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.

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 degrees C (optimum, 25 degrees C and 30 degrees 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 alpha-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 beta-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.

Automated summary

Two novel bacterial strains, CBA3104(T) and CBA3105(T), isolated from kimchi, were identified as a new species of Brachybacterium genus (Brachybacterium kimchii sp. nov.) and a new subspecies of B. halotolerans (B. halotolerans subsp. kimchii subsp. nov.), respectively. These strains showed differences in growth conditions and genetic similarity.