Genome Sequence of Kocuria atrinae C3-8, Isolated from Jeotgal, a Traditional Korean Fermented Seafood

Abstract

Kocuria is a Gram-positive coccus, catalase-positive, coagulase-negative, strictly aerobic bacterial genus in the family Micrococcaceae. Kocuria atrinae C3-8 was isolated from a traditional Korean fermented seafood. This study describes the first genome sequence of K. atrinae strain C3-8, which has a 3.19-Mbp genome and a G+C content of 63.8%.

GENOME ANNOUNCEMENT

Jeotgal is a salted and fermented seafood which is commonly used as an additive in Korea to improve the taste of various foods, or it may be eaten alone as a side dish. Jeotgal is made by adding large amounts of salt (20 to 30%) to a diverse range of marine organisms such as shrimp, shellfish, or fish but without the inoculation of microorganisms (2). Jeotgal has a high nutritional content and a unique taste due to fermentation. The fermentation process is caused by a large range of microorganisms, which are derived naturally from the manufacturing environment (7). Kocuria is a coccoid, Gram-positive bacterium that belongs to the family Micrococcaceae in the Actinomycetales order, and the genus Kocuria was created by subdivision of the genus Micrococcus (9). Members of the genus Kocuria have been isolated from a diverse range of environments, including mammalian skin, soil, clinical specimens, freshwater, and marine sediments (10). In particular, the type strains of K. koreensis, K. salsicia, and K. atrinae were isolated from Korean jeotgal (5, 6, 10). In this study, a new isolate, K. atrinae C3-8, was obtained from shrimp jeotgal. The genome sequence of this Kocuria strain will allow us to investigate its roles in the fermentation of traditional foods.

The draft genome of K. atrinae C3-8 was sequenced by using an Ion Torrent Personal Genome Machine with 316 (100-Mb) sequencing chips in accordance with the manufacturer's instructions (8). This produced 2,116,953 reads with an average length of 123 bases covering 261 Mb. The sequence reads were assembled into 221 contigs (>1 kb in size; 246 contigs greater than 500 bases) with approximately 82-fold coverage using the CLC Genomics Workbench 5.0.1 program (CLC Bio, Aarhus, Denmark). The draft genome of K. atrinae C3-8 is 3.19 Mbp long with a G+C content of 63.8%. Single copies of the 5S, 16S, and 23S rRNAs and 45 tRNAs were identified using RNAmmer 1.2 (3) and tRNA scan-SE (4), respectively. A total of 3,959 predicted protein-coding sequences were annotated by RAST server 4.0 (1). Of the predicted protein-coding genes, 1,243 (31.4%) were assigned as encoding hypothetical proteins. These included 497 genes related to carbohydrate metabolism, i.e., monosaccharides (49 genes), oligosaccharides (47 genes), polysaccharides (20 genes), amino sugars (5 genes), and the utilization of organic acids (47 genes) and sugar alcohols (17 genes). A total of 205 genes were related to protein metabolism, including 31 protease- and 46 peptidase-related genes. A single gene for histidinol phosphate phosphatase (EC 3.3.3.15), which catalyzes the biosynthesis of histidine, was identified. Eight genes were related to molybdopterin synthesis. A more detailed analysis of this genome will provide useful information related to the application of microorganisms in the food industry.

Nucleotide sequence accession numbers.

The draft genome sequence of K. atrinae C3-8 is available in DDBJ/EMBL/GenBank under accession number AJXN00000000. The version described here is the first version, AJXN00000000.