Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov., Isolated from Freshwater and Soil

Two novel bacterial strains CJ74T and CJ75T belonging to the genus Flavobacterium were isolated from freshwater of Han River and ginseng soil, South Korea, respectively. Strain CJ74T was Gram-stain-negative, aerobic, rod-shaped, non-motile, and non-flagellated, and did not produce flexirubin-type pigments. Strain CJ75T was Gram-stain-negative, aerobic, rod-shaped, motile by gliding, and non-flagellated, and produced flexirubin-type pigments. Both strains were shown to grow optimally at 30 °C in the absence of NaCl on R2A medium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ74T and CJ75T belonged to the genus Flavobacterium and were most closely related to Flavobacterium niveum TAPW14T and Flavobacterium foetidum CJ42T with 96.17% and 97.29% 16S rRNA sequence similarities, respectively. Genomic analyses including the reconstruction of phylogenomic tree, average nucleotide identity, and digital DNA-DNA hybridization suggested that they were novel species of the genus Flavobacterium. Both strains contained menaquinone 6 (MK-6) as the primary respiratory quinone and phosphatidylethanolamine as a major polar lipid. The predominant fatty acids of both strains were iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). Based on the polyphasic taxonomic study, strains CJ74T and CJ75T represent novel species of the genus Flavobacterium, for which names Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov. are proposed, respectively. The type strains are CJ74T (=KACC 19819T =JCM 32889T) and CJ75T (=KACC 23149T =JCM 36132T).

The fish pathogen Flavobacterium columnare represents four distinct species: Flavobacterium columnare, Flavobacterium covae sp. nov., Flavobacterium davisii sp. nov. and Flavobacterium oreochromis sp. nov., and emended description of Flavobacterium columnare

Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish and four discrete genetic groups exist within the species, suggesting that the species designation requires revision. The present study determined the taxonomic status of the four genetic groups of F. columnare using polyphasic and phylogenomic approaches and included five representative isolates from each genetic group (including type strain ATCC 23463^T; genetic group 1). 16S rRNA gene sequence analysis revealed genetic group 2 isolate AL-02-36^T, genetic group 3 isolate 90-106^T, and genetic group 4 isolate Costa Rica 04-02-TN^T shared less than <98.8 % sequence identity to F. columnare ATCC 23463^T. Phylogenetic analyses of 16S rRNA and gyrB genes using different methodologies demonstrated the four genetic groups formed well-supported and distinct clades within the genus Flavobacterium. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (GGDC) values between F. columnare ATCC 23463^T, genetic group 2 isolate AL-02-36^T, genetic group 3 isolate 90-106^T, and genetic group 4 isolate Costa Rica 04-02-TN^T were less than 90.84% and 42.7%, respectively. Biochemical and physiological characteristics were similar among the four genetic groups; however, quantitative differences in fatty acid profiles were detected and MALDI-TOF analyses demonstrated numerous distinguishing peaks unique to each genetic group. Chemotaxonomic, MALDI-TOF characterization and ANI/GGDC calculations afforded differentiation between the genetic groups, indicating each group is a discrete species. Herein, the names F. covae sp. nov. (AL-02-36^T), F. davisii sp. nov. (90-106^T), and F. oreochromis sp. nov. (Costa Rica 04-02-TN^T) are proposed to represent genetic groups 2, 3, and 4, respectively.

Flavobacterium hydrophilum sp. nov. and Flavobacterium cheongpyeongense sp. nov., isolated from freshwater

Two Gram-stain-negative, non-motile, yellow-pigmented bacterial strains, designated IMCC34758^T and IMCC34759^T, were isolated from freshwater. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains formed a distinct clade within the genus Flavobacterium and they shared 97.9 % sequence similarity. The average nucleotide identity (ANI) and digital DNA-DNA hybridization values (dDDH) between the two strains were 85.5 and 30.2 %, respectively, indicating that they are separate species. The two strains showed ≤98.5 % 16S rRNA gene sequence similarities, 80.6-81.3 % of ANI and 24.7-25.1 % of dDDH values to closely related species of the genus Flavobacterium, indicating that the two strains each represent novel Flavobacteriumspecies. The respiratory quinone detected in both strains was menaquinone-6 (MK-6). The major polar lipids of the two strains were phosphatidylethanolamine, an unidentified aminolipid, an unidentified aminophospholipid and an unidentified polar lipid. The DNA G+C contents of strains IMCC34758^T and IMCC34759^T were 34.0 and 34.1 mol%, respectively. The major fatty acids of the two strains were very similar to each other, comprising iso-C15 : 0, iso-C15 : 1 G, anteiso-C15 : 0 and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). Phenotypic characteristics including enzyme activities and carbon source utilization differentiated the two strains from other Flavobacteriumspecies. Based on these results, strains IMCC34758^T and IMCC34759^T were considered to represent novel species in the genus Flavobacterium, for which the names Flavobacterium hydrophilum (IMCC34758^T=KACC 19591^T=NBRC 113423^T) and Flavobacterium cheongpyeongense (IMCC34759^T=KACC 19592^T=NBRC 113424^T) are proposed, respectively.

Flavobacterium parvum sp. nov., isolated from soil polluted by sewer water

A novel Gram-stain-negative, motile by means of gliding, and short rod-shaped bacterium, designated HS916T, was isolated from soil polluted by sewer water in Cheonan-si, South Korea. Growth occurred at 10-35°C (optimum 30°C), pH 6.0-8.0 (optimum pH 7.0), and 0-1% sodium chloride (NaCl, w/v). Based on similarities of 16S rRNA gene sequences, strain HS916^T was closely related to members of the genus Flavobacterium, exhibiting the highest sequence similarities with Flavobacterium glycines Gm-149^T (96.4%), followed by F. granuli Kw05^T (96.3%), F. fluminis 3R17^T (96.3%), F. aquicola TMd3a3^T (96.2%), and F. nitratireducens N1^T (96.2%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HS916T was placed in a monophyletic cluster with F. nitratireducens N1^T and F. fluminis 3R17^T. The predominant fatty acids (> 5% of the total) of strain HS916^T were iso-C_15:0, anteiso-C_15:0, iso-C_15:0 3-OH, C_17:1ω6с, C_16:0 3-OH, iso-C_17:0 3-OH, and summed feature 3 (C_16:1ω7с and/or C_16:1ω6с). The major polar lipids of the strain comprised phosphatidylethanolamine, unidentified aminolipids, and five unidentified lipids. The predominant respiratory quinone and the major polyamine were menaquinone-6 (MK-6) and symhomospermidine, respectively. The DNA G + C content of strain HS916^T was 34.9 mol%. Based on polyphasic analyses, strain HS916^T represents a novel species belonging to the genus Flavobacterium, for which the name Flavobacterium parvum sp. nov. is proposed. The type strain is HS916T (= KACC 19448^T = JCM 32368^T).