Journal of Microbiology

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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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Abstract PDF Supplementary Material: Two Gram-stain-positive, facultatively anaerobic, rod-shaped, and non-motile lactic acid bacterial strains, designated as strains CBA3605^T and CBA3606^T, 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 CBA3605^T and CBA3606^T were most closely related to Lactiplantibacillus (Lp.) pingfangensis 382-1^T with 16S rRNA sequence similarity of 99.4% and 99.1%, respectively. However, the orthologous average nucleotide identities between CBA3605^T and CBA3606^T were 91.7%, and those with strain 382-1^T were 76.9% and 76.5%, respectively. Digital DNA–DNA hybridization values between CBA3605^T and CBA3606^T were 45.0%, and those with strain 382-1^T were 21.4% and 21.0%, respectively. The major fatty acids detected in both strains included C_16:0, C_18:1 ω9c, and summed features 7 (C_19:1 ω7c, C_19:1 ω6c, C_19:0 cyclo ω10c, and/or C_19:0 ω6c). The peptidoglycan of both strains CBA3605^T and CBA3606^T contained meso-diaminopimelic acid and was classified as A4α type (L-Lys–D-Asp). In polar lipid analyses, only strain CBA3605^T contained aminophosphoglycolipid, which was absent in CBA3606^T, although both strains harbored same major polar lipids (diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine). Based on phenotypic, phylogenetic, genomic, biochemical, and chemotaxonomic analyses, strains CBA3605^T and CBA3606^T represent two novel species of the genus Lactiplantibacillus, for which the names Lactiplantibacillus koreensis sp. nov. and Lactiplantibacillus kimchii sp. nov. are proposed, with CBA3605^T (= KACC 81073BP^T = JCM 37965^T), and CBA3606^T (= KACC 81074BP^T = JCM 37966^T) as the type strains.

Journal Article

Leuconostoc aquikimchii sp. nov., a Lactic Acid Bacterium Isolated from Cabbage Watery Kimchi: Subin Kim, Se Hee Lee, Ki Hyun Kim, Misun Yun; J. Microbiol. 2024;62(12):1089-1097. Published online December 2, 2024; DOI: https://doi.org/10.1007/s12275-024-00188-z

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Two Gram-stain-positive, facultatively anaerobic, non-hemolytic, coccoid-shaped bacterial strains, designated MS01(T) and MS02, were isolated from cabbage watery kimchi in the Republic of Korea. Cellular growth occurred at 5-25 ℃ (optimum, 20 ℃), pH 5-8 (optimum, pH 7) and in the presence of 0-5% (w/v) NaCl (optimum, 1%). Results of 16S rRNA gene-based phylogenetic analyses showed that strains MS01(T) and MS02 shared identical sequences, clustered within the Leuconostoc clade in phylogenetic trees, and were most closely related to Leuconostoc inhae IH003(T) and Leuconostoc gasicomitatum LMG 18811(T) with sequence similarities of 98.74%. The complete whole-genome sequences of strains MS01(T) and MS02 measured 2.04-2.06 Mbp and harbored a 50.6 kb plasmid, with DNA G + C contents of 37.7% for both. Based on average nucleotide identities (ANI) and digital DNA-DNA hybridization (dDDH) values, both strains were confirmed to belong to the same species but showed ≤ 85.9% ANI and ≤ 29.9% dDDH values to other Leuconostoc species, indicating that they represent a novel species. Metabolic pathway reconstruction revealed that both strains perform heterolactic acid fermentation, producing lactate, acetate, and ethanol. Chemotaxonomic analyses, including cellular fatty acids, polar lipids, and peptidoglycan amino acid, confirmed the inclusion of both strains within the genus Leuconostoc. Based on the phylogenetic, genomic, and phenotypic characterization, strains MS01(T) and MS02 were considered to represent a novel species within the genus Leuconostoc, for which the name Leuconostoc aquikimchii sp. nov. is proposed with MS01(T) (= KACC 23748(T) = JCM 37028(T)) as the type strain.

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Validation List no. 224. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef

Review

Application of Microbiome‑Based Therapies in Chronic Respiratory Diseases: Se Hee Lee, Jang Ho Lee, Sei Won Lee; J. Microbiol. 2024;62(3):201-216. Published online April 18, 2024; DOI: https://doi.org/10.1007/s12275-024-00124-1

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Abstract PDF

The application of microbiome-based therapies in various areas of human disease has recently increased. In chronic respiratory disease, microbiome-based clinical applications are considered compelling options due to the limitations of current treatments. The lung microbiome is ecologically dynamic and afected by various conditions, and dysbiosis is associated with disease severity, exacerbation, and phenotype as well as with chronic respiratory disease endotype. However, it is not easy to directly modulate the lung microbiome. Additionally, studies have shown that chronic respiratory diseases can be improved by modulating gut microbiome and administrating metabolites. Although the composition, diversity, and abundance of the microbiome between the gut and lung are considerably diferent, modulation of the gut microbiome could improve lung dysbiosis. The gut microbiome infuences that of the lung via bacterial-derived components and metabolic degradation products, including short-chain fatty acids. This phenomenon might be associated with the cross-talk between the gut microbiome and lung, called gut-lung axis. There are multiple alternatives to modulate the gut microbiome, such as prebiotics, probiotics, and postbiotics ingestion and fecal material transplantation. Several studies have shown that high-fber diets, for example, present benefcial efects through the production of short-chain fatty acids. Additionally, genetically modifed probiotics to secrete some benefcial molecules might also be utilized to treat chronic respiratory diseases. Further studies on microbial modulation to regulate immunity and potentiate conventional pharmacotherapy will improve microbiome modulation techniques, which will develop as a new therapeutic area in chronic respiratory diseases.

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Journal Articles

Sala cibi gen. nov., sp. nov., an extremely halophilic archaeon isolated from solar salt: Hye Seon Song , Juseok Kim , Yeon Bee Kim , Se Hee Lee , Tae Woong Whon , Seong Woon Roh; J. Microbiol. 2022;60(9):899-904. Published online July 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2137-5

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Two novel halophilic archaeal strains, CBA1133T and CBA- 1134, were isolated from solar salt in South Korea. The 16S rRNA gene sequences of the isolates were identical to each other and were closely related to the genera Natronomonas (92.3–93.5%), Salinirubellus (92.2%), Halomarina (91.3– 92.0%), and Haloglomus (91.4%). The isolated strains were coccoid, Gram-stain-negative, aerobic, oxidase-positive, and catalase-negative. Growth occurred under temperatures of 25–50°C (optimum, 45°C), NaCl levels of 10–30% (optimum, 15%), pH levels of 6.0–8.5 (optimum, 7.0), and MgCl2 concentrations of 0–500 mM (optimum, 100 mM). Digital DNADNA hybridization values between the strains and related genera ranged from 18.3% to 22.7%. The major polar lipids of the strains were phosphatidyl glycerol, phosphatidyl glycerol phosphate methyl ester, and phosphatidyl glycerol sulfate. Genomic, phenotypic, physiological, and biochemical analyses of the isolates revealed that they represent a novel genus and species in the family Halobacteriaceae. The type strain is CBA1133T (= KACC 22148T = JCM 34265T), for which the name Sala cibi gen. nov., sp. nov. is proposed.

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Dominance and diversity of archaea in food-grade salts: insights for histamine degradation in salt-fermented foods
Jing Hou, Ya-Ling Mao, Na Li, Xiao-Yan Yang, Chidiebele Nwankwo, Heng-Lin Cui
International Journal of Food Science and Technology.2024; 59(12): 9490. CrossRef
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Halorarius litoreus gen. nov., sp. nov., Halorarius halobius sp. nov., Haloglomus halophilum sp. nov., Haloglomus salinum sp. nov., and Natronomonas marina sp. nov., extremely halophilic archaea isolated from tidal flat and marine solar salt
Ya-Ping Sun, Bei-Bei Wang, Zhang-Ping Wu, Xi-Wen Zheng, Jing Hou, Heng-Lin Cui
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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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Abstract 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.

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Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia
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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
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Paracoccus jeotgali sp. nov., isolated from Korean salted and fermented shrimp: Juseok Kim , Joon Yong Kim , Hye Seon Song , In-Tae Cha , Seong Woon Roh , Se Hee Lee; J. Microbiol. 2019;57(6):444-449. Published online May 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8704-8

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A Gram-stain-negative and facultatively aerobic bacterium, designated as strain CBA4604T, was isolated from a traditional Korean salted and fermented shrimp food (saeu-jeot). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBA4604T formed a clearly distinct phyletic lineage from closely related species within the genus Paracoccus. Strain CBA4604T was the most closely related to P. koreensis Ch05T (97.5% 16S rRNA gene sequence similarity) and other type strains (≤ 97.0%). The genome comprised a chromosome and two plasmids of 3,299,166 bp with 66.5% G+C content. The DNA-DNA relatedness values between strain CBA4604T and P. koreensis Ch05T, P. alcaliphilus DSM 8512T, and P. stylophorae KTW-16T were 30.5%, 22.9%, and 16.7%, respectively. Cells of the strain were short rod-shaped and oxidase- and catalase-positive. The growth of strain CBA- 4604T was observed at 10–40°C (optimum, 37°C), pH 6.0–10.0 (optimum, pH 7.0), and in the presence of 0–8.0% (w/v) NaCl (optimum, 0–2.0%). Strain CBA4604T contained ubiquinone 10 as the sole isoprenoid quinone and summed feature 8 (C18:1 ω7c/C18:1 ω6c) and C18:0 as the major cellular fatty acids. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phospholipid, an unidentified aminolipid, an unidentified glycolipid, and three unidentified lipids. Based on its phylogenetic, genomic, phenotypic, and chemotaxonomic features, we concluded that strain CBA- 4604T represents a novel species in the genus Paracoccus and we propose the name Paracoccus jeotgali sp. nov. The type strain is CBA4604T (= KACC 19579T = JCM 32510T).

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