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Lactiplantibacillus koreensis sp. nov. and Lactiplantibacillus kimchii sp. nov., isolated from kimchi, a traditional Korean fermented food
Min Ji Lee, Jisu Lee, Sohee Nam, Mi-Ja Jung, Yeon Bee Kim, Yujin Kim, Jeong Ui Yun, Seong Woon Roh, Tae Woong Whon, Che Ok Jeon, Se Hee Lee
J. Microbiol. 2025;63(11):e2507007.   Published online November 30, 2025
DOI: https://doi.org/10.71150/jm.2507007
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AbstractAbstract PDFSupplementary Material

Two Gram-stain-positive, facultatively anaerobic, rod-shaped, and non-motile lactic acid bacterial strains, designated as strains CBA3605T and CBA3606T, were isolated from kimchi, a traditional Korean fermented food. Both strains were oxidase- and catalase-negative, non-spore-forming, non-hemolytic, and non-gas-producing. Optimal growth conditions for the two strains were observed at 30°C, pH 5.0, and 0% NaCl. The two genomes were composed of a circular chromosome and three plasmids and the DNA G + C content of 43.0%, respectively. Strains CBA3605T and CBA3606T were most closely related to Lactiplantibacillus (Lp.) pingfangensis 382-1T with 16S rRNA sequence similarity of 99.4% and 99.1%, respectively. However, the orthologous average nucleotide identities between CBA3605T and CBA3606T were 91.7%, and those with strain 382-1T were 76.9% and 76.5%, respectively. Digital DNA–DNA hybridization values between CBA3605T and CBA3606T were 45.0%, and those with strain 382-1T were 21.4% and 21.0%, respectively. The major fatty acids detected in both strains included C16:0, C18:1 ω9c, and summed features 7 (C19:1 ω7c, C19:1 ω6c, C19:0 cyclo ω10c, and/or C19:0 ω6c). The peptidoglycan of both strains CBA3605T and CBA3606T contained meso-diaminopimelic acid and was classified as A4α type (L-Lys–D-Asp). In polar lipid analyses, only strain CBA3605T contained aminophosphoglycolipid, which was absent in CBA3606T, although both strains harbored same major polar lipids (diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine). Based on phenotypic, phylogenetic, genomic, biochemical, and chemotaxonomic analyses, strains CBA3605T and CBA3606T represent two novel species of the genus Lactiplantibacillus, for which the names Lactiplantibacillus koreensis sp. nov. and Lactiplantibacillus kimchii sp. nov. are proposed, with CBA3605T (= KACC 81073BPT = JCM 37965T), and CBA3606T (= KACC 81074BPT = JCM 37966T) as the type strains.

Journal Article
Brachybacterium kimchii sp. nov. and Brachybacterium halotolerans subsp. kimchii subsp. nov., isolated from the Korean fermented vegetables, kimchi, and description of Brachybacterium halotolerans subsp. halotolerans subsp. nov.
Yujin Kim , Yeon Bee Kim , Juseok Kim , Joon Yong Kim , Tae Woong Whon , Won-Hyong Chung , Eun-Ji Song , Young-Do Nam , Se Hee Lee , Seong Woon Roh
J. Microbiol. 2022;60(7):678-688.   Published online July 4, 2022
DOI: https://doi.org/10.1007/s12275-022-1581-6
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AbstractAbstract PDF
Two Gram-stain-positive, oxidase-negative, catalase-positive, and coccus-shaped bacterial strains, designated CBA3104T and CBA3105T, were isolated from kimchi. Strain CBA3104T and CBA3105T grew at 10–35°C (optimum, 25°C and 30°C, respectively), at pH 6.0–8.5 (optimum, pH 6.5), and in the presence of 0–15% (w/v) NaCl (optimum, 5%). A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CBA3104T formed a distinct phylogenetic lineage within the genus Brachybacterium whereas strain CBA3105T was closely positioned with Brachybacterium halotolerans MASK1Z-5T. The 16S rRNA gene sequence similarity between strains CBA3104T and CBA3105T was 99.9%, but ANI and dDDH values between strains CBA3104T and CBA3105T were 93.61% and 51.5%, respectively. Strain CBA3104T showed lower ANI and dDDH values than species delineation against three closely related strains and type species of the genus Brachybacterium, however, strain CBA3105T showed 96.63% ANI value and 69.6% dDDH value with Brachybacterium halotolerans MASK1Z-5T. Among biochemical analysis results, strain CBA3104T could uniquely utilize bromo-succinic acid whereas only strain CBA3105T was positive for alkaline phosphatase and α-fucosidase among two novel strains, closely related strains, and type species of the genus Brachybacterium. Compared with strain CBA3105T and Brachybacterium halotolerans JCM 34339T, strain CBA3105T was differentially positive for acid production of D-arabinose, D-adonitol, and potassium 5-ketogluconate and enzyme activity of β-glucuronidase. Both strains contained menaquinone-7 as the dominant quinone. The cell-wall peptidoglycan of two novel strains contained meso-diaminopimelic acid. The major fatty acids of strains CBA3104T and CBA3105T were anteiso-C15:0, anteiso-C17:0, and iso-C16:0. The major polar lipids of both strains were phosphatidylglycerol and diphosphatidylglycerol. Strain CBA3104T possessed a uniquely higher abundance of tRNA (97 tRNAs) than four Brachybacterium strains used for comparative taxonomic analysis (54–62 tRNAs). Both the CBA3104T and CBA3105T strain harbored various oxidoreductase, transferase, hydrolase, and lyase as strain-specific functional genes compared to closely related strains and Brachybacterium type species. The results of biochemical/physiological, chemotaxonomic, and genomic analyses demonstrated that strains CBA3104T and CBA3105T represent a novel species of the genus Brachybacterium and a novel subspecies of B. halotolerans, respectively, for which the names Brachybacterium kimchii sp. nov. and B. halotolerans subsp. kimchii subsp. nov. are proposed. The type strains of the novel species and the novel subspecies are CBA3104T (= KCCM 43417T = JCM 34759T) and CBA3105T (= KCCM 43418T = JCM 34760T), respectively.

Citations

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  • Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia
    Alexander G. Elcheninov, Kseniya S. Zayulina, Alexandra A. Klyukina, Mariia K. Kremneva, Ilya V. Kublanov, Tatiana V. Kochetkova
    Microorganisms.2023; 12(1): 16.     CrossRef
  • Validation List no. 208. Valid publication of new names and new combinations effectively published outside the IJSEM
    Aharon Oren, George M. Garrity
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Complete Genome Sequence of Brachybacterium sp. Strain NBEC-018, Isolated from Nematode-Infected Potatoes
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    Microbiology Resource Announcements.2022;[Epub]     CrossRef

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