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Complete genome sequence of Staphylococcus xylosus strain DMSX03 from fermented soybean, meju
Korean J. Microbiol. 2021;57(1):52-54
Published online March 31, 2021
© 2021 The Microbiological Society of Korea.

Sojeong Heo1, Jong-Hoon Lee2, and Do-Won Jeong1*

1Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Republic of Korea
2Department of Food Science and Biotechnology, Kyonggi University, Suwon 16227, Republic of Korea
Correspondence to: E-mail:;
Tel.: +82-2-940-4463;Fax: +82-2-940-4610
Received November 23, 2020; Revised December 22, 2020; Accepted December 24, 2020.
Staphylococcus xylosus strain DMSX03 was isolated from fermented soybean, meju, and its complete genome sequence was determined. It contains a single circular 2,825,246-bp chromosome and a 48,816-bp plasmid. The G + C content of the genome is 32.76%. Strain DMSX03, having protease and lipase activities, encodes 44 protease and 8 lipase genes. Thus, the genetic background corroborates the enzymatic activities reported for strain DMSX03, making it a potential starter candidate.
Keywords : Staphylococcus xylosus, genome, meju, starter

Coagulase-negative Staphylococcus have been detected predominantly in protein-rich fermented foods (Cocolin et al., 2001; Blaiotta et al., 2004; Corbière Morot-Bizot et al., 2006; Drosinos et al., 2007). In particular, Staphylococcus xylosus has usually been isolated from fermented sausages, and it displays protease and lipase activities involved in protein and lipid degradation, respectively (Martín et al., 2006; Jeong et al., 2016; dos Santos Cruxen, 2017). These extracellular enzymatic activities contribute to flavor enhancement through the production of aroma compounds (Sondergaard and Stahnke, 2002; Jeong et al., 2016). Owing to these properties, S. xylosus has been used in fermented sausage as a meat starter (Leroy et al., 2017). Here, S. xylosus strain DMSX03 was isolated from fermented soybean, meju, as a starter candidate. Strain DMSX03 exhibited proteolytic and lipolytic activities on tryptic soy agar (BD Diagnostic Systems) containing 1.5% and 4% NaCl, respectively, and its complete genome sequence was determined to confirm its genetic background.

The whole-genome sequencing of S. xylosus strain DMSX03 was performed using the PacBio RSII platform (Pacific Bioscience) at ChunLab, Inc. Two contigs were constructed from 49,384 reads generated using the PacBio system (226.61× coverage) by HGAP2 assembler in SMRT Link (ver. 7.0.1; Pacific Bioscience). The NCBI Prokaryotic Genome Annotation Pipeline was used for genome annotation (Tatusova et al., 2016), and Glimmer 3 was used to predict open reading frames (Delcher et al., 1999). Then, a search against the Clusters of Orthologous Groups (COG) database was performed to determine putative protein functions (Tatusov et al., 1997).

The complete genome of strain DMSX03 consists of a single circular 2,825,246-bp chromosome and a 48,816-bp plasmid (Table 1). The G + C content of genome is 32.76%. The genome was predicted to contain 2,704 open reading frames, 59 tRNA genes, and 22 rRNA genes. In total, 2,407 genes were functionally assigned to categories on the basis of the COG results. The genomic fractions in the COG categories related to amino acid transport and metabolism, to carbohydrate transport and metabolism, and to lipid transport and metabolism were 9.97% (240 genes), 8.14% (196 genes), and 2.87% (69 genes), respectively. Strain DMSX03 possesses 38 protease genes belonging to Enzyme Class (E.C.) 3.4.-.-. and 2 protease genes belonging to E.C. 3.5.1.-. An additional four protease genes were not assigned E.C. numbers. The genome of strain DMSX03 encodes four triacylglycerol lipase (E.C., three lysophospholipase (E.C. and one putative esterase (E.C. 3.1.-.-) genes. These annotated genes may contribute to the protease and lipase activities of strain DMSX03. Additionally, the DMSX03 genome does not possess α-hemolysin, β-hemolysin, and enterotoxin genes, which have been detected in pathogenic Staphylococcus aureus (Kane et al., 2018). Although hemolysin III family protein gene (DMSX03_RS03685) was detected in DMSX03 genome, it is not clear the contribution of these gene into hemolysis (Robertson et al., 2006). In previous our study, these gene in S. equorum was not related with hemolysis (Jeong et al., 2017). Moreover, DMSX03 did not exhibited the hemolysis, thus we still assumed that hemolysin III family protein gene in DMSX03 may not function in hemolysis. These results suggested that DMSX03 strain might be safe bacteria. The lack of these pathogenicity-related genes is a desired trait of safe candidate starter strains. Consequently, the genome of strain DMSX03 indicates that it utilizes proteins and lipids during fermentation and might contribute to flavor enhancements.

Genome features of Staphylococcus xylosus strain DMSX03

Feature Value
Genome size (bp) 2,874,062
G + C content (%) 32.76
Number of plasmids 1
Open reading frames 2,704
CDS assigned by COG 2,407
rRNA genes 22
tRNA genes 59

Abbreviations: CDS, coding DNA sequence; COG, Cluster of Orthologous Groups of proteins.

Nucleotide sequence accession number(s)

The complete genome sequence of S. xylosus DMSX03 has been deposited in DDBJ/ENA/GenBank under accession numbers CP060271 and CP060272, and the strain has been deposited in the Korean Culture Center of Microorganisms under accession number KFCC 11860P.

적 요

Staphylococcus xylosus DMSX03 균주를 메주로부터 분리하여 유전체를 분석하였다. 균주 DMSX03은 유전체는 약 2.8-Mb 크기의 chromosome과 48-kb 크기의 플라스미드를 보유하고 있었다. DMSX03 균주의 GC 함량은 32.76%였다. 해당 균주는 단백질 분해활성과 지방분해활성을 보였고, 유전체 분석 결과 44개의 단백질 분해효소 유전자와 8개 지방분해효소 유전자를 보유하고 있었다. 이는 DMSX03 균주의 효소활성에 대한 유전적 배경을 이해하는데 활용될 수 있음을 제공한다.


This research was supported by the Basic Science Research Program through the National Research Foundation of Korea funded by the Ministry of Education (NRF-2019R1A2C1003639 for DWJ and NRF-2020R1A6A3A13077341 for SH). We thank Lesley Benyon, PhD, from Edanz Group ( for editing a draft of this manuscript.

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March 2021, 57 (1)