urine samples were obtained from children who presented for voiding cystourethrogram (VCUG) between 12/1/2020 and 10/3/2023. Children were excluded if they had any surgical procedures of the genitourinary tract in the 30 days prior to VCUG or were on treatment antibiotics at the time of VCUG. 16S rRNA gene sequencing and taxonomical classification identified the urobiome. …