Characterization and comparative genomic analysis of virulent and temperateBacillus megateriumbacteriophages

Abstract

Next-Generation Sequencing (NGS) technologies provide unique possibilities for the comprehensive assessment of the environmental diversity of bacteriophages. Several Bacillus bacteriophages have been isolated, but very few Bacillus megaterium bacteriophages have been characterized. In this study, we describe the biological characteristics, whole genome sequences, and annotations for two new isolates of the B. megaterium bacteriophages (BM5 and BM10), which were isolated from Egyptian soil samples. Growth analyses indicated that the phages BM5 and BM10 have a shorter latent period (25 and 30 min, respectively) and a smaller burst size (103 and 117 PFU, respectively), in comparison to what is typical for Bacillus phages. The genome sizes of the phages BM5 and BM10 were 165,031 bp and 165,213 bp, respectively, with modular organization. Bioinformatic analyses of these genomes enabled the assignment of putative functions to 97 and 65 putative ORFs, respectively. Comparative analysis of the BM5 and BM10 genome structures, in conjunction with other B. megaterium bacteriophages, revealed relatively high levels of sequence and organizational identity. Both genomic comparisons and phylogenetic analyses support the conclusion that the sequenced phages (BM5 and BM10) belong to different sub-clusters (L5 and L7, respectively), within the L-cluster, and display different lifestyles (lysogenic and lytic, respectively). Moreover, sequenced phages encode proteins associated with Bacillus pathogenesis. In addition, BM5 does not contain any tRNA sequences, whereas BM10 genome codes for 17 tRNAs.

Virulent Drexlervirial Bacteriophage MSK, Morphological and Genome Resemblance With Rtp Bacteriophage Inhibits the Multidrug-Resistant Bacteria

“…Thus, the phage MSK has a mosaic genome structure and morphology similar to related phages, indicating the extensive genetic exchange and horizontal gene transfer within the phage community ( Rohwer and Edwards, 2002 ). Furthermore, the phage genome also has the one tRNA-arg (78 bp), which also supports the hypothesis that bacteriophages with tRNA genes have larger burst size as a result of their virulence and propagation in their host increases ( Delesalle et al, 2016 ; Sharaf et al, 2018 ).…”

“…In contrast, T1 bacteriophage exhibit a latent period of 13 min and produces 100 virions per infected phage ( Borchert and Drexler, 1980 ). Further, several factors like mutation, host cell size, host physiology, and culture condition might reflect the short burst size and the latent period during the propagation in the host ( Sharaf et al, 2018 ). These results suggest that the latent period of the phage MSK is almost closed to other Drexlerviridae family bacteriophages, and this could be a potential candidate for phage therapy.…”

Evidence for shared ancestry between Actinobacteria and Firmicutes bacteriophages

“…The results (Figure 3, Figure S2, Data S3) show consistent branching (99.9% bootstrap support) of the actinobacteriophage supercluster with both Lactococcus and Faecalibacterium phages, clearly establishing that these Firmicutes phages and the actinobacteriophage supercluster phages share more gene content with each other than with reference actinobacteriophages and Firmicutes phages. To further validate and support this result, we performed phylogenetic inference on the protein sequence of the large terminase subunit (Figure 4, Data S2), a very common marker for bacteriophage phylogenetic analysis (Casjens et al 2005 p. 18; Bardina et al 2016;Merrill et al 2016;Sharaf et al 2018). Due to the high diversity among the phages included in the analysis, the alignment of TerL sequences yielded no conserved blocks with GBlocks for Bayesian inference analysis (Castresana 2000).…”

Evidence for shared ancestry between Actinobacteria and Firmicutes bacteriophages

“…The results (Figure 3, Figure S2, Data S3) show consistent branching (99.9% bootstrap support) of the Actinobacteriophage supercluster with both Lactococcus and Faecalibacterium phages, clearly establishing that these Firmicutes phages and the Actinobacteriophage supercluster phages share more gene content with each other than with reference Actinobacteriophages and Firmicutes phages. To further validate and support this result, we performed phylogenetic inference on the protein sequence of the large terminase subunit (Figure 4, Data S2), a very common marker for bacteriophage phylogenetic analysis [31][32][33][34]. Due to the high diversity among the phages included in the analysis, the alignment of TerL sequences yielded no conserved blocks with GBlocks for maximum likelihood or Bayesian inference analysis [35].…”