Population Genomics of Bacteriophages

Abstract

Due to their small genome size, an abundance equaling or surpassing that of bacteria, and an obligatory dependence on their host bacteria, bacteriophages are an ideal study object for population genomics. However, due to a certain research neglect, less than 2,700 phage genomes were deposited in the NCBI database, far less than the 90,000 prokaryotic genomes. Large and ecologically representative phage genome sequencing projects have so far only conducted for a small number of phage systems. Phages of dairy bacteria belong to this group since they were systematically collected and extensively sequenced due to their negative impact on industrial milk fermentation. More than ten different phage species were defined for Lactococcus lactis and four for Streptococcus thermophilus, the two most important starter bacteria in cheese and yogurt production, respectively. The genetic interrelationship between the phages infecting the same host species and between phages infecting phylogenetically (L. lactis vs. L. garvieae and S. thermophilus vs. S. salivarius phages) or ecologically closely related host bacteria (L. lactis vs. S. thermophilus dairy phages) is here reviewed. Dairy phages allowed the study of population genomics as a function of time, geography, and distinct fermentation technologies. The elucidation of the CRISPR-Cas antiviral defense system in S. thermophilus provided first insights into the phage-bacterium arms race at the level of phage and bacterial population genomics. Phages studied by applied microbiologists thus became important study objects for fundamental questions of biology.