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

Grose JH, Jensen GL, Burnett SH, Breakwell DP - BMC Genomics (2014)

Bottom Line: In addition, 3,058 (62%) of phams were orphams (phams containing a gene product from a single phage).These included several genes that may contribute to the pathogenicity of Bacillus strains.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.

View Article: PubMed Central - PubMed

Affiliation: Microbiology and Molecular Biology Department, Brigham Young University, Provo, UT, USA. julianne_grose@byu.edu.

ABSTRACT

Background: 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. 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.

Results: Whole 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.

Conclusions: This 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.

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Nucleotide and amino acid dot plot analysis of 93 fully sequencedBacillusphages reveals 12 clusters (A-L) and 14 singletons. Nucleotide (A) and amino acid (C) dot plot of Bacillus genomes of less than 100 kb organized by similarity reveals 10 clusters of related phages. Nucleotide (B) and amino acid (D) dot plot of Bacillus genomes of greater than 100 kb organized by similarity reveals 2 clusters of related phages. Thick lines indicate cluster assignments, which are provided on the Y-axis (A-L). Dot plots were produced using Gepard [61] and whole genome amino acid sequences were retrieved from Phamerator [62].
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Fig1: Nucleotide and amino acid dot plot analysis of 93 fully sequencedBacillusphages reveals 12 clusters (A-L) and 14 singletons. Nucleotide (A) and amino acid (C) dot plot of Bacillus genomes of less than 100 kb organized by similarity reveals 10 clusters of related phages. Nucleotide (B) and amino acid (D) dot plot of Bacillus genomes of greater than 100 kb organized by similarity reveals 2 clusters of related phages. Thick lines indicate cluster assignments, which are provided on the Y-axis (A-L). Dot plots were produced using Gepard [61] and whole genome amino acid sequences were retrieved from Phamerator [62].

Mentions: Dot plot analysis of the Bacillus phages revealed 12 clusters of phages with similarity over at least 50% of their genomes (clusters A through L) and 14 phages that are singletons, having little to no nucleotide similarity to any other Bacillus phages. Genomic dot plot analysis consists of placing the nucleotide sequences across both the X- and Y-axis. A dot is placed where the sequences are identical resulting in a diagonal line down the center of the plot when a sequence is compared to itself. The phages were aligned on two separate plots due to the wide range in genome size and the fact that no additional nucleotide similarity was seen in a combined plot. Figure 1A contains phage genomes less than 100 kb while 1C contains the larger phage genomes. As stated above, assignment of a phage to a cluster was based on nucleotide similarity over at least 50% of the genome when compared to at least one other phage in the cluster. Thus, a phage could be placed into the same cluster by weak similarity over most of the genome, by strong similarity over about half of the genome, or by a combination of relatedness. The ANI values were also calculated within each cluster and found to be at least 55% between a phage and another phage within a cluster. From the total of 26 clusters just over half (14) are singleton clusters containing a single phage member, suggesting that the isolation of unique Bacillus phages is far from complete.Figure 1


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

Grose JH, Jensen GL, Burnett SH, Breakwell DP - BMC Genomics (2014)

Nucleotide and amino acid dot plot analysis of 93 fully sequencedBacillusphages reveals 12 clusters (A-L) and 14 singletons. Nucleotide (A) and amino acid (C) dot plot of Bacillus genomes of less than 100 kb organized by similarity reveals 10 clusters of related phages. Nucleotide (B) and amino acid (D) dot plot of Bacillus genomes of greater than 100 kb organized by similarity reveals 2 clusters of related phages. Thick lines indicate cluster assignments, which are provided on the Y-axis (A-L). Dot plots were produced using Gepard [61] and whole genome amino acid sequences were retrieved from Phamerator [62].
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4197329&req=5

Fig1: Nucleotide and amino acid dot plot analysis of 93 fully sequencedBacillusphages reveals 12 clusters (A-L) and 14 singletons. Nucleotide (A) and amino acid (C) dot plot of Bacillus genomes of less than 100 kb organized by similarity reveals 10 clusters of related phages. Nucleotide (B) and amino acid (D) dot plot of Bacillus genomes of greater than 100 kb organized by similarity reveals 2 clusters of related phages. Thick lines indicate cluster assignments, which are provided on the Y-axis (A-L). Dot plots were produced using Gepard [61] and whole genome amino acid sequences were retrieved from Phamerator [62].
Mentions: Dot plot analysis of the Bacillus phages revealed 12 clusters of phages with similarity over at least 50% of their genomes (clusters A through L) and 14 phages that are singletons, having little to no nucleotide similarity to any other Bacillus phages. Genomic dot plot analysis consists of placing the nucleotide sequences across both the X- and Y-axis. A dot is placed where the sequences are identical resulting in a diagonal line down the center of the plot when a sequence is compared to itself. The phages were aligned on two separate plots due to the wide range in genome size and the fact that no additional nucleotide similarity was seen in a combined plot. Figure 1A contains phage genomes less than 100 kb while 1C contains the larger phage genomes. As stated above, assignment of a phage to a cluster was based on nucleotide similarity over at least 50% of the genome when compared to at least one other phage in the cluster. Thus, a phage could be placed into the same cluster by weak similarity over most of the genome, by strong similarity over about half of the genome, or by a combination of relatedness. The ANI values were also calculated within each cluster and found to be at least 55% between a phage and another phage within a cluster. From the total of 26 clusters just over half (14) are singleton clusters containing a single phage member, suggesting that the isolation of unique Bacillus phages is far from complete.Figure 1

Bottom Line: In addition, 3,058 (62%) of phams were orphams (phams containing a gene product from a single phage).These included several genes that may contribute to the pathogenicity of Bacillus strains.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.

View Article: PubMed Central - PubMed

Affiliation: Microbiology and Molecular Biology Department, Brigham Young University, Provo, UT, USA. julianne_grose@byu.edu.

ABSTRACT

Background: 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. 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.

Results: Whole 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.

Conclusions: This 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.

Show MeSH
Related in: MedlinePlus