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Draft genome sequence of Bacillus velezensis strain KMUS1 from Kimchi
Korean J. Microbiol. 2021;57(2):122-124
Published online June 30, 2021
© 2021 The Microbiological Society of Korea.

Sojeong Heo1, Jong-Hoon Kim2, Mi-Sun Kwak2, Do-Won Jeong1*, and Moon-Hee Sung2,3*

1Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Republic of Korea
2The Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul 02707, Republic of Korea
3KookminBio Corporation, Seoul 02826, Republic of Korea
Correspondence to: (M.H. Sung) E-mail: smoonhee@kookmin.ac.kr; Tel.: +82-2-910-4808; Fax: +82-2-910-5739 / (D.W. Jeong) E-mail: jeongdw@dongduk.ac.kr; Tel.: +82-2-940-4463; Fax: +82-2-940-4610
Received March 10, 2021; Revised June 2, 2021; Accepted June 8, 2021.
Abstract
The whole-genome sequence of Bacillus velezensis strain KMUS1 from kimchi was analyzed with the Illumina HiSeq 4000 platform. The genome comprises a 3,810,818-bp chromosome with a G + C content of 46.63%. Strain KMUS1 encodes 20 protease and 61 peptidase genes, as well as nattokinase. Therefore, the genetic background of strain KMUS1 potentially confers the functional properties of a starter or probiotic candidate.
Keywords : Bacillus velezensis, genome, kimchi, probiotic, starter
Body

The genus Bacillus contains Gram-positive, spore-forming, aerobic or facultatively anaerobic bacteria and is divided into two groups, the B. subtilis group and B. cereus group. The B. subtilis group contains not only the dominant bacteria in fermented foods, but also bacteria widely used in traditional and industrial fermentation (Jung et al., 2016). Bacillus velezensis belongs to the B. subtilis group and produces exoenzymes such as proteases and amylases, and is predominantly detected in several fermented foods (Jang et al., 2019; Lee et al., 2020). Exoenzymes from B. velezensis are involved in protein and starch degradation and contribute to the sensory properties of fermented foods by producing aromatic compounds (Moon et al., 2018). Based on these properties, B. velezensis has been suggested as a starter candidate for fermented foods. Here, B. velezensis strain KMUS01 was isolated from kimchi as a candidate starter strain. Strain KMUS1 displayed proteolytic activities on tryptic soy agar (BD Diagnostic Systems), and its genome sequence was determined to confirm its genetic background.

The genomic DNA of strain KMUS1 was extracted with the Maxwell RSC Tissue DNA Kit (Promega), and the draft genome was sequenced with 100-bp paired-end reads on the Illumina HiSeq 4000 platform (Macrogen, Inc.). The DNA library was prepared with the TruSeq DNA PCR-Free kit, according to the instructions of the manufacturer (Macrogen, Inc.). The DNA quality checks of the sequencing data were made with FastQC (ver. 0.11.7) and the data were assembled with SPAdes (ver. 3.10.0). The NCBI Prokaryotic Genome Annotation Pipeline was used for genome annotation and then a search against the Clusters of Orthologous Groups (COG) database was performed to determine the putative protein functions (Tatusov et al., 2016). Additional prediction of genes and functional roles was performed with the RAST server in USA (https://rast.nmpdr.org/rast.cgi) and the SEED database (Aziz et al., 2008).

It has been known for many years that Bacillus species are difficult to distinguish with traditional phenotypic methods or by their entire 16S rRNA genes (Freitas et al., 2008). Strain KMUS1 was isolated as B. amyloliquefaciens in 2018 on the basis of its 16S rRNA gene sequence. The average nucleotide identity (ANI) of the KMUS1 genomic sequence showed 98.6%, 94.4%, and 94.1% similarity with B. velezensis GH1-13, B. siamensis SCSIO 05746, and B. amyloliquefaciens DSM7T, respectively. Therefore, strain KMUS1 was redefined as B. velezensis.

The draft genome of strain KMUS1 consists of 14 contigs with a total length of 3,810,818 bp (Table 1). The depth of sequencing coverage was 228.12× and the G + C content of the genome is 46.63%. The genome was predicted to contain 3,765 open reading frames and 3,497 genes were functionally assigned to categories on the basis of the COG results. The fractions of the genome related to the COG categories amino acid transport and metabolism, transcription, and carbohydrate transport and metabolism were 8.41% (294 genes), 7.43% (260 genes), and 6.72% (235 genes), respectively. Strain KMUS1 contains 20 protease genes and 61 peptidase genes, and a leucine aminopeptidase gene (KMUS1_02911; EC 3.4.11.1) was detected among them. Bacterial protease activity confers unique characteristic upon fermented foods by breaking down proteins to peptides and various amino acids during fermentation. In particular, leucine aminopeptidases contribute to the flavor development in soybean fermentation products (Zhao et al., 2018). These enzymes also reduce the bitterness of soybean fermentation products by hydrolyzing hydrophobic amino acid residues, such as leucine, at the amino termini of proteins and/or peptides (Kim et al., 2017). The KMUS1 genome also contains a subtilisin gene (KMUS1_00971; EC 3.4.21.62), which encodes a well-known nattokinase. Nattokinase has shown therapeutic pharmacological effects, including antithrombotic and antihypertensive properties (Fujita et al., 2011). Therefore, KMUS1 may be a potential probiotic strain for the production of pharmaceutical products. The draft genome sequence of strain KMUS1 provides further genetic insight into its strain-specific properties and its utility as a starter and probiotic.

Genome features of Bacillus velezensis strain KMUS1

Features Value
No. contigs 14
Depth (×) 228.1
Genome size (bp) 3,810,818
G + C content (%) 46.63
Open reading frames 3,765
tRNA genes 35
rRNA genes -
CDSs assigned with COG 3,497
GenBank accession no. JAEIJC000000000

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



Nucleotide sequence accession number

The draft genome sequence of B. velezensis KMUS1 has been deposited in DDBJ/ENA/GenBank under accession number JAEIJC000000000. The strain has been deposited in the Korean Collection for Type Cultures under accession number KCTC 13635BP.

적 요

Bacillus velezensis KMUS1 균주를 김치로부터 분리하여 유전체를 분석하였다. 균주 KMUS1은 유전체는 약 3.8-Mb 크기로 GC 함량은 46.63%였다. 유전체 분석 결과 단백질 분해효소 및 펩타이드 분해효소 유전자를 다양하게 보유하고 있었으며, 나토키나이제 유전자 또한 보유하고 있었다. 이는 KMUS1 균주의 단백질 분해 활성과 프로바이오틱 특성에 대한 유전적 배경을 이해하는데 활용될 수 있음을 제공한다.

Acknowledgments

This work was supported by the Innopolis Korea innovation Foundation 2020 grant funded by the Korea government (MEST) (No. 2020-JB-RD-0218) and Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (No. 2020R1 A6A3A13077341). We thank Janine Miller, PhD, from Edanz Group (https://en-author-services.edanz.com/ac) for editing a draft of this manuscript.

Conflict of Interest

The authors have no conflicts of interest to report.

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