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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2023; 51(3): 289-292

Received: August 21, 2023; Revised: September 12, 2023; Accepted: September 20, 2023

Complete Genome Sequence of Bacillus subtilis NIB353 Isolated from Nuruk

Jeong-Ah Yoon1, Se-Young Kwun1, Eun-Hee Park2, and Myoung-Dong Kim1,2,3*

1Department of Food Biotechnology and Environmental Science, 2Department of Food Science and Biotechnology, 3Institute of Fermentation and Brewing, Kangwon National University, Chuncheon 24341, Republic of Korea

Correspondence to :
Myoung-Dong Kim,

Thermotolerant Bacillus subtilis NIB353 was isolated from Nuruk, a traditional Korean fermentation starter. The complete B. subtilis NIB353 genome sequence was obtained using MinION and Illumina (MiSeq) platforms. The B. subtilis NIB353 genome sequence was 4,247,447 bp with a GC content of 43%. The B. subtilis NIB353 strain exhibited orthologous average nucleotide identity values of 98.39% and 98.38% with B. subtilis 168 and B. subtilis ATCC6051a, respectively. The genome has been deposited in GenBank under the accession number NZ_CP089148.1.

Keywords: Bacillus subtilis, complete genome sequence, whole-genome analysis, fermentation starter culture, Nuruk

Bacillus subtilis is a culture starter commonly used in the preparation of traditional fermented foods, such as cheonggukjang, natto, and kinema [1]. Due to its highly efficient protein secretion system and adaptive metabolism, B. subtilis is widely used in industrial applications [2]. In the present study, we describe B. subtilis NIB353, which can grow at 57℃ and was isolated from Nuruk, a traditional Korean fermentation starter.

B. subtilis NIB353 was inoculated in nutrient broth and incubated at 37℃ with agitation for 24 h. Following incubation, bacterial cells were harvested by centrifugation at 20,000 × g for 10 min. Subsequently, genomic DNA was extracted using the ExiPrep™ Plus Bacteria Genomic DNA Kit (Bioneer, Korea), according to the manufacturer's instructions. The complete B. subtilis NIB353 genome was sequenced using the MinION and Illumina (MiSeq) platforms. The read set was assembled de novo into one contig sequence using Unicycler (v0.4.8). B. subtilis NIB353 genome annotation was performed using rapid prokaryotic genome annotation (Prokka v1.14.6) [3] and rapid annotation using subsystems technology (RAST) [4]. Average nucleotide identity (ANI) values among the B. subtilis NIB353 genome and genomes of closely related species (B. subtilis, Bacillus halotolerans, Bacillus mojavensis, Bacillus amyloliquefaciens, Bacillus velezensis, Bacillus licheniformis, and Bacillus paralicheniformis) were calculated using the Orthologous Average Nucleotide Identity Software Tool (OAT, v0.93.1) [5].

The genomic features of B. subtilis NIB353 and the other Bacillus species are highlighted in Table 1. The B. subtilis NIB353 genome, which consists of one contig, was 4,247,447 bp long with a GC content of 43%. The genome size and GC content are in alignment with those of Bacillus species. In addition, the B. subtilis NIB353 genome was predicted to contain 4,350 coding sequences, 30 rRNAs, and 87 tRNA genes. Using RASTbased annotation, 337 functional subsystems were revealed (Table 2).

Table 1 . Comparison of genomes between B. subtilis NIB353 and several other Bacillus species.

StrainGC content (%)Contig N50 (bp)Predicted CDSrRNAstRNAsGenBank accession NO.Reference
B. subtilis NIB35343.04,247,4474,3503087NZ_CP089148.1This study
B. subtilis ATCC6051a43.54,215,6334,2443086NZ_CP011115.1[6]
B. subtilis 16843.54,215,6064,2373088NC_000964.3[7]
B. halotolerans ZB20170243.84,154,2454,0233088NZ_CP029364.1[8]
B. mojavensis UCMB507543.84,031,1213,9503087NZ_CP051464.1-
B. amyloliquefaciens IT-4546.63,928,8573,7253095NC_020272.1[9]
B. velezensis JS25R46.44,006,0023,7612181NZ_CP009679.1-
B. licheniformis SCEB1446.34,136,9864,0702481NZ_CP014842-
B. paralicheniformis Bac8445.84,376,8314,2372481NZ_CP023665.1[10]

Abbreviations: B., Bacillus; CDS, coding sequence; rRNA, ribosomal RNA; tRNA, transfer RNA

Table 2 . Overview of the subsystem categories among B. subtilis NIB353 and closely related strains (B. subtilis ATCC6051a and B. subtilis 168).

B. subtilis NIB353B. subtilis ATCC6051aB. subtilis 168
Number of subsystems337334334
Subsystem coverage
In subsystem1,205 (27%)1,180 (27%)1,179 (27%)
Non in subsystem3,429 (73%)3,226 (73%)3,230 (73%)
Subsystem category distribution
Cofactors, vitamins, prosthetic groups, Pigments143145145
Cell wall and capsule928384
Virulence, disease and defense353939
Potassium metabolism333
Phages, prophages, transposable elements, plasmids2677
Membrane transport444242
Iron acquisition and metabolism313131
RNA metabolism565656
Nucleosides and nucleotides104101101
Protein metabolism216174174
Cell division and cell cycle444
Motility and chemotaxis74645
Regulation and cell signaling302828
Secondary metabolism866
DNA metabolism646464
Fatty acids, lipids, and isoprenoids474849
Nitrogen metabolism191919
Dormancy and sporulation969797
Stress response454747
Metabolism of aromatic compounds131212
Amino acids and derivatives295302300
Sulfur metabolism888
Phosphorus metabolism111111

The B. subtilis NIB353 strain exhibited orthologous ANI values of 98.39% and 98.38% with B. subtilis 168 and B. subtilis ATCC6051a, respectively (Fig. 1). These insights into the genomic characteristics of B. subtilis NIB353 highlight its potential industrial use as a fermentation starter culture.

Figure 1.Heatmap of the orthologous average nucleotide identity values of Bacillus subtilis NIB353 and other Bacillus species.

The complete B. subtilis NIB353 genome sequence has been deposited in the DDBJ/ENA/GenBank database under accession number NZ_CP089148.1.

This research was funded by the Research Program for Agricultural Science and Technology Development (Project No. RS-2022-RD010225) and the National Institute of Agricultural Science, Rural Development Administration, Republic of Korea.

The authors have no financial conflicts of interest to declare.

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