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

• Published in: The journal of microbiology Vol. 60; no. 7; pp. 678 - 688
• Main Authors: Kim, Yujin, Kim, Yeon Bee, Kim, Juseok, Kim, Joon Yong, Whon, Tae Woong, Chung, Won-Hyong, Song, Eun-Ji, Nam, Young-Do, Lee, Se Hee, Roh, Seong Woon
• Format: Journal Article
• Language: English
• Published: Seoul The Microbiological Society of Korea 01.07.2022; Springer Nature B.V; 한국미생물학회
• Subjects: Acid production; Alkaline phosphatase; Arabinose; Biochemical analysis; Biomedical and Life Sciences; Cardiolipin; Catalase; DNA sequencing; Enzymatic activity; Enzyme activity; Fatty acids; Fermentation; Fermented food; Gene sequencing; Genomic analysis; Hydrolase; Kimchi; Life Sciences; Lipids; Menaquinones; Microbial Systematics and Evolutionary Microbiology; Microbiological strains; Microbiology; New species; Oxidoreductase; Oxidoreductases; Peptidoglycans; pH effects; Phosphatase; Phosphatidylglycerol; Phylogenetics; Phylogeny; Potassium; Quinones; rRNA 16S; Sodium chloride; Strains (organisms); Succinic acid; Transfer RNA; tRNA; 생물학; CBA3105; CBA3104; kimchi; subsp; polyphasic taxonomy
• ISSN: 1976-3794; 1225-8873; 1976-3794
• DOI: 10.1007/s12275-022-1581-6

Two Gram-stain-positive, oxidase-negative, catalase-positive, and coccus-shaped bacterial strains, designated CBA3104 T and CBA3105 T , were isolated from kimchi. Strain CBA3104 T and CBA3105 T 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 CBA3104 T formed a distinct phylogenetic lineage within the genus Brachybacterium whereas strain CBA3105 T was closely positioned with Brachybacterium halotolerans MASK1Z-5 T . The 16S rRNA gene sequence similarity between strains CBA3104 T and CBA3105 T was 99.9%, but ANI and dDDH values between strains CBA3104 T and CBA3105 T were 93.61% and 51.5%, respectively. Strain CBA3104 T showed lower ANI and dDDH values than species delineation against three closely related strains and type species of the genus Brachybacterium , however, strain CBA3105 T showed 96.63% ANI value and 69.6% dDDH value with Brachybacterium halotolerans MASK1Z-5 T . Among biochemical analysis results, strain CBA3104 T could uniquely utilize bromo-succinic acid whereas only strain CBA3105 T 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 CBA3105 T and Brachybacterium halotolerans JCM 34339 T , strain CBA3105 T 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 CBA3104 T and CBA3105 T were anteiso-C 15:0 , anteiso-C 17:0 , and iso-C 16:0 . The major polar lipids of both strains were phosphatidylglycerol and diphosphatidylglycerol. Strain CBA3104 T possessed a uniquely higher abundance of tRNA (97 tRNAs) than four Brachybacterium strains used for comparative taxonomic analysis (54–62 tRNAs). Both the CBA3104 T and CBA3105 T 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 CBA3104 T and CBA3105 T 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 CBA3104 T (= KCCM 43417 T = JCM 34759 T ) and CBA3105 T (= KCCM 43418 T =JCM 34760 T ), respectively.