Genome Sequence of Strain TW25, a Novel Member of the Genus Ornithinibacillus in the Family Bacillaceae

Abstract

Ornithinibacillus sp. strain TW25, belonging to the family Bacillaceae, was isolated from a dead ark clam during a mass mortality event. Here, the draft genome sequence of strain TW25 (3,843,870 bp, with a G+C content of 36.7%) is reported. This is the first Ornithinibacillus genome to be sequenced.

TEXT

Mass mortality of cage-cultured invertebrates is an annual event along the south coast of Korea. The novel strain TW25 belonging to the genus Ornithinibacillus was cultivated as part of an attempt to isolate and characterize putative pathogenic bacterioplankton. The genus Ornithinibacillus currently comprises three species; O. bavariensis was isolated from pasteurized milk, O. californiensis from coastal surface sediments (8), and O. contaminans from a human blood sample obtained from a 75-year-old woman (5). Based on 16S rRNA gene sequences of validly published species, the isolate TW25 shows the closest similarity to O. californiensis (98.5%). Within the family Bacillaceae, a major feature that differentiates the genus Ornithinibacillus from Oceanobacillus is the inclusion of l-ornithine in the peptidoglycan (5). This study presents the genome of Ornithinibacillus sp. TW25; genome sequencing had not been completed or initiated for any strain in this genus when the present sequencing project was begun. Ornithinibacillus sp. TW25 genomic DNA was isolated from a tissue homogenate obtained from the ark clam. This strain is the first member of the genus Ornithinibacillus to be sequenced.

A whole-genome shotgun strategy was used for genomic DNA sequencing. Roche 454 GS FLX Titanium pyrosequencing (216,931 reads totaling ∼86 Mb, ∼22.4-fold coverage of the genome) was performed by GnCBIO, Inc. (Daejeon, Republic of Korea), and genome sequences were processed with Roche software, according to the manufacturer's instructions. A total of 216,931 reads were assembled using 454 Newbler assembler version 2.3 software (454 Life Science), which generated 75 large contigs with bases containing quality scores of 40 and above. The RAST (Rapid Annotation using Subsystem Technology) pipeline (1) and the Glimmer 3.02 modeling software package (4) were used for the preliminary prediction of 3,867 and 4,019 coding sequences (CDSs), respectively, within the genome.

The unclosed draft genome includes 3,843,870 bases with a G+C content of 36.7%. tRNAscan-SE 1.23 (7) and RNAmmer 1.2 (6) analyses of the genome predicted 54 tRNA genes, two 5S rRNA genes, one 23S rRNA gene, and one 16S rRNA gene. l-Ornithine is the characteristic diamino acid in the peptidoglycan of Ornithinibacillus species, and 15 genes were predicted to be involved in the conversion or degradation of l-ornithine, including arginase (EC 3.5.3.1), ornithine aminotransferase (EC 2.6.1.13), and ornithine cyclodeaminase (EC 4.3.1.12) (2, 3, 10).

Among the publicly available genomes for the family Bacillaceae, Ornithinibacillus sp. strain TW25 shows the closest relationship to Oceanobacillus iheyensis HTE831^T (9), with which it shares 2,266 genes, in addition to containing 1,645 unique genes. There are 51 and 30 predicted genes that correspond to virulence, disease, and defense in the genomes of TW25 and O. iheyensis HTE831^T, respectively. However, only the TW25 genome contains genes putatively involved in adhesion, bile hydrolysis, vancomycin resistance, and multidrug resistance efflux.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AEWH00000000. The version described in this paper is the first version, AEWH01000000. The 75 large contigs contained in the genome have been deposited under accession numbers AEWH01000001 through AEWH01000075.