Genome Sequence of Staphylococcus lentus F1142, a Strain Isolated from Korean Soybean Paste

Abstract

This report describes the draft genome sequence of Staphylococcus lentus F1142, which was isolated from a Korean fermented soybean paste (doenjang). The draft genome sequence contained 2.79 Mbp with a G+C content of 31.8%; this is the first S. lentus genome to be reported.

GENOME ANNOUNCEMENT

Staphylococcus lentus is a member of the Staphylococcus sciuri group, which are Gram-positive, oxidase-positive, and coagulase-negative cocci (11). The S. sciuri group is part of the normal flora of animal skin and mucosal surfaces, and they are frequently isolated from various animal-derived fermented food products (1, 4). Members of the S. sciuri group and the Staphylococcus saprophyticus group are commonly found in traditional Korean fermented soybean foods such as doenjang (9) and cheonggukjang (8). Members of the S. sciuri group are not commonly considered to be pathogenic, but there is a pressing need to confirm the safety of this Staphylococcus group in food products because there have been frequent reports of S. sciuri group members being isolated in hospital environments (5), and a large proportion of strains isolated from various environments have the potential for enterotoxin production (3). In this study, a new strain, Staphylococcus lentus F1142, was isolated from doenjang, which is a Korean soybean paste. This report contains the draft genome sequence of this Staphylococcus strain, which participates in soybean fermentation.

The draft genome sequence of S. vitulinus F1142 was determined using an Ion Torrent personal genome machine (PGM) with 316 (100-Mb) sequencing chips (150-bp library), according to the manufacturer's instructions (10). This produced 3,151,336 reads with an average length of 127 bases (total, 399 Mb). The reads were assembled into 169 contigs (>1 kb in size) with an approximate 143-fold coverage using the CLC Genomics Workbench 5.0.1 program (CLC Bio, Denmark). The draft genome of S. lentus F1142 measured 2.79 Mbp in length with a G+C content of 31.8%. Gene prediction and annotation were conducted using open databases: i.e., RNAmmer 1.2 for rRNAs (6), tRNA scan-SE 1.23 for tRNAs (7), and RAST 4.0 (Rapid Annotation using Subsystem Technology) for proteins (2). The genome of S. lentus F1142 contained one 16S rRNA gene, one 23S rRNA, and 55 tRNA genes. Based on the RAST results, the draft genome contained 2,827 predicted protein-coding sequences (CDSs), of which 73% (2,089) were annotated based on known proteins with biological functions, and 27% (738) were annotated as hypothetical proteins. Most of the protein-coding genes were related to metabolic traits, such as carbohydrate (14%), protein (6%), and RNA metabolism (4.5%). There were no toxin- or superantigen-related genes, but the draft genome contained four bacteriocin-related genes. A more detailed analysis of this genome and a comparative analysis with other Staphylococcus genomes will provide insights into the genetic basis of its involvement in the fermentation of traditional foods.

Nucleotide sequence accession numbers.

The draft genome sequence of S. lentus F1142 is available in DDBJ/EMBL/GenBank under accession no. AJXO00000000. The version described here is the first version, AJXO00000000.