Understanding the enormous diversity of bacteriophages: The tailed phages that infect the bacterial family Enterobacteriaceae

Abstract

Bacteriophages are the predominant biological entity on the planet. The recent explosion of sequence information has made estimates of their diversity possible. We describe the genomic comparison of 337 fully sequenced tailed phages isolated on 18 genera and 31 species of bacteria in the Enterobacteriaceae. These phages were largely unambiguously grouped into 56 diverse clusters (32 lytic and 24 temperate) that have syntenic similarity over >50% of the genomes within each cluster, but substantially less sequence similarity between clusters. Most clusters naturally break into sets of more closely related subclusters, 78% of which are correlated with their host genera. The largest groups of related phages are superclusters united by genome synteny to lambda (81 phages) and T7 (51 phages). This study forms a robust framework for understanding diversity and evolutionary relationships of existing tailed phages, for relating newly discovered phages and for determining host/phage relationships.

Characterization and genome sequencing of a Citrobacter freundii phage CfP1 harboring a lysin active against multidrug-resistant isolates

“…All these five Citrobacter phages were isolated from sewage samples in USA, and their genomes were recently announced without being characterized in vitro (Edwards et al 2015;Hwang et al 2015;LeSage et al 2015). Overall, CfP1 characteristics fall into the T4 virus major subtype (Grose and Casjens 2014), although having less identity at nucleotide (46.1 %) and protein (41 %) level when compared to Enterobacteria phage T4.…”

Dark Matter of the Biosphere: the Amazing World of Bacteriophage Diversity

“…Interestingly, rarefaction analysis of mycobacteriophage gene contents suggests that this population is not closed and that sequencing new phage isolates will continue to reveal new genes (7). Enterobacteriophages can be similarly grouped into clusters according to nucleotide sequence similarity, suggesting that these relationships reflect a broader feature of phage populations (11).…”

The lambda - P22 problem

“…The distinctiveness of l and P22 is indeed recognized by Grose and Casjens when they classify l and P22 into different subclusters within a l supercluster. 3 Thus, if l and P2 are related, this is not a close relationship. Rather, it can be said that they became related by "marriage" of unrelated ancestors and fall presently into 2 distinct clades.…”

“…1 The situation was summarized in 2005 2 and needs to be reconsidered as Grose and Casjens recently classified tailed enterobacteriophages into clusters. 3 Botstein and Herskovitz (1974) created viable hybrids of l and P22, in which the immunity, early control and replication genes are substitued for the analogous l genes. 4 Susskind and Botstein (1978) noted a similar genome organization and lysogeny regulation genes in l and P22.…”