Bacteriophages are the most abundant biological entities in the human gut, yet their metabolic contributions remain poorly understood. Recent metagenomic studies have identified phage-encoded bile salt hydrolase (BSH) homologs, enzymes canonically responsible for deconjugating host bile acids, raising a fundamental question: do phages actively contribute to bile acid metabolism, and what functional role do these auxiliary metabolic genes (AMGs) play in bacterial fitness under bile acid stress? This project investigates phage-encoded BSH AMGs through integrated genomic and genetic approaches. Building on prior bioinformatic identification and structural validation of high-confidence phage BSH candidates, I constructed genome neighborhood diagrams and performed phylogenetic analyses to characterize the evolutionary relationship between phage-encoded and bacterial BSH homologs. In parallel, I designed a gene knockout protocol targeting endogenous BSH activity in a bacterium identified through prophage mapping, establishing a genetic toolkit for studying these viral AMGs in their native host context. Phylogenetic analyses revealed that phage BSH candidates cluster distinctly from characterized bacterial homologs, suggesting functional divergence acquired through horizontal gene transfer. This work advances our understanding of how the gut virome shapes host bile acid metabolism and opens new avenues for investigating phage-bacteria metabolic interactions with direct implications for gut health and disease.

Gram-positive bacteria rely on covalently polymerized virulence factors called pili to mediate adhesion to host tissue, biofilm formation, and resistance to immune responses during infection. Because of their essential role in infection, pilus assembly is a critical target for therapeutic intervention as an alternative to antibiotics. This project investigates how class C sortase enzymes perform the dual function of processing pilin substrates and catalyzing interpilin crosslinks, a capability not shared by other sortase classes. Despite many proteins containing similar cell wall sorting signals, class C sortases exhibit remarkable substrate specificity, and the molecular basis of this selectivity remains unclear. To address this, we use the pilin biogenesis system in Corynebacterium diphtheriae. We developed a fluorescence-activated cell sorting (FACS) assay to quantitatively monitor pilus assembly in vivo, enabling systematic analysis of pilin and sortase variants. These experiments were complemented by molecular modeling to examine interactions between sortase enzymes and pilin substrates at the membrane. Our results show that sortase recognition extends beyond the LPXTG motif to include additional regions of the sorting signal, forming a transmembrane helix-helix complex required for activation. These findings provide mechanistic insight into how sortases distinguish substrates and identify targets for disrupting pilus assembly, supporting the development of new therapeutics against antibiotic-resistant bacteria.

Nanoparticles are widely researched in modern science due to the unique size-dependent optical and physical properties they exhibit compared to their bulk counterparts. Within nanoparticles, titanium dioxide nanoparticles are among the most widely used commercially due to its high refractive index. Surface modification of the titanium dioxide nanoparticles can greatly alter their dispersity, chemical reactivity, and optical properties, leading to changes in the nanoparticle size-dependent properties and the potential to enable new functionality within these particles. The coverage of surface ligands can be tailored by varying deposition conditions, such as solution pH, as it controls ligand binding and surface charge. In this study, the functionalized titanium dioxide nanoparticles were characterized using microscopy techniques (SEM, TEM, AFM), spectroscopic analysis (UV-Vis), crystallographic analysis (XRD), surface chemical analysis (XPS), and particle size analysis (NTA). Through those experiments, this research study aims to investigate and explore how the concentration and pH of the solution affect the titanium dioxide surface modification and nanoparticle functionality.

The human oral cavity is both one of the most densely colonized microbiomes in the human body. Relative to the gut microbiome, the oral microbiome is enriched with biosynthetic gene clusters (BGCs), which are capable of producing structurally complex secondary metabolites, known as natural products. These natural products often have potent bioactivities that can influence the health and diseased states of the oral cavity. Polyketides represent a structurally diverse and biologically potent family of natural products, possessing antibacterial, antifungal, anticancer, and anti-inflammatory properties, which remain underexplored in the human oral microbiome. We developed a large-scale bioinformatic pipeline for the identification and prioritization of bacterial polyketide BGCs enriched in healthy mouths. We developed a high-throughput bioinformatic analysis pipeline using the BGC prediction algorithm, antiSMASH, to process 5,114 genomes from the Human Reference Oral Microbiome (HROM) to construct a dataset of 8,598 BGCs. We then utilized BiG-SCAPE to generate sequence similarity networks, or gene cluster families, from the identified BGCs. Finally, we utilize BiG-MAP to map these networks against metagenomic and metatranscriptomic datasets to identify clusters that are both highly abundant and highly expressed in metagenomics and metatranscriptomics datasets, respectively, from healthy subjects. These findings are discussed herein.

This abstract has been withheld from publication.