Date of Award

Fall 9-5-2025

Degree Type

Thesis

Degree Name

Master of Science (MS)

Department

Bioinformatics & Computational Biology

First Advisor

Catherine Putonti

Abstract

The ongoing evolutionary arms race between bacteria and bacteriophages (phages) is a prime example of Red Queen hypothesis, where continuous adaptation drives survival. This study focuses on Escherichia coli-infecting temperate phages, which dominate natural environments and contribute to bacterial resistance mechanisms. Despite their prevalence, temperate phages are less suited for phage therapy due to their lysogenic life cycle, where they integrate into bacterial genomes instead of lysing the host. In contrast, obligately lytic phages, which directly lyse bacterial cells, are ideal for therapeutic use but occur less frequently in nature. This research aims to select for lytic behavior in temperate phages through experimental evolution. Aim 1 involves inducing temperate phages from a collection of E. coli lysogens isolated from urinary tract infections (UTIs) in females. These phages were characterized through transmission electron microscopy (TEM) and host range assays. Aim 2 applies the Appelmans' Protocol to select for lytic behavior through iterative co-cultures of phage cocktails and E. coli strains over 30 days. Aim 3 uses the BRESEQ pipeline to identify mutations linked to lytic conversion, focusing on integrase genes and other loci involved in host interaction. By characterizing temperate phages and evolving them, this study addresses the urgent need for supplementation to antibiotic treatments, particularly in regards to UTIs. Beyond clinical applications, it expands our understanding of temperate phage evolution, mutation dynamics, and ecological roles. This approach offers new insights into the adaptability of phages and their potential to combat antibiotic resistance.

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