Complete Genome Sequence of Croceibacter atlanticus HTCC2559T

Here we announce the complete genome sequence of Croceibacter atlanticus HTCC2559^T, which was isolated by high-throughput dilution-to-extinction culturing from the Bermuda Atlantic Time Series station in the Western Sargasso Sea. Strain HTCC2559^T contained genes for carotenoid biosynthesis, flavonoid biosynthesis, and several macromolecule-degrading enzymes. The genome confirmed physiological observations of cultivated Croceibacter atlanticus strain HTCC2559^T, which identified it as an obligate chemoheterotroph.The phylum Bacteroidetes comprises 6 to ∼30% of total bacterial communities in the ocean by fluorescence in situ hybridization (8-10). Most marine Bacteroidetes are in the family Flavobacteriaceae, most of which are aerobic respiratory heterotrophs that form a well-defined clade by 16S rRNA phylogenetic analyses (4). The members of this family are well known for degrading macromolecules, including chitin, DNA, cellulose, starch, and pectin (17), suggesting their environmental roles as detritus decomposers in the ocean (6). Marine Polaribacter and Dokdonia species in the Flavobacteriaceae have also shown to have photoheterotrophic metabolism mediated by proteorhodopsins (11, 12).Several strains of the family Flavobacteriaceae were isolated from the Sargasso Sea and Oregon coast, using high-throughput culturing approaches (7). Croceibacter atlanticus HTCC2559^T was cultivated from seawater collected at a depth of 250 m from the Sargasso Sea and was identified as a new genus in the family Flavobacteriaceae based on its 16S rRNA gene sequence similarities (6). Strain HTCC2559^T met the minimal standards for genera of the family Flavobacteriaceae (3) on the basis of phenotypic characteristics (6).Here we report the complete genome sequence of Croceibacter atlanticus HTCC2559^T. The genome sequencing was initiated by the J. Craig Venter Institute as a part of the Moore Foundation Microbial Genome Sequencing Project and completed in the current announcement. Gaps among contigs were closed by Genotech Co., Ltd. (Daejeon, Korea), using direct sequencing of combinatorial PCR products (16). The HTCC2559^T genome was analyzed with a genome annotation system based on GenDB (14) at Oregon State University and with the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (15, 16).The HTCC2559^T genome is 2,952,962 bp long, with 33.9 mol% G+C content, and there was no evidence of plasmids. The number of protein-coding genes was 2,715; there were two copies of the 16S-23S-5S rRNA operon and 36 tRNA genes. The HTCC2559^T genome contained genes for a complete tricarboxylic acid cycle, glycolysis, and a pentose phosphate pathway. The genome also contained sets of genes for metabolic enzymes involved in carotenoid biosynthesis and also a serine/glycine hydroxymethyltransferase, which is often associated with the assimilatory serine cycle (13). The potential for HTCC2559^T to use bacterial type III polyketide synthase (PKS) needs to be confirmed because this organism had a naringenin-chalcone synthase (CHS) or chalcone synthase (EC 2.3.1.74), a key enzyme in flavonoid biosynthesis. CHS initiates the addition of three molecules of malonyl coenzyme A (malonyl-CoA) to a starter CoA ester (e.g., 4-coumaroyl-CoA) (1) and takes part in a few bacterial type III polyketide synthase systems (1, 2, 5, 18).The complete genome sequence confirmed that strain HTCC2559^T is an obligate chemoheterotroph because no genes for phototrophy were found. As expected from physiological characteristics (6), the HTCC2559^T genome contained a set of genes coding for enzymes required to degrade high-molecular-weight compounds, including peptidases, metallo-/serine proteases, pectinase, alginate lyases, and α-amylase.     

Complete Genome Sequence of Vibrio parahaemolyticus Bacteriophage vB_VpaM_MAR

Vibrio parahaemolyticus is a major pathogen that is mainly associated with seafood and is a global food safety issue. Our objective was to isolate and completely sequence a specific phage against this bacterium. Phage vB_VpaM_MAR is able to lyse 76% of the V. parahaemolyticus strains tested. MAR belongs to the Myoviridae family and has a genome comprised of double-stranded DNA with a size of 41,351 bp, a G+C content of 51.3%, and 62 open reading frames (ORFs). Bioinformatic analysis showed that phage MAR is closely related to Vibrio phages VHML, VP58.5, and VP882 and Halomonas aquamarina phage ΦHAP-1.     

Complete Genome Sequence of Staphylococcus aureus Bacteriophage GH15

GH15 is a polyvalent phage that shows activity against a wide range of Staphylococcus aureus strains. In this work, the complete genome sequence of GH15 was determined. With a genome size of 139,806 bp (double-stranded DNA), GH15 is the largest staphylococcal phage sequenced to date. The complete genome encodes 214 open reading frames (ORFs) and 4 tRNAs. The closest relatives are the class III staphylococcal myobacteriophages, including K, A5W, ISP, Sb-1, and G1. Interestingly, although corresponding gene sequences demonstrate very high similarity, all the introns and inteins present in the phages listed above are absent in GH15. As such, GH15 can be considered phylogenetically unique among the staphylococcal myobacteriophages, indicating the diversity of this family.     

Complete Genome Sequence of Salmonella Bacteriophage SS3e

A Salmonella lytic bacteriophage, SS3e, was isolated, and its genome was sequenced completely. This phage is able to lyse not only various Salmonella serovars but also Escherichia coli, Shigella sonnei, Enterobacter cloacae, and Serratia marcescens, indicating a broad host specificity. Genomic sequence analysis of SS3e revealed a linear double-stranded DNA sequence of 40,793 bp harboring 58 open reading frames, which is highly similar to Salmonella phages SETP13 and MB78.     

Complete Genome Sequence of Cronobacter sakazakii Bacteriophage vB_CsaM_GAP161

Cronobacter sakazakii is an opportunistic pathogen that causes infant meningitis and is often associated with milk-based infant formula. We have fully sequenced the genome of a newly isolated lytic C. sakazakii myovirus, vB_CsaM_GAP161, briefly named GAP161. It consists of 178,193 bp and has a G+C content of 44.5%. A total of 277 genes, including 275 open reading frames and two tRNA-encoding genes, were identified. This phage is closely related to coliphages RB16 and RB43 and Klebsiella pneumoniae phage KP15.     

Complete Genome Sequence of the Enterobacter cancerogenus Bacteriophage Enc34

Enterobacter cancerogenus is widely distributed in nature and is generally recovered from environmental or vegetal sources. In some cases, it has also been associated with human infections. In this study, the complete genomic sequence of virulent E. cancerogenus bacteriophage Enc34 was determined. The Enc34 genome is 60,364 bp in length and contains 80 open reading frames. To our knowledge, this is the first report of a bacteriophage infecting E. cancerogenus.     

Complete Genome Sequence of Caulobacter crescentus Bacteriophage {varphi}CbK

?CbK is a B3 morphotype bacteriophage of the Siphoviridae family that infects Caulobacter crescentus, the preeminent model system for bacterial cell cycle studies. The last 4 decades of research with ?CbK as a genetic and cytological tool to study the biology of the host warrant an investigation of the phage genome composition. Herein, we report the complete genome sequence of ?CbK and highlight unusual features that emerged from its annotation. The complete genome analysis of the ?CbK phage provides new insight into its characteristics and potential interactions with its Caulobacter crescentus host, setting the stage for future functional studies with ?CbK.     

Whole Genome Sequence Analysis of Lactiplantibacillus Plantarum Bacteriophage P2

Phage P2 was isolated from failed fermentation broth carried out by Lactiplantibacillus plantarum IMAU10120. A previous study in our laboratory showed that this phage belonged to the Siphoviridae family. In this study, this phage’s genomic characteristics were analyzed using whole-genome sequencing. It was revealed that phage P2 was 77.9 kb in length and had 39.28% G + C content. Its genome included 96 coding sequences (CDS) and two tRNA genes involved in the function of the structure, DNA replication, packaging, and regulation. Phage P2 had higher host specificity; many tested strains were not infected. Cell wall adsorption experiments showed that the adsorption receptor component of phage P2 might be a part of the cell wall peptidoglycan. This research might enrich the knowledge about genomic information of lactobacillus phages and provide some primary data to establish phage control measures.     

Complete Genome Sequence of Pectobacterium carotovorum subsp. carotovorum Bacteriophage My1

Pectobacterium carotovorum subsp. carotovorum, a member of the Enterobacteriaceae family, is an important plant-pathogenic bacterium causing significant economic losses worldwide. P. carotovorum subsp. carotovorum bacteriophage My1 was isolated from a soil sample. Its genome was completely sequenced and analyzed for the development of an effective biological control agent. Sequence and morphological analyses revealed that phage My1 is a T5-like bacteriophage and belongs to the family Siphoviridae. To date, there is no report of a Pectobacterium-targeting siphovirus genome sequence. Here, we announce the complete genome sequence of phage My1 and report the results of our analysis.     

Complete Genome Sequence of T4-Like Escherichia coli Bacteriophage HX01

Phage T4 is among the best-characterized biological systems (S. Kanamaru and F. Arisaka, Seikagaku 74:131-135, 2002; E. S. Miller et al., Microbiol. Mol. Biol. Rev. 67:86-156, 2003; W. B. Wood and H. R. Revel, Bacteriol. Rev. 40:847-868, 1976). To date, several genomes of T4-like bacteriophages are available in public databases but without any APEC bacteriophages (H. Jiang et al., Arch. Virol. 156:1489-1492, 2011; L. Kaliniene, V. Klausa, A. Zajanckauskaite, R. Nivinskas, and L. Truncaite, Arch. Virol. 156:1913-1916, 2011; J. H. Kim et al., Vet. Microbiol. 157:164-171, 2012; W. C. Liao et al., J. Virol. 85:6567-6578, 2011). We isolated a bacteriophage from a duck factory, named HX01, that infects avian pathogenic Escherichia coli (APEC). Sequence and morphological analyses revealed that phage HX01 is a T4-like bacteriophage and belongs to the family Myoviridae. Here, we announce the complete genome sequence of phage HX01 and report the results of our analysis.     

Complete Genome Sequence Analysis of the Cold-active Siphoviridae Bacteriophage from Pseudomonas fluorescens

Microbiology - Phages are considered the most abundant and diverse biological entities on Earth. Although many phages have been isolated, most of this diversity remains completely unexplored....     

Complete Genome Sequence of Bacteriophage phiAC-1 Infecting Acinetobacter soli Strain KZ-1

To date, a number of bacteriophages (phages) infecting Acinetobacter species have been reported and characterized. However, Acinetobacter phages which infect A. soli have not been investigated yet. Here, we report the complete genome sequence of Acinetobacter phage phiAC-1, which belongs to the Myoviridae, infecting Acinetobacter soli strain KZ-1.     

Complete Genome Sequence of IME11, a New N4-Like Bacteriophage

N4-like bacteriophages are a class of virulent Podoviridae phages for which few genome sequences are present in GenBank. IME11, a novel lytic Escherichia bacteriophage with a wide host range, was isolated, and the whole genome was sequenced. It has a circular double-stranded DNA genome of 72,570 bp. Genomic analysis showed that it resembles another Escherichia phage, vB_EcoP_G7C. Here we announce its complete genome and major findings from its annotation.     

Complete Genome Sequence of Phytopathogenic Pectobacterium carotovorum subsp. carotovorum Bacteriophage PP1

Pectobacterium carotovorum subsp. carotovorum is a phytopathogen causing soft rot disease on diverse plant species. To control this plant pathogen, P. carotovorum subsp. carotovorum-targeting bacteriophage PP1 was isolated and its genome was completely sequenced to develop a novel biocontrol agent. Interestingly, the 44,400-bp genome sequence does not encode any gene involved in the formation of lysogen, suggesting that this phage may be very useful as a biocontrol agent because it does not make lysogen after host infection. This is the first report on the complete genome sequence of the P. carotovorum subsp. carotovorum-targeting bacteriophage, and it will enhance our understanding of the interaction between phytopathogens and their targeting bacteriophages.     

Complete Genome Sequence of Bacteriophage BC-611 Specifically Infecting Enterococcus faecalis Strain NP-10011

Enterococcus faecalis is an opportunistic pathogen that causes serious infections in humans and animals and is also an important bacterium for dairy and probiotic supplement production. Therefore, bacteriophages infecting E. faecalis may be useful for phage therapy against multidrug-resistant strains or may threaten industrial fermentation. We isolated a virulent Siphoviridae bacteriophage, BC-611, specifically infecting E. faecalis strain NP-10011 but not infecting other E. faecalis strains or other enterococci. Although the genome sequence of BC-611 resembled that of enterococcal bacteriophage SAP6, BC-611 was marked by its narrow host specificity.     

Complete Genome Sequence of Bacteriophage SSU5 Specific for Salmonella enterica serovar Typhimurium Rough Strains

Salmonella enterica serovar Typhimurium rough strain-specific phage SSU5 was isolated, and its whole genome was sequenced. The 103,229-bp-long double-stranded DNA genome of SSU5 encodes 130 open reading frames with one tRNA for asparagine. Genomic analysis revealed that SSU5 might be the phylogenetic origin of cryptic plasmid pHCM2 harbored by Salmonella Typhi CT18.     

Complete Genome Sequence of Mycobacterium massiliense

Mycobacterium massiliense is a rapidly growing bacterium associated with opportunistic infections. The genome of a representative isolate (strain GO 06) recovered from wound samples from patients who underwent arthroscopic or laparoscopic surgery was sequenced. To the best of our knowledge, this is the first announcement of the complete genome sequence of an M. massiliense strain.     

Complete Genome Sequence of Bp7, an Escherichia coli Bacteriophage with a Wide Host Range

Chicken colibacillosis is caused by some pathogenic Escherichia coli strains. Thirty-five pathogenic antibiotic-resistant E. coli strains were used in the host range detection of bacteriophage Bp7. The phage showed a wide range of E. coli hosts (46%). The complete genome of bacteriophage Bp7 was sequenced, assembled, and analyzed. The results revealed a linear double-stranded DNA sequence of 168,066 bp harboring 791 open reading frames. The major findings from its annotation are described.     

Complete Genome Sequence of Temperate Bacteriophage AcaML1 from the Extreme Acidophile Acidithiobacillus caldus ATCC 51756

Development of reproducible genetic tools in the industrially important acidithiobacilli is urgently required. Inducible temperate phages which may be modified in vitro, propagated in suitable hosts, and used to transduce relevant genetic information to other strains and/or species are potentially valuable tools in this field of research. In order to address these current limitations, the genome sequence of an inducible temperate Myoviridae-like bacteriophage from the Acidithiobacillus caldus type strain was annotated and analyzed bioinformatically. Here, we announce the genome sequence of AcaML1 and report major findings from its annotation.     

The Complete Genome Sequence of Bacteriophage CP21 Reveals Modular Shuffling in Campylobacter Group II Phages

Campylobacter group II phages described so far share a high degree of sequence similarity. We report the 182,833-bp genomic sequence of the closely related group II phage CP21 and show that it has a completely different genomic organization. As in other group II phages, the CP21 genome is composed of large modules separated by long DNA repeat regions which obviously trigger recombination and modular shuffling.