Genome Sequences of Two Bacillus Phages Isolated from Indonesia (original) (raw)
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Evaluation of Genome Sequences of the Bacteriophages JeTaime and Luna22
Microbiology Resource Announcements
The mycobacteriophages JeTaime (E cluster) and Luna22 (Q cluster) were isolated from soil in Providence, Rhode Island, and Charleston, South Carolina, respectively, using a Mycobacterium smegmatis mc 2 155 host. The genome of JeTaime is 75,099 bp (142 predicted genes), and that of Luna22 is 53,730 bp (87 predicted genes). Both phages exhibit Siphoviridae morphology.
Microbiology Resource Announcements, 2021
Here, we report genome sequences of 10 Bacillus cereus group-infecting bacteriophages. Each virus was isolated from an environmental sample, contained a double-stranded DNA genome, and belonged to the Myoviridae family. Nine phages exhibit a conserved genome structure, and one phage appears novel in genome structure, sequence, and protein content. ABSTRACT Here, we report genome sequences of 10 Bacillus cereus group-infecting bacteriophages. Each virus was isolated from an environmental sample, contained a double-stranded DNA genome, and belonged to the Myoviridae family. Nine phages exhibit a conserved genome structure, and one phage appears novel in genome structure, sequence, and protein content.
Genomic characterization of six novel Bacillus pumilus bacteriophages
Virology, 2013
Twenty-eight bacteriophages infecting the local host Bacillus pumilus BL-8 were isolated, purified, and characterized. Nine genomes were sequenced, of which six were annotated and are the first of this host submitted to the public record. The 28 phages were divided into two groups by sequence and morphological similarity, yielding 27 cluster BpA phages and 1 cluster BpB phage, which is a BL-8 prophage. Most of the BpA phages have a host range restricted to distantly related strains, B. pumilus and B. simplex, reflecting the complexities of Bacillus taxonomy. Despite isolation over wide geographic and temporal space, the six cluster BpA phages share most of their 23 functionally annotated protein features and show a high degree of sequence similarity, which is unique among phages of the Bacillus genera. This is the first report of B. pumilus phages since 1981.
Complete genome equences of Microbacterium bacteriophages Danno, Otwor and Scumberland isolated in Clarksville, Tennessee. , 2021
This paper reports the genome sequences of bacteriophages isolated from soil samples using Microbacterium foliorum. Phages Danno and Otwor (cluster EE) have genomes of 17,452 bp and 17,454 bp, respectively, and 25 predicted genes. The phage Scumberland (cluster EC) has a genome of 53,276 bp with 92 predicted genes.
Novel Bacteriophages Containing a Genome of Another Bacteriophage within Their Genomes
2012
A novel bacteriophage infecting Staphylococus pasteuri was isolated during a screen for phages in Antarctic soils. The phage named SpaA1 is morphologically similar to phages of the family Siphoviridae. The 42,784 bp genome of SpaA1 is a linear, double-stranded DNA molecule with 39 protruding cohesive ends. The SpaA1 genome encompasses 63 predicted proteincoding genes which cluster within three regions of the genome, each of apparently different origin, in a mosaic pattern. In two of these regions, the gene sets resemble those in prophages of Bacillus thuringiensis kurstaki str. T03a001 (genes involved in DNA replication/transcription, cell entry and exit) and B. cereus AH676 (additional regulatory and recombination genes), respectively. The third region represents an almost complete genome (except for the short terminal segments) of a distinct bacteriophage, MZTP02. Nearly the same gene module was identified in prophages of B. thuringiensis serovar monterrey BGSC 4AJ1 and B. cereus Rock4-2. These findings suggest that MZTP02 can be shuttled between genomes of other bacteriophages and prophages, leading to the formation of chimeric genomes. The presence of a complete phage genome in the genome of other phages apparently has not been described previously and might represent a 'fast track' route of virus evolution and horizontal gene transfer. Another phage (BceA1) nearly identical in sequence to SpaA1, and also including the almost complete MZTP02 genome within its own genome, was isolated from a bacterium of the B. cereus/B. thuringiensis group. Remarkably, both SpaA1 and BceA1 phages can infect B. cereus and B. thuringiensis, but only one of them, SpaA1, can infect S. pasteuri. This finding is best compatible with a scenario in which MZTP02 was originally contained in BceA1 infecting Bacillus spp, the common hosts for these two phages, followed by emergence of SpaA1 infecting S. pasteuri.
Genome Sequences of 38 Bacteriophages Infecting Escherichia coli, Isolated from Raw Sewage
Microbiology Resource Announcements, 2020
Here, we report the complete genome sequences of 38 novel bacteriophages infecting Escherichia coli, isolated from a raw sewage source in Washington. Of these phages, 26 are under 100 kb, 11 are near 170 kb, and 1 352-kb jumbo phage was discovered. ABSTRACT Here, we report the complete genome sequences of 38 novel bacteriophages infecting Escherichia coli, isolated from a raw sewage source in Washington. Of these phages, 26 are under 100 kb, 11 are near 170 kb, and 1 352-kb jumbo phage was discovered.
Complete Genome Sequence of Bacteriophage Loca, Isolated on a Microbacterium foliorum Culture
Microbiology resource announcements, 2022
Microbacteriophage Loca was extracted from a shopping cart handle swab sample in Stephenville, TX, and isolated on a Microbacterium foliorum NRRL-24224 culture. The 17,475-bp double-stranded DNA genome contains 25 predicted protein-coding genes and has .96% nucleotide identity to bacteriophages Quaker and Livingwater. M icrobacterium bacteriophages are genetically diverse and composed of several types of genomic architectures containing multiple genes of unknown function (1). To expand our knowledge of the diversity of microbacteriophages isolated from central and north Texas (2-4), we report the genome sequence of microbacteriophage Loca, collected from a swab sample of a shopping cart handle in Stephenville, TX (global positioning system [GPS] coordinates, 32.206238 N, 98.23701 W). The sample was submerged in peptone-yeast extract-calcium (PYCa) liquid medium and incubated while shaking for 2 h at 220 rpm and 29°C. The supernatant was filtered through a 0.22-mm filter and incubated with the bacterial host strain Microbacterium foliorum NRRL B-24224 in PYCa liquid medium for 6 days at 29°C (5, 6). The bacteria were pelleted and the supernatant passed through 0.22-mm filters. The filtrates were 10-fold serially diluted in phage buffer (10 mM Tris [pH 7.5], 10 mM MgSO 4 , 68 mM NaCl, 1 mM CaCl 2 , 10% glycerol) and incubated with M. foliorum in a soft agar overlay on PYCa agar plates for 48 h at 29°C. Bacteriophage replication formed clear, circular plaques approximately 5 mm in diameter within the soft agar overlay. Loca was isolated by two rounds of picking a single, well-separated plaque, followed by 10-fold serial dilution of the bacteriophage sample and plating it with M. foliorum as before. High-titer lysates were prepared by flooding "webbed" plates with phage buffer overnight at 4°C, as described in Phage Discovery Guide (5). Negative-staining transmission electron microscopy showed that Loca exhibited Siphoviridae morphology (Fig. 1), and ImageJ v1.53m (7) was used to measure an approximate tail length of 105 nm and capsid diameter of 40 nm (n = 9). Genomic DNA was extracted from the high-titer lysate using a modified zinc chloride precipitation method (5, 8). The Pittsburgh Bacteriophage Institute prepared sequencing libraries using the NEBNext Ultra II DNA library prep kit (New England Biolabs, Ipswich, MA) and sequenced them using an Illumina MiSeq instrument to produce 20,276 single-end 150-bp reads. The raw reads were assembled using Newbler v2.9 to generate a single contig with 75Â coverage that was checked for completeness and genomic termini using Consed v29 (9, 10). The 17,475-bp double-stranded DNA genome contains 9-nucleotide 39 singlestranded cohesive ends (59-CCCGCCCCA-39) and 68.7% G1C content. A BLASTn (11) query of the sequence against the nonredundant/nucleotide (nr/nt) database returned .96% nucleotide sequence identity to the cluster EE bacteriophages Quaker (GenBank accession number MH371111) and Livingwater (MT498040) (1). Auto-annotation with GLIMMER v3.02 (12) and GeneMark v2.5p (13) was manually refined using Phamerator (14), PECAAN, and DNA Master v5.23.3 (http://phagesdb.org/DNAMaster/). No tRNA genes were identified using Aragorn v1.1 (15) or tRNAscan-SE v2.0 (16). Putative functions for 18 of