1887

Abstract

The novel strain CBA3628 was isolated from kimchi, a Korean fermented vegetable. CBA3628 is a cocci-shaped, Gram-stain-positive, catalase- and oxidase-negative and facultatively anaerobic bacterium. The results of phylogenetic analysis based on 16S rRNA gene sequencing indicated that CBA3628 represented a member of the genus of the family . CBA3628 has a circular chromosomal genome and three plasmids of 1 864 558 bp (37% DNA G+C content), containing 1,887 genes, 1,762 predicted protein-coding genes, 4 complete rRNA loci and 70 tRNA genes. The cells were non-haemolytic, non-motile and non-spore forming. The optimal growth of CBA3628 occurred at 30 °C, pH 6.0 and with 0–2% (w/v) NaCl. The major polar lipids of CBA3628 were diphosphatidylglycerol and phosphatidylglycerol. The major fatty acids (>10%) of CBA3628 were C, C and C cyclo ω8. CBA3628 contained A3α-type peptidoglycans. CBA3628 was most closely related to subsp. ATCC 8293, subsp. DSM 20484 and DSM 20241 with 99.52% 16S rRNA gene sequence similarity. However, the average nucleotide identities of 91.9%, 91.7% and 91.1% and the digital DNA–DNA hybridisation values of 45.6%, 45.4% and 45.4% indicated that the novel isolate represented a distinct species. Phylogenetic analyses of both the 16S rRNA gene and genome sequences revealed that CBA3628 formed a distinct phylogenetic lineage within the genus and was most closely related to MB7. The ANI and dDDH values between CBA3628 and MB7 were 84.9 and 22.8%, respectively. Functional genes belonging to COG categories E, J and K were enriched in the genome of CBA3628 (>7.9%). On the basis of its physiological, chemotaxonomic, phylogenetic and genomic properties, strain CBA3628 represents a novel species from the genus , for which we propose the name sp. nov., with the type strain CBA3628 (= KACC 23049 = DSM 116836).

Funding
This study was supported by the:
  • Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (Award RS-2024-00397218)
    • Principle Award Recipient: SeHee Lee
  • National Research Foundation of Korea (Award 2021R1C1C1013859)
    • Principle Award Recipient: SeHee Lee
  • World Institute of Kimchi (Award KE2401-1-1)
    • Principle Award Recipient: TaeWoong Whon
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006533
2024-10-18
2024-11-10
Loading full text...

Full text loading...

References

  1. Lee SH, Whon TW, Roh SW, Jeon CO. Unraveling microbial fermentation features in kimchi: from classical to meta-omics approaches. Appl Microbiol Biotechnol 2020; 104:7731–7744 [View Article] [PubMed]
    [Google Scholar]
  2. Chun BH, Kim KH, Jeon HH, Lee SH, Jeon CO. Pan-genomic and transcriptomic analyses of Leuconostoc mesenteroides provide insights into its genomic and metabolic features and roles in kimchi fermentation. Sci Rep 2017; 7:11504 [View Article] [PubMed]
    [Google Scholar]
  3. Jung JY, Lee SH, Jeon CO. Kimchi microflora: history, current status, and perspectives for industrial kimchi production. Appl Microbiol Biotechnol 2014; 98:2385–2393 [View Article] [PubMed]
    [Google Scholar]
  4. Kim J, Chun J, Han H-U. Leuconostoc kimchii sp. nov., a new species from kimchi. Int J Syst Evol Microbiol 2000; 50 Pt 5:1915–1919 [View Article] [PubMed]
    [Google Scholar]
  5. Kim B, Lee J, Jang J, Kim J, Han H. Leuconostoc inhae sp. nov., a lactic acid bacterium isolated from kimchi. Int J Syst Evol Microbiol 2003; 53:1123–1126 [View Article] [PubMed]
    [Google Scholar]
  6. Lee SH, Park MS, Jung JY, Jeon CO. Leuconostoc miyukkimchii sp. nov., isolated from brown algae (Undaria pinnatifida) kimchi. Int J Syst Evol Microbiol 2012; 62:1098–1103 [View Article] [PubMed]
    [Google Scholar]
  7. Chambel L, Chelo IM, Zé-Zé L, Pedro LG, Santos MA et al. Leuconostoc pseudoficulneum sp. nov., isolated from a ripe fig. Int J Syst Evol Microbiol 2006; 56:1375–1381 [View Article] [PubMed]
    [Google Scholar]
  8. Chen Y-S, Wang L-T, Wu Y-C, Mori K, Tamura T et al. Leuconostoc litchii sp. nov., a novel lactic acid bacterium isolated from lychee. Int J Syst Evol Microbiol 2020; 70:1585–1590 [View Article] [PubMed]
    [Google Scholar]
  9. Dicks LMT, Fantuzzi L, Gonzalez FC, Du Toit M, Dellaglio F. Leuconostoc argentinum sp. nov., isolated from argentine raw milk. Int J Syst Bacteriol 1993; 43:347–351 [View Article]
    [Google Scholar]
  10. Ehrmann MA, Freiding S, Vogel RF. Leuconostoc palmae sp. nov., a novel lactic acid bacterium isolated from palm wine. Int J Syst Evol Microbiol 2009; 59:943–947 [View Article] [PubMed]
    [Google Scholar]
  11. Wu Y, Gu CT. Leuconostoc falkenbergense sp. nov., isolated from a lactic culture, fermentating string beans and traditional yogurt. Int J Syst Evol Microbiol 2021; 71:004602 [View Article] [PubMed]
    [Google Scholar]
  12. Shaw BG, Harding CD. Leuconostoc gelidum sp. nov. and Leuconostoc carnosum sp. nov. from chill-stored meats. Int J Syst Bacteriol 1989; 39:217–223 [View Article]
    [Google Scholar]
  13. Lee KW, Kim GS, Baek AH, Hwang HS, Kwon DY et al. 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 [View Article] [PubMed]
    [Google Scholar]
  14. Lane DJ. 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics 1991 pp 125–175
    [Google Scholar]
  15. Burland TG. DNASTAR’s Lasergene sequence analysis software. Methods Mol Biol 2000; 132:71–91 [View Article] [PubMed]
    [Google Scholar]
  16. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
    [Google Scholar]
  17. Thompson JD, Gibson TJ, Higgins DG. Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics 2002; Chapter 2:Unit [View Article] [PubMed]
    [Google Scholar]
  18. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
    [Google Scholar]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  20. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
    [Google Scholar]
  21. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [View Article] [PubMed]
    [Google Scholar]
  22. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article] [PubMed]
    [Google Scholar]
  23. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  24. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  25. Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2019; 47:D309–D314 [View Article] [PubMed]
    [Google Scholar]
  26. Na S-I, Kim YO, Yoon S-H, Ha S, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article]
    [Google Scholar]
  27. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009; 26:1641–1650 [View Article] [PubMed]
    [Google Scholar]
  28. Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol 2021; 38:5825–5829 [View Article] [PubMed]
    [Google Scholar]
  29. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  30. Pritchard L, Harrington B, Cock P, Davey R, Waters N et al. Pyani: whole-genome classification using average nucleotide identity; 2015
  31. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
  32. Gomori G. Preparation of buffers for use in enzyme studies. In Handbook of Biochemistry and Molecular Biology 2010 p 721
    [Google Scholar]
  33. Agarwal S, Sharma K, Swanson BG, Yüksel GU, Clark S. Nonstarter lactic acid bacteria biofilms and calcium lactate crystals in Cheddar cheese. J Dairy Sci 2006; 89:1452–1466 [View Article] [PubMed]
    [Google Scholar]
  34. Whittenbury R. Hydrogen peroxide formation and catalase activity in the lactic acid bacteria. J Gen Microbiol 1964; 35:13–26 [View Article] [PubMed]
    [Google Scholar]
  35. Shields P, Cathcart L. Oxidase test protocol. In American Society for Microbiology 2010 pp 1–9
    [Google Scholar]
  36. Cappuccino JG, Sherman N. Microbiology: A laboratory manual, 8th. edn San Francisco: Benjamin Cummings Pearson Education; 2008
    [Google Scholar]
  37. Kent DJ, Chauhan K, Boor KJ, Wiedmann M, Martin NH. Spore test parameters matter: mesophilic and thermophilic spore counts detected in raw milk and dairy powders differ significantly by test method. J Dairy Sci 2016; 99:5180–5191 [View Article] [PubMed]
    [Google Scholar]
  38. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
    [Google Scholar]
  39. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  40. Miller L, Berger T. Bacteria identification by gas chromatography of whole cell fatty acids. Hewlett-Packard Application Note 1985; 2281–8
    [Google Scholar]
  41. Binda E, Carrano L, Marcone GL, Marinelli F. Extraction and analysis of peptidoglycan cell wall precursors. Methods Mol Biol 2016; 1440:153–170 [View Article] [PubMed]
    [Google Scholar]
  42. Jeon HH, Kim KH, Chun BH, Ryu BH, Han NS et al. 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. Int J Syst Evol Microbiol 2017; 67:2225–2230 [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006533
Loading
/content/journal/ijsem/10.1099/ijsem.0.006533
Loading

Data & Media loading...

Supplements

 Supplementary material 1 

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error