The odd one out: Bacillus ACT bacteriophage CP-51 exhibits unusual properties compared to related Spounavirinae W.Ph. and Bastille

Klumpp, Jochen; Schmuki, Martina; Sozhamannan, Shanmuga; Beyer, Wolfgang; Fouts, Derrick E.; Bernbach, Vanessa; Calendar, Richard; Loessner, Martin J.

doi:10.1016/j.virol.2014.06.012

Cited by 17 publications

(9 citation statements)

References 66 publications

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“…Illumina library preparation by a PCR-free library protocol, which required significantly higher amounts of input DNA, produced DNA libraries sequencable by Illumina MiSeq. Modification or base substitution of phage DNA has been reported as an impediment to sequencing for other phages, such as the 5-hydroxymethyluracil substitution for thymine found in the Bacillus phage CP-51 (39), or uracil substitution for thymine in the Bacillus jumbo phage AR9 (40). Phage AR9 was sequenced by Illumina following library amplification using a uracil-compatible DNA polymerase (40) and CP-51 was only sequencable by a combination of PacBio and Sanger sequencing (39).…”

Section: Resultsmentioning

confidence: 99%

“…The copyright holder for this preprint this version posted December 15, 2020. ; https://doi.org/10.1101/2020.12.14.422802 doi: bioRxiv preprint sequencing for other phages, such as the 5-hydroxymethyluracil substitution for thymine found in the Bacillus phage CP-51 (39), or uracil substitution for thymine in the Bacillus jumbo phage AR9 (40). Phage AR9 was sequenced by Illumina following library amplification using a uracil-compatible DNA polymerase (40) and CP-51 was only sequencable by a combination of PacBio and Sanger sequencing (39). The previously reported S. aureus jumbo phage S6 was also determined to contain DNA with thymine completely replaced by uracil (14).…”

Section: Dna Sequencing and Genomic Characterizationmentioning

confidence: 99%

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Comparative Genomics of Three Novel Lytic Jumbo Bacteriophages InfectingStaphylococcus aureus

Korn

Hillhouse

Sun

et al. 2020

Preprint

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The majority of previously described Staphylococcus aureus bacteriophages belong to three major groups: P68-like Podoviridae, Twort-like or K-like Myoviridae, and a more diverse group of temperate Siphoviridae. Here we present three novel S. aureus 'jumbo' phages: MarsHill, Madawaska, and Machias. These phages were isolated from swine production environments in the United States and represent a novel clade of S. aureus Myoviridae that is largely unrelated to other known S. aureus phages. The average genome size for these phages is ~269 kb with each genome encoding ~263 predicted protein-coding genes. Phage genome organization and content is most similar to known jumbo phages of Bacillus, including AR9 and vB_BpuM-BpSp. All three phages possess genes encoding complete viral and non-viral RNA polymerases, multiple homing endonucleases, and a retron-like reverse transcriptase. Like AR9, all of these phages are presumed to have uracil-substituted DNA which interferes with DNA sequencing. These phages are also able to transduce host plasmids, which is significant as these phages were found circulating in swine production environments and can also infect human S. aureus isolates.

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Section: Resultsmentioning

confidence: 99%

Section: Dna Sequencing and Genomic Characterizationmentioning

confidence: 99%

Comparative Genomics of Three Novel Lytic Jumbo Bacteriophages InfectingStaphylococcus aureus

Korn

Hillhouse

Sun

et al. 2020

Preprint

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“…BLASTn comparison of Bacillus phage Crookii on NCBI revealed a viral strain relationship to a Myoviridae Bacillus phage WPh., isolated from an anthrax positive zebra carcass in Namibia [ 50 , 51 ]. The whole genome of Bacillus phage Crookii was compared and aligned with Bacillus phage WPh.…”

Section: Resultsmentioning

confidence: 99%

“…was isolated from an anthrax positive zebra carcass in Etosha National Park, Namibia [ 50 , 51 ]. Both phages are Myoviridae dsDNA bacteriophages based on similar GC content and sequence identity with characteristics of Spounaviruses [ 51 , 66 ]. These bacteriophages infect members of the B. cereus sensu lato group.…”

Section: Discussionmentioning

confidence: 99%

A Unique Isolation of a Lytic Bacteriophage Infected Bacillus anthracis Isolate from Pafuri, South Africa

Hassim

Lekota

Dyk³

et al. 2020

Microorganisms

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Bacillus anthracis is a soil-borne, Gram-positive endospore-forming bacterium and the causative agent of anthrax. It is enzootic in Pafuri, Kruger National Park in South Africa. The bacterium is amplified in a wild ungulate host, which then becomes a source of infection to the next host upon its death. The exact mechanisms involving the onset (index case) and termination of an outbreak are poorly understood, in part due to a paucity of information about the soil-based component of the bacterium’s lifecycle. In this study, we present the unique isolation of a dsDNA bacteriophage from a wildebeest carcass site suspected of having succumbed to anthrax. The aggressively lytic bacteriophage hampered the initial isolation of B. anthracis from samples collected at the carcass site. Classic bacteriologic methods were used to test the isolated phage on B. anthracis under different conditions to simulate deteriorating carcass conditions. Whole genome sequencing was employed to determine the relationship between the bacterium isolated on site and the bacteriophage-dubbed Bacillus phage Crookii. The 154,012 bp phage belongs to Myoviridae and groups closely with another African anthrax carcass-associated Bacillus phage WPh. Bacillus phage Crookii was lytic against B. cereus sensu lato group members but demonstrated a greater affinity for encapsulated B. anthracis at lower concentrations (<1 × 108 pfu) of bacteriophage. The unusual isolation of this bacteriophage demonstrates the phage’s role in decreasing the inoculum in the environment and impact on the life cycle of B. anthracis at a carcass site.

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“…Genome wide comparisons with sequences in the GenBank nr/nt database revealed no significant matches. Phage vB_EalM-132 shares very low similarity with well-studied Bacillus phage SP01 (GenBank: KC595513.2), a representative phage of the Myoviridae family [31] and Bacillus phage CP-51 (GenBank: KF554508.2) [32]. Phage vB_BpsS-136 also had very low similarity to Bacillus phage vB_BanS-Tsamsa (GenBank: KC481682.1), barely detectable by a diagonal dotplot analysis.…”

Section: Resultsmentioning

confidence: 99%

Comparative genomic analysis of eight novel haloalkaliphilic bacteriophages from Lake Elmenteita, Kenya

Akhwale

Rohde

et al. 2019

PLoS ONE

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We report complete genome sequences of eight bacteriophages isolated from Haloalkaline Lake Elmenteita found on the floor of Kenyan Rift Valley. The bacteriophages were sequenced, annotated and a comparative genomic analysis using various Bioinformatics tools carried out to determine relatedness of the bacteriophages to each other, and to those in public databases. Basic genome properties like genome size, percentage coding density, number of open reading frames, percentage GC content and gene organizations revealed the bacteriophages had no relationship to each other. Comparison to other nucleotide sequences in GenBank database showed no significant similarities hence novel. At the amino acid level, phages of our study revealed mosaicism to genes with conserved domains to already described phages. Phylogenetic analyses of large terminase gene responsible for DNA packaging and DNA polymerase gene for replication further showed diversity among the bacteriophages. Our results give insight into diversity of bacteriophages in Lake Elmenteita and provide information on their evolution. By providing primary sequence information, this study not only provides novel sequences for biotechnological exploitation, but also sets stage for future studies aimed at better understanding of virus diversity and genomes from haloalkaline lakes in the Rift Valley.

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The odd one out: Bacillus ACT bacteriophage CP-51 exhibits unusual properties compared to related Spounavirinae W.Ph. and Bastille

Cited by 17 publications

References 66 publications

Comparative Genomics of Three Novel Lytic Jumbo Bacteriophages InfectingStaphylococcus aureus

Comparative Genomics of Three Novel Lytic Jumbo Bacteriophages InfectingStaphylococcus aureus

A Unique Isolation of a Lytic Bacteriophage Infected Bacillus anthracis Isolate from Pafuri, South Africa

Comparative genomic analysis of eight novel haloalkaliphilic bacteriophages from Lake Elmenteita, Kenya

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