Abstract
Lactobacillus sakei MBEL1397(=KCTC14037BP) was isolated from kimchi, a traditional Korean fermented food, in Gangwon province, Republic of Korea. MBEL1397 is an acid-tolerant strain with antimicrobial activity and α-glucosidase inhibitory activity, which might be preliminary indications of its probiotic properties. Complete genome sequencing of L. sakei MBEL1397 was performed using the PacBio RSII platform. MBEL1397 has a 1,994,569 bp circular chromosome with 41.04% G+C content. The genome includes 1,946 protein-coding genes, 66 transfer RNA genes, and 21 ribosomal RNA genes. The BioProject has been deposited at DDBJ/EMBL/GenBank. The GenBank accession numbers are PRJNA598112 for the BioProject, SAMN13698554 for the BioSample, and CP048116 for the chromosome.
Keywords: Complete genome, Lactobacillus sakei, Kimchi, Probiotics
Specifications table
| Subject | Genetics |
| Specific subject area | Genomics and Molecular Biology |
| Type of data | Figure and Table |
| How data were acquired | The complete genome sequence was determined using the PacBio RSII platform. The reads were assembled de novo into 1 contig using FALCON (v.2.1.4). |
| Data format | Raw and Analyzed |
| Parameters for data collection | Isolation of L. sakei MBEL1397 from kimchi, a traditional Korean fermented food. Genomic DNA extraction and sequencing procedure. |
| Description of data collection | Whole-genome sequencing followed by genome assembly. |
| Data source location | L. sakei MBEL1397 was isolated from kimchi in Chuncheon, Gangwon province, Republic of Korea. Latitude: 37°87’ N and Longitude: 127°74’ E. |
| Data accessibility | Data are publically available at NCBI GenBank under the following accession numbers: BioSample, SAMN13698554 (https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN13698554); BioProject, PRJNA598112 (https://www.ncbi.nlm.nih.gov/bioproject/598112); assembly/WGS, CP048116 (https://www.ncbi.nlm.nih.gov/nuccore/CP048116). The raw data have been deposited in the Mendeley database (https://data.mendeley.com/datasets/sxk2sr5tf2/draft?a=3f3c4635-391a-45c8-8403-7f928ccbaba8). |
Value of the Data
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The complete genome of L. sakei MBEL1397, isolated from kimchi, allows studying the genetic information of this strain because of its potential use as a probiotic strain.
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L. sakei MBEL1397 genome data presented here can be valuable for researchers involved in the field of genomic analysis of lactic acid bacteria and food fermentations.
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This genomic sequence could contribute to the understanding of the molecular information of L. sakei and related characteristics of this strain.
1. Data Description
We present the complete genome sequence of L. sakei MBEL1397 isolated from kimchi. L. sakei MBEL1397 survived in MRS broth adjusted to pH 2.5 and showed survival rates of over 97% both at low pH and in bile, and had antimicrobial activity against Bacillus cereus. Also, it has the α-glucosidase inhibitory activity. This strain was deposited to the Korean Collection for Type Cultures (KCTC) as KCTC14037BP.
The reads were assembled de novo into one contig using FALCON (v2.1.4). The genome contained 1,994,569 base pairs (bp) with a GC content of 41.04%. We were able to annotate a total of 2,033 genes, including 1,946 protein-coding genes, 66 tRNA, and 21 rRNA genes (Table 1). The genome of L. sakei MBEL1397 showed the highest average nucleotide identity (ANI) value (98.92%) with that of L. sakei LT-13.
Table 1.
Genome features of six different Lactobacillus sakei strains.
| Length (bp) | G+C content (%) | Protein-coding genes | rRNA genes | tRNA genes | Reference | |
|---|---|---|---|---|---|---|
| MBEL1397 | 1,994,569 | 41.0 | 1,946 | 21 | 66 | This study |
| LT-13 | 1,943,136 | 41.2 | 1,825 | 15 | 65 | [4] |
| LK-145 | 1,994,264 | 41.2 | 1,878 | 15 | 65 | [3] |
| 23K | 1,884,661 | 41.3 | 1,770 | 21 | 64 | [2] |
| FBL1 | 2,032,158 | 41.2 | 1,922 | 10 | 56 | [5] |
| Wikim22 | 2,185,902 | 40.6 | 1,869 | 9 | 58 | [7] |
L. sakei MBEL1397 exhibited ANI value of 97.46% with L. sakei FAM18311, another strain that was below the species boundary value (ANI, >95%) (Fig. 1) [6].
Fig. 1.
Heatmap generated by OAT software indicating the OrthoANI values of Lactobacillus sakei strain MBEL1397 and related Lactobacillus species.
The α-glucosidase inhibitory activity of L. sakei MBEL1397, as well as its acid tolerance and antimicrobial activity, suggest that it might become a prominent probiotic with potential hypoglycemic effects.
2. Experimental Design, Materials, and Methods
The genomic DNA of L. sakei MBEL1397 was prepared from cells in the exponential growth phase. Genomic DNA was extracted using a G-DEXTMIIc Genomic DNA Extraction Kit (iNtRON, Daejeon, Korea) according to the manufacturer's instructions.
The complete genome of L. sakei MBEL1397 was sequenced using the PacBio RSII (P6-C4) platform (Pacific Biosciences, Menlo Park, CA, USA). The reads were assembled de novo into one contig (652-fold coverage) using a FALCON genome assembly process (https://pb-falcon.readthedocs.io/en/latest).
Prokka (http://www.vicbioinformatics.com/software.prokka.shtml) was used to predict and subsequently annotate open reading frames. The ANI with closely related species was determined using the Orthologous Average Nucleotide Identity Software Tool (OAT) [6]. The antiSMASH bacterial version 5.1.1 (https://antismash.secondarymetabolites.org) was used to identify putative genes in the L. sakei MBEL1397 genome [1].
Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships which have, or could be perceived to have, influenced the work reported in this article.
Acknowledgments
This research was financially supported by the Ministry of Trade Industry and Energy (MOTIE), Korea, under the “Regional Specialized Industry Development Program”(reference number P0002815) supervised by the Korea Institute for Advancement of Technology (KIAT).
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