Genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity

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 93 extant Bacillus phages revealed 12 distinct clusters, 28 subclusters and 14 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 of the group. Analysis of the proteins conserved among these phages reveals enormous diversity and the uncharacterized nature of these phages, with a total of 4,922 protein families (phams) of which only 951 (19%) had a predicted function. In addition, 3,058 (62%) of phams were orphams (phams containing a gene product from a single phage). 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 phages 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.

Comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica

“…4 and Figure S1). A similar phenomenon was also observed for Cluster Mycobacterium (56.3 to 69.1%) [23][24][25][26][27]. Salmonella and Pseudomonas both belong to the Enterobacteriaceae family and their phages share very similar genome sizes and GC content.…”

“…of a large number of phage genomes in the GenBank (about 13,703 phage genomes were present as of June 2019) (http://millardlab.org/bioinformatics/bacteriophage-genomes/phage-genomes-june-2019/) has provided insights into the impact on the evolution of both the virus and host [23]. Wholegenome comparative analysis has been successfully applied to study phages present or infecting several bacterial genera including Mycobacteria [24], Staphylococcus [25], Bacillus [26], Gordonia [27], Pseudomonas [23] and as well as the Enterobacteriaceae family [28]. Phage genomes are commonly grouped into clusters, but outlier phages lacking strong nucleotide identity relationships with other clustered genome are often designed as 'singletons' [27].…”

Genomic diversification of marine cyanophages into stable ecotypes

“…A comparison of 108 lytic cyanophage isolates collected from the same locations over time revealed well‐supported cyanophage genomic clusters and subclusters that remained consistent for a decade or longer. Previous studies of mycobacteriophages, Bacillus phages, and Enterobacteriaceae phages have examined genomic diversity by sampling widely from diverse environments and locations (Grose and Casjens, ; Grose et al ., ; Hatfull, ; Pope et al ., ). Although the phages in these studies can be broadly organized into clusters (ANI values of at least 55% over 50% of genome) and subclusters (ANI values at least 60%), it has been suggested that these groups do not necessarily reflect real boundaries between bacteriophages, but incomplete sampling of a continuum of diversity (Hatfull, ; Pope et al ., ).…”

The Efficacy of Isolated Bacteriophages from Pig Farms against ESBL/AmpC-Producing Escherichia coli from Pig and Turkey Farms

“…Phages for this purpose may be easily isolated from the environment, but the question whether distant locations and different environments are better sources of active phages remains open. Although phages are considered one of the least known entities on our planet (Grose et al, 2014) and further studies regarding their biology need to be conducted, they undoubtedly could provide a novel approach to the prevention and treatment of infections caused by drug-resistant bacteria.…”