Abstract
Kimchi, a traditional Korean fermented food, contains many lactic acid bacteria. Leuconostoc mesenteroides KNU-2 strain with low-temperature tolerance and Weissella hellenica MBEL1842 with antibacterial activity were isolated from kimchi. The genomes of L. mesenteroides KNU-2 and W. hellenica MBEL1842 are composed of one circular chromosomal genome of 1,973,419 bp (37.9% G+C content) and 1,887,056 bp (37.9% G+C content), as well as four and one plasmids, respectively, The sequence data of the strains were deposited in GenBank under the accession numbers CP089782 (L. mesenteroides KNU-2) and CP086020 (W. hellenica MBEL1842).
Keywords: Complete genome, Kimchi, Lactic acid bacteria, Leuconostoc mesenteroides, Weissella hellenica
Specifications Table
| Subject | Genetics: General |
| Specific subject area | Genomics and Molecular Biology |
| Type of data | Table and Figure |
| How the data were acquired | The PacBio RSII platform was used for genome sequencing. PacBio long-reads of L. mesenteroides KNU-2 were assembled using RS HGAP(v3.0) and annotated using Prokka (v1.12b), while those of W. hellenica MBEL1842 were assembled using FALCON (v.2.1.4) and annotated using Prokka (v1.12b). |
| Data format | Raw and analyzed |
| Description of data collection | Genomic DNA of L. mesenteroides KNU-2 and W. hellenica MBEL1842 was extracted and used. |
| Data source location | • Institution: Kangwon National University • City/Region: Chuncheon, Kangwon-do • Country: Republic of Korea • Latitude and longitude: 37°87′ N and 127°74′ E |
| Data accessibility | The draft genome sequence of L. mesenteroides KNU-2 was deposited in GenBank under the following Biosample, Bioproject, Sequence Read Archive and GenBank accession number, SAMN10492388 (https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN10492388), PRJNA507406 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA507406), SRX12232645 (https://www.ncbi.nlm.nih.gov/sra/SRX12232645), and CP089782 (https://www.ncbi.nlm.nih.gov/nuccore/CP089782). That of W. hellenica MBEL1842 was deposited under SAMN13968964 (https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN13968964), PRJNA604418 (https://www.ncbi.nlm.nih.gov/bioproject/604418), SRX12745381-SRX12745386 (https://www.ncbi.nlm.nih.gov/sra/?term=SRP342772) and CP086020 (https://www.ncbi.nlm.nih.gov/nuccore/CP086020). |
Value of the Data
-
•
The genome sequence of L. mesenteroides KNU-2 and W. hellenica MBEL1842 provides fundamental knowledge about genes related to lactic acid bacteria isolated from kimchi.
-
•
The genome data of the strains will be useful for comparative genomic analysis with other lactic acid bacteria.
-
•
The data can be useful in understanding the characterization of enzymes and genes related to kimchi fermentation.
1. Data Description
Kimchi is a traditional Korean fermented food consisting of vegetables such as Chinese cabbage, radish, and various ingredients [3]. Lactic acid bacteria (LAB), such as Leuconostoc, Lactobacillus, and Weissella genera, play an important role in kimchi fermentation [4,9]. Therefore, LAB are considered fermentation starters that produce standardized, high-quality kimchi [9]. L. mesenteroides KNU-2 strain with low-temperature tolerance and W. hellenica MBEL1842 with antibacterial activity were isolated from kimchi.
The PacBio reads of L. mesenteroides KNU-2 and W. hellenica MBEL1842 were assembled. Only the L. mesenteroides KNU-2 reads were assembled using RS HGAP (v3.0) to make a circular genome [1]. However, W. hellenica MBEL1842 reads were then assembled again using Falcon (v2.1.4) to obtain a circular genome [2]. The genome coverage of L. mesenteroides KNU-2 was 560 × and that of W. hellenica MBEL1842 was 366 ×.
Table 1 summarizes the genomic features of L. mesenteroides and W. hellenica strains. The genome of L. mesenteroides KNU-2 comprises one circular chromosomal genome of 1973,419 bp (37.9% G+C content) and four circular plasmids. The chromosome contains 1957 predicted protein-coding, 12 rRNA, and 71 tRNA genes. The genome of W. hellenica MBEL1842 was identified as a 1,887,056 bp (36.9% G+C content) circular chromosome with one circular plasmid. The chromosome has 1,779 predicted protein-coding, 25 rRNA, and 76 tRNA genes. The average nucleotide identity (ANI) value for L. mesenteroides KNU-2 and other L. mesenteroides strains was over 99%, indicating a high species boundary value (ANI > 95%) (Fig. 2) [8]. The W. hellenica MBEL1842 and other W. hellenica strains also showed a high ANI value of over 99% (Fig. 3). The whole-genome comparisons of L. mesenteroides (Fig. 4) and W. hellenica strains (Fig. 5) showed high synteny and no large rearrangements.
Table 1.
Genomic features of L. mesenteroides and W. hellenica strains.
| Lactic acid bacteria | Strain | Length (bp) | G+C content (%) | Protein-coding genes | rRNA genes | tRNA genes | Plasmid No. | GenBank No. | Refs. |
|---|---|---|---|---|---|---|---|---|---|
| L. mesenteroides | KNU-2 | 1,973,419 | 37.9 | 1,957 | 12 | 71 | 4 | CP089782 | This study |
| LK151 | 2,090,103 | 37.8 | 1,974 | 9 | 67 | 3 | AP017936 | [6] | |
| ATCC8293 | 2,038,396 | 37.7 | 1,925 | 12 | 70 | 1 | CP000414 | [10] | |
| J18 | 1,900,740 | 37.8 | 1,769 | 12 | 70 | 4 | CP003101 | [5] | |
| DRC1506 | 1,893,478 | 37.7 | 1,707 | 12 | 70 | 3 | CP014611 | [7] | |
| W. hellenica | MBEL1842 | 1,887,056 | 36.9 | 1,779 | 25 | 76 | 1 | CP086020 | This study |
| 0916–4–2 | 1,875,603 | 38.9 | 1,834 | 25 | 76 | 2 | CP033608 | [12] | |
| CBA3632 | 1,900,683 | 36.8 | 1,834 | 25 | 75 | 4 | CP042399 | - | |
Fig. 2.
Heatmap generated with Ortho-ANI values between Leuconostoc mesenteroides KNU-2 and other closely related species.
Fig. 3.
The Heatmap of the Ortho-ANI values of W. hellenica MBEL1842 and related Weissella species.
Fig. 4.
Whole-genome alignment of Leuconostoc mesenteroides strains.
Fig. 5.
Whole-genome alignment of Weissella hellenica strains.
The genome sequence of L. mesenteroides KNU-2 was deposited in GenBank under the accession number CP089782 (https://www.ncbi.nlm.nih.gov/nuccore/CP089782) and W. hellenica MBEL1842 was deposited under the accession number CP086020 (https://www.ncbi.nlm.nih.gov/nuccore/CP086020). The genome sequence data provide essential information for understanding LAB in kimchi.
2. Experimental Design, Materials, and Methods
The L. mesenteroides KNU-2 (KCTC18324P) and W. hellenica MBEL1842 strains were cultured in MRS (de Man, Rogosa and Sharpe) broth at 37 °C for 24 h. Genomic DNA was extracted from the strains grown to an exponential phase using the G-DEX™IIc Genomic DNA Extraction kit (iNtRON, Daejeon, Korea). Whole-genome sequencing was performed using the PacBio RSII platform (Pacific Biosciences, CA, USA). If it was estimated that the total number of bases in the PacBio reads would result in less than 100 × genome coverage, additional sequencing was performed, and all the output raw data were used for assembly.
The reads of L. mesenteroides KNU-2 and W. hellenica MBEL1842 were assembled using RS HGAP (v3.0) and FALCON (v2.1.4), respectively, [1,2]. Polishing was performed using the Quiver algorithm of SMRT® analysis (v2.3.0) and the assessment was performed using BUSCO (v3.0) [11]. Gene prediction was performed using Prokka (v1.12b) to predict and annotate the open reading frame [13]. Fig. 1 shows the whole-genome sequencing steps and the parameters.
Fig. 1.
Steps and parameters of whole-genome sequencing.
The ANI values for closely related species were calculated using the Orthologous Average Nucleotide Identity Software Tool (OAT). Whole-genome alignment of strains was visualized using the CLC Genomics Workbench 20.0.4 (CLC bio) software program.
Ethics Statements
Not applicable.
CRediT authorship contribution statement
J.A. Yoon: Methodology, Software, Data curation, Writing – original draft, Visualization. S.Y. Kwun: Methodology, Software, Data curation, Writing – original draft. E.H. Park: Writing – review & editing, Data curation. M.D. Kim: Conceptualization, Supervision, Funding acquisition.
Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Acknowledgments
This work was supported by the “Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ009477)”, Rural Development Administration Republic of Korea, and 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).
Data Availability
Leuconostoc mesenteroides KNU-2 Genome sequencing and assembly (Reference data) (National Center for Biotechnology Information Search database)
Weissella hellenica strain:MBEL1842 Genome sequencing and assembly (Reference data) (National Center for Biotechnology Information Search database)
References
- 1.Chin C.S., Alexander D.H., Marks P., Klammer A.A., Drake J., Heiner C., Clum A., Copeland A., Huddleston J., Eichler E.E., Turner S.W., Korlach J. Nonhybrid, finished microbial genome assemblies from long-read smrt sequencing data. Nat. Methods. 2013;10:563–569. doi: 10.1038/nmeth.2474. [DOI] [PubMed] [Google Scholar]
- 2.Chin C.S., Peluso P., Sedlazeck F.J., Nattestad M., Concepcion G.T., Clum A., Dunn C., O'Malley R., Balderas R.F., Cruz A.M., Cramer G.R., Delledonne M., Luo C., Ecker J.R., Cantu D., Rank D.R., Schatz M.C. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods. 2016;13:1050–1054. doi: 10.1038/nmeth.4035. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Cho E.J., Rhee S.H., Park K.Y. Standardization of materials of baechu kimchi recipe. J. Korean Soc. Food Sci. Nutr. 1999;30:1456–1463. [Google Scholar]
- 4.Jeong S.E., Chun B.H., Kim K.H., Park D., Roh S.W., Lee S.H., Jeon C.O. Genomic and metatranscriptomic analyses of weissella koreensis reveal its metabolic and fermentative features during kimchi fermentation. Food Microbiol. 2018;76:1–10. doi: 10.1016/j.fm.2018.04.003. [DOI] [PubMed] [Google Scholar]
- 5.Jung J.Y., Lee S.H., Lee S.H., Jeon C.O. Complete genome sequence of Leuconostoc mesenteroides subsp. mesenteroides strain J18, isolated from kimchi. J. Bacteriol. 2012;194:730–731. doi: 10.1128/JB.06498-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Kato S., Oikawa T. Genome sequence of Leuconostoc mesenteroides LK-151 isolated from a Japanese sake cellar as a high producer of d-amino acids. Genome Announc. 2022;5 doi: 10.1128/genomeA.00661-17. e00661–00617. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Kato S., Oikawa T. A proposal of Leuconostoc mesenteroides subsp. Jonggajibkimchii subsp. nov. and reclassification of Leuconostoc mesenteroides subsp. Suionicum (Gu et al., 2012) as Leuconostoc suionicum sp. nov. based on complete genome sequences. Genome Announc. 2017;27 doi: 10.1099/ijsem.0.001930. e00661-00617. [DOI] [PubMed] [Google Scholar]
- 8.Lee I., Kim Y.O., Park S.C., Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int. J. Syst. Evol. Microbiol. 2016;66:1100–1103. doi: 10.1099/ijsem.0.000760. [DOI] [PubMed] [Google Scholar]
- 9.Lee K.W., Kim G.S., Baek A.H., Hwang H.S., Kwon D.Y., Kim S.G., Lee S.Y. Isolation and characterization of kimchi starters Leuconostoc mesenteroides PBio03 and Leuconostoc mesenteroides PBio104 for manufacture of commercial kimchi. J. Microbiol. Biotechnol. 2020;30:1060–1066. doi: 10.4014/jmb.2001.01011. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Makarova K., Slesarev A., Wolf Y., Sorokin A., Mirkin B., Koonin E., Pavlov A., Pavlova N., Karamychev V., Polouchine N., Shakhova V., Grigoriev I., Lou Y., Rohksar D., Lucas S., Huang K., Goodstein D., Hawkins T., Plengvidhya V., Welker D., Hughes J., Goh Y., Benson A., Baldwin K., Lee J., Díaz-Muñiz I., Dosti B., Smeianov V., Wechter W., Barabote R., Lorca G., Altermann E., Barrangou R., Ganesan B., Xie Y., Rawsthorne H., Tamir D., Parker C., Breidt F., Broadbent J., Hutkins R., O'Sullivan D., Steele J., Unlu G., Saier M., Klaenhammer T., Richardson P., Kozyavkin S., Weimer B., Mills D. Comparative genomics of the lactic acid bacteria. Proc. Natl. Acad. Sci. U. S. A. 2006;103:15611–15616. doi: 10.1073/pnas.0607117103. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Manni M., Berkeley M.R., Seppey M., Zdobnov E.M. BUSCO: assessing genomic data qualityand beyond. Curr. Protoc. 2021;1:e323. doi: 10.1002/cpz1001.1323. [DOI] [PubMed] [Google Scholar]
- 12.Panthee S., Paudel A., Blom J., Hamamoto H., Sekimizu K. Complete genome sequence of Weissella hellenica 0916-4-2 and its comparative genomic analysis. Front. Microbiol. 2019;10:1619. doi: 10.3389/fmicb.2019.01619. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–2069. doi: 10.1093/bioinformatics/btu153. [DOI] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
Leuconostoc mesenteroides KNU-2 Genome sequencing and assembly (Reference data) (National Center for Biotechnology Information Search database)
Weissella hellenica strain:MBEL1842 Genome sequencing and assembly (Reference data) (National Center for Biotechnology Information Search database)