Six bacterial strains (BT523T, BT559T, 15J16-1T3BT, BT730T, DG25AT, and DG25BT) were isolated from soil samples in Korea and assigned to the family Hymenobacteraceae (order Cytophagales, class Cytophagia). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains formed distinct lineages within the genus Hymenobacter. Strains BT523T, BT559T, and 15J16-1T3BT exhibited highest sequence similarities to Hymenobacter armeniacus BT189T (97.6%), Hymenobacter polaris RP-2-7 T (97.8%), and Hymenobacter paludis KBP-30 T (98.3%), respectively, while strains BT730T, DG25AT, and DG25BT were most closely related to Hymenobacter tibetensis XTM003T, with similarities of 96.3–96.6%. All strains were Gram-negative, aerobic, rod-shaped, and formed red to pink pigmented colonies. Whole-genome analysis revealed genome sizes ranging from 3.78 to 6.33 Mb with G + C contents of 55.5–65.0%. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the strains and their closest relatives were below the accepted thresholds for species delineation, supporting their classification as novel species. Functional annotation indicated the presence of genes associated with core metabolism, stress response, and pigment biosynthesis, reflecting adaptation to soil environments. Secondary metabolite analysis further revealed the presence of biosynthetic gene clusters, including terpene and siderophore pathways. Based on polyphasic taxonomic evidence, the six strains are proposed to represent six novel species of the genus Hymenobacter, for which the names Hymenobacter miniatus sp. nov., Hymenobacter madidus sp. nov., Hymenobacter convexus sp. nov., Hymenobacter rubellus sp. nov., Hymenobacter erythromyxa sp. nov., and Hymenobacter radioresistens sp. nov. are proposed. The type strains are BT523T (= KCTC 72341 T = NBRC 114851 T), BT559T (= KACC 21821 T = NBRC 114852 T), 15J16-1T3BT (= KCTC 42995 T = NBRC 112818 T), BT730T (= KACC 22457 T = NBRC 116482 T), DG25AT (= KCTC 32451 T = TBRC 19856 T), and DG25BT (= KCTC 32452 T = JCM 19444 T).

Genomic and polyphasic characterization of six novel Hymenobacter species isolated from soil in Korea

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发表日期：

2026年8月3日

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Yuna Park,
Seona Park,
Soohyun Maeng,
Myung Kyum Kim

摘要

Six bacterial strains (BT523^T, BT559^T, 15J16-1T3B^T, BT730^T, DG25A^T, and DG25B^T) were isolated from soil samples in Korea and assigned to the family Hymenobacteraceae (order Cytophagales, class Cytophagia). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains formed distinct lineages within the genus Hymenobacter. Strains BT523^T, BT559^T, and 15J16-1T3B^T exhibited highest sequence similarities to Hymenobacter armeniacus BT189^T (97.6%), Hymenobacter polaris RP-2-7^T (97.8%), and Hymenobacter paludis KBP-30^T (98.3%), respectively, while strains BT730^T, DG25A^T, and DG25B^T were most closely related to Hymenobacter tibetensis XTM003^T, with similarities of 96.3–96.6%. All strains were Gram-negative, aerobic, rod-shaped, and formed red to pink pigmented colonies. Whole-genome analysis revealed genome sizes ranging from 3.78 to 6.33 Mb with G + C contents of 55.5–65.0%. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the strains and their closest relatives were below the accepted thresholds for species delineation, supporting their classification as novel species. Functional annotation indicated the presence of genes associated with core metabolism, stress response, and pigment biosynthesis, reflecting adaptation to soil environments. Secondary metabolite analysis further revealed the presence of biosynthetic gene clusters, including terpene and siderophore pathways. Based on polyphasic taxonomic evidence, the six strains are proposed to represent six novel species of the genus Hymenobacter, for which the names Hymenobacter miniatus sp. nov., Hymenobacter madidus sp. nov., Hymenobacter convexus sp. nov., Hymenobacter rubellus sp. nov., Hymenobacter erythromyxa sp. nov., and Hymenobacter radioresistens sp. nov. are proposed. The type strains are BT523^T (= KCTC 72341^T = NBRC 114851^T), BT559^T (= KACC 21821^T = NBRC 114852^T), 15J16-1T3B^T (= KCTC 42995^T = NBRC 112818^T), BT730^T (= KACC 22457^T = NBRC 116482^T), DG25A^T (= KCTC 32451^T = TBRC 19856^T), and DG25B^T (= KCTC 32452^T = JCM 19444^T).