Abstract
BackgroundThe Bacillus genus of Firmicutes bacteria is ubiquitous in nature and includes one of the best characterized model organisms, B. subtilis, as well as medically significant human pathogens, the most notorious being B. anthracis and B. cereus. As the most abundant living entities on the planet, bacteriophages are known to heavily influence the ecology and evolution of their hosts, including providing virulence factors. Thus, the identification and analysis of Bacillus phages is critical to understanding the evolution of Bacillus species, including pathogenic strains.ResultsWhole genome nucleotide and proteome comparison of the 83 extant, fully sequenced Bacillus phages revealed 10 distinct clusters, 24 subclusters and 15 singleton phages. Host analysis of these clusters supports host boundaries at the subcluster level and suggests phages as vectors for genetic transfer within the Bacillus cereus group, with B. anthracis as a distant member. Analysis of the proteins conserved among these phages reveals enormous diversity and the uncharacterized nature of these phages, with a total of 4,442 protein families (phams) of which only 894 (20%) had a predicted function. In addition, 2,583 (58%) of phams were orphams (phams containing a single member). The most populated phams were those encoding proteins involved in DNA metabolism, virion structure and assembly, cell lysis, or host function. These included several genes that may contribute to the pathogenicity of Bacillus strains.ConclusionsThis analysis provides a basis for understanding and characterizing Bacillus and other related phages as well as their contributions to the evolution and pathogenicity of Bacillus cereus group bacteria. The presence of sparsely populated clusters, the high ratio of singletons to clusters, and the large number of uncharacterized, conserved proteins confirms the need for more Bacillus phage isolation in order to understand the full extent of their diversity as well as their impact on host evolution.
Highlights
The Bacillus genus of Firmicutes bacteria is ubiquitous in nature and includes one of the best characterized model organisms, B. subtilis, as well as medically significant human pathogens, the most notorious being B. anthracis and B. cereus
Correction The version of this article published in BMC genomics 2014 15(1):855, contains unpublished genomes downloaded from the public website phagesdb.org
Whole genome nucleotide and amino acid comparison of the Bacillus family of phages reveals 10 diverse clusters of related phages and 15 singleton clusters In order to determine the relationship of the 83 extant, fully-sequenced Bacillus phages, we analyzed the published phage genomes by methods similar to those of Hatfull et al [15,16], including whole genome dot plot analysis, pairwise average nucleotide identities (ANI) and genomic maps
Summary
The Bacillus genus of Firmicutes bacteria is ubiquitous in nature and includes one of the best characterized model organisms, B. subtilis, as well as medically significant human pathogens, the most notorious being B. anthracis and B. cereus. Bacteriophages are the most abundant biological entities on the planet, with at least 1031 bacteriophages in Earth’s biosphere [1,2,3,4,5] Their ability to infect and kill their bacterial hosts makes them key factors in both the evolution of bacteria and the maintenance of ecological balance (for recent reviews see [6,7,8,9,10,11,12]). Identical mycobacteriophages have only been isolated independently twice (Graham Hatfull, personal communication) Beyond these Mycobacterium phages, the bacterial family with the most phages isolated is the Gram-negative Enterobacteriaceae family (337 fully sequenced genomes available in GenBank). They have recently been grouped into 38 clusters of related phages and 18 singleton clusters [14]
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