UC Merced

Bacteriophages (phages) are viruses that target and infect bacteria. The impact of phages on a biological ecosystem could result in devastation to the system or augmentation. T/., For example, in the bacterium Staphylococcus aureus, phages have important roles in virulence, antibiotic resistance, and genome evolution. In agricultural ecosystems, bacteria and phages offer the host plant protection from pathogens, and provide resilience against stressful environments. Determining the presence of virulence and beneficial genes helps us uncover more about the relationship between the host, bacteria and phages.Identifying and analyzing phages in bacterial genome sequences through experimentation can be costly in both time and resources. Rapid growth in the number of sequenced bacterial genomes allows for an investigation of prophage sequences at an unprecedented scale. Computational pipelines and systems can be used to explore how phages impact the host and ecosystem through techniques such as: (1) alignment-based methods that leverage sequence homology and sequence similarity, (2) alignment-free methods centered around sequence composition and genomic features, and (3) machine-learning-based methods. In this dissertation, I leverage the above techniques and others to explore the role of phages in biological ecosystems through bacterial genome sequences.