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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 6

sp. nov., a novel lactic acid bacterium isolated from kimchi Open Access

Abstract

A short, rod-shaped, Gram-positive, catalase-negative and facultative anaerobic bacterium, designated strain P0083, was isolated from kimchi, a traditional Korean fermented vegetable. Phylogenetic analysis based on the nearly complete 16S rRNA and gene sequences placed the isolate within a distinct group from other closely related species within the genus. Under anaerobic conditions on de Man, Rogosa and Sharpe agar, the bacterium formed beige, circular colonies of moderate size. Growth occurred between 4 and 25 °C, with optimal growth at 20 °C and limited growth at 30 °C. The bacterium grew at pH 5–8 and tolerated 3% NaCl. The main cellular fatty acids included C16 : 0 fatty acid methyl esters (FAME) and C18 : 1 CIS 9 FAME. Digital DNA–DNA hybridization confirmed that strain P0083 represents a novel genomic species, with species sharing less than 84.22% DNA homology with strain P0083. The genomic, phenotypic and biochemical characteristics of support the hypothesis that strain P0083 (=JCM 37383=KCTC 25916) represents a novel species, sp. nov., with P0083 as the type strain.

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  • Accepted:
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Keyword(s): Dellaglioa kimchii , kimchi , lactic acid bacteria , new taxon , P0083 and taxonomy
Funding
This study was supported by the:
  • Ministry of Science and ICT, South Korea (Award KE2403-1)
    • Principal Award Recipient: Tae-WoonKim
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2025-06-30
2026-02-12

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References

  1. Ko HI, Jeong CH, Park SJ, Kim SR, Eun JB et al. Influence of isolation temperature on isolating diverse lactic acid bacteria from kimchi and cultural characteristics of psychrotrophs. J Microbiol Biotechnol 2023; 33:1066–1075 [View Article] [PubMed]
     [Google Scholar]
  2. Yang H-I, Min S-G, Seo H-Y, Lee SY, Yang J-H et al. Nondestructive prediction of physicochemical properties of kimchi sauce with artificial and convolutional neural networks. Int J Food Prop 2023; 26:2924–2938 [View Article]
     [Google Scholar]
  3. Lee H-G, Jeong S, Yoo S. Development of a calcium hydroxide–dye kimchi ripening indicator and its application in kimchi packaging. Food Chemistry 2023; 400:134039 [View Article]
     [Google Scholar]
  4. Jung M-J, Kim J, Lee SH, Whon TW, Sung H et al. Role of combinated lactic acid bacteria in bacterial, viral, and metabolite dynamics during fermentation of vegetable food, kimchi. Food Res Int 2022; 157:111261 [View Article] [PubMed]
     [Google Scholar]
  5. Yun Y-R, Kwon M-S, Lee H-J, Lee W, Lee J-E et al. Anti-obesity activity of lactic acid bacteria-starter-based kimchi in high-fat diet-induced obese mice. J Funct Foods 2024; 112:105966 [View Article]
     [Google Scholar]
  6. Mun SY, Seo YJ, Chang HC. Characterization of the psychrotrophic lactic acid bacterium Leuconostoc gelidum subsp. aenigmaticum LS4 isolated from kimchi based on comparative analyses of its genomic and phenotypic properties. Foods 2021; 10:1899 [View Article] [PubMed]
     [Google Scholar]
  7. Rahkila R, De Bruyne K, Johansson P, Vandamme P, Björkroth J. Reclassification of Leuconostoc gasicomitatum as Leuconostoc gelidum subsp. gasicomitatum comb. nov., description of Leuconostoc gelidum subsp. aenigmaticum subsp. nov., designation of Leuconostoc gelidum subsp. gelidum subsp. nov. and emended description of Leuconostoc gelidum.. Int J Syst Evol Microbiol 2014; 64:1290–1295 [View Article] [PubMed]
     [Google Scholar]
  8. 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]
  9. Zheng J, Wittouck S, Salvetti E, Franz CMAP, Harris HMB et al. A taxonomic note on the genus Lactobacillus: description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol 2020; 70:2782–2858 [View Article]
     [Google Scholar]
  10. Werum V, Ehrmann M. Dellaglioa spp. an underestimated genus isolated from high-oxygen modified-atmosphere packaged meat. Food Microbiol 2024; 117:104398 [View Article] [PubMed]
     [Google Scholar]
  11. Werum V, Ehrmann M. Description of Dellaglioa carnosa sp. nov., a novel species isolated from high-oxygen modified-atmosphere packaged meat. Syst Appl Microbiol 2023; 46:126423 [View Article] [PubMed]
     [Google Scholar]
  12. 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]
  13. Thompson JD, Gibson TJ, Higgins DG. Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinform 2003; 00:2 [View Article]
     [Google Scholar]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  15. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  16. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  17. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  18. Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 2005; 33:W686–9 [View Article] [PubMed]
     [Google Scholar]
  19. Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 2013; 29:2933–2935 [View Article] [PubMed]
     [Google Scholar]
  20. Edgar RC. PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics 2007; 8:18 [View Article] [PubMed]
     [Google Scholar]
  21. Bland C, Ramsey TL, Sabree F, Lowe M, Brown K et al. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 2007; 8:209 [View Article] [PubMed]
     [Google Scholar]
  22. UniProt Consortium UniProt: a hub for protein information. Nucleic Acids Res 2015; 43:D204–12 [View Article] [PubMed]
     [Google Scholar]
  23. Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 2014; 42:D199–205 [View Article] [PubMed]
     [Google Scholar]
  24. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H-Y et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 2005; 33:5691–5702 [View Article] [PubMed]
     [Google Scholar]
  25. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010; 26:2460–2461 [View Article] [PubMed]
     [Google Scholar]
  26. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  27. Yoon S-H, Ha S, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article]
     [Google Scholar]
  28. Chung J, Otoguro M, Yanagida F, Wu H, Chang Y et al. Enterococcus alishanensis sp. nov., a novel lactic acid bacterium isolated from fresh coffee beans. Int J Syst Evol Microbiol 2022; 72:005255 [View Article]
     [Google Scholar]
  29. Li Y, Li W, Luo R, Sakandar HA, Zhang H et al. Lentilactobacillus rapi subsp. dabitei subsp. nov., a lactic acid bacterium isolated from naturally fermented dairy product. Int J Syst Evol Microbiol 2022; 72:005359 [View Article]
     [Google Scholar]
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Dellaglioa kimchii sp. nov., a novel lactic acid bacterium isolated from kimchi
Int J Syst Evol Microbiol 75, 006829 (2025); https://doi.org/10.1099/ijsem.0.006829
/content/journal/ijsem/10.1099/ijsem.0.006829
/content/journal/ijsem/10.1099/ijsem.0.006829
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