Document Type


Degree Name

Master of Science (MSc)



Program Name/Specialization

Integrative Biology


Faculty of Science

First Advisor

Gabriel Moreno-Hagelsieb

Advisor Role



Bacteriophage (or ‘phage’) are viruses that infect and reproduce within their bacterial hosts. They have a major global impact on bacterial evolution and ecology, and might influence the pathogenicity of their host bacterium by providing virulence factors. Phage can either be described as “virulent” or “temperate”; the distinguishing feature between the two is their method of replication.

This study sought to identify phage sequences within bacterial host genomes and determine the life cycle of the phage, exploring whether there is a connection between defective phage and previously virulent phage. It would normally be expected that any phage sequences identified within a bacterial host would have a temperate life cycle, since only temperate phage enter the lysogenic cycle and insert their DNA into the host as a ‘prophage,’ while virulent phage replicate via the lytic cycle, in which phage DNA replicates separately from that of the host’s and infected cells are lysed.

Defective phage–‘zombies’ in bacterial genomes–are dormant phage that have become inactive through mutational decay or some other process. It is possible that some of these defective phage are in fact previously virulent phage that have become accidentally inserted within the host genome.

This study detected phage within bacterial genomes using the prophage identification tools PHAge Search Tool (PHAST) and Prophage Finder. Identified sequences were categorized as ‘intact,’ ‘questionable,’ or ‘incomplete’; questionable and incomplete phage were classified as defective. The lifestyles of the uncovered phage sequences were then determined using PHACTS; six phage were identified as possibly virulent. The life cycles of the phage were further analyzed by assessing the genomic signature distances (GSD) and codon adaptation indexes (CAI) for each phage. Three phage were shown to have a GSD consistent with a virulent life cycle, and the CAI values of four phage corresponded with that of virulent phage. Although previous studies have indicated that some virulent phage may have a temperate lineage, identifying prophage as previously virulent is a novel finding. This has implications for our understanding of phage life cycles and the infection process, as it challenges the idea that only temperate phage insert their DNA into the host genome.

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