Infection kinetics, phylogenetics, and host interactions of bacteriophages

Abstract

Bacteriophages, or as they are most commonly referred to as phages, are viruses which are capable of infecting bacteria. They are environmentally plenty, found everywhere from the ground we walk on to contributing to our microbiome. They are highly diverse, coming in various sizes, shapes, and genomic compositions. Compared to animal viruses, phages have larger genomes that are highly mosaic, with different segments having diverse evolutionary backgrounds. Around 96% of all phages found are tailed phages with double stranded DNA genomes, belonging to the order Caudovirales.

Phage infection can be categorized into three stages; adsorption whereby the phage attaches to its host bacterial cell wall followed by the maturation and lysis stages, whereby a phage primarily replicates either via the lytic (i.e. progressively take over bacterial transcription machinery and materials in favor of its own and results in bacterial lysis) or the lysogenic cycle (i.e. integration of its genome into the host genome). As phages are ubiquitous and require a bacterial host for replication, it is not surprising that they interact with their surrounding environments and other phages (e.g. influencing global nutrient cycling as well as affecting bacterial pathogenicity), constantly coevolving. With the continuing rise in antibiotic resistance and dawning of the “post-antibiotic” era, there has been renewed interest in phage research and their therapeutic potential. However, there are many obstacles that must be overcome before phages can reach clinical settings and be widely applied (e.g. regulatory issues and phage pharmacology). The main element behind these obstacles is a phage’s inherent biology. As such, this thesis aimed to improve the understanding of phage biology by addressing specific components such as infection kinetics, phylogenetics, and host interactions.

In Papers I and II, phages vB_EcoD_SU57 (SU57) and vB_EcoP_SU7 (SU7) were characterized based on their infection kinetics and phylogenetics. SU57 was determined to be a T1-like Drexlerviridae phage with a relatively fast infection kinetics (short latent time of 14 minutes and small burst size) whereas SU7 was determined to be a Podoviridae phage belonging to the Kuravirus genus, with the rare C3 morphology of an elongated capsid. It was also shown to be a slower infecting phage (long latent time of 30 minutes and small burst size). Paper III delved into the evolutionary origins of phages with the rare C3 morphotype making up the Kuravirus genus. These phages were found to be monophyletic in origins, closely related to marine Vibrio phages. Interestingly, these phages have a unique genomic end comprising of 33 genes which encode for hypothetical proteins of unknown function and a tRNA. In Paper IV, the population dynamics between two phages (SU10 and SU57) and one bacterial host (ECOR57) were studied in terms of population structure, size, and cell viability (i.e. resistance and/or susceptibility).

From the papers presented in this thesis, one thing is certain: phages are highly complex organisms. They come in a variety of morphologies with highly mosaic genomes of various sizes, which often hampers bioinformatics and phylogenetic analyses. Phages also have unique infection kinetics which influences how they interact and coevolve with other phages and bacteria.

Keywords: bacteriophage biology, infection kinetics, phylogenetics, host interactions, phage therapy, phage ecology and evolution.