Takuji Kudo

Surugapyrone A from Streptomyces coelicoflavus strain USF-6280 as a new DPPH radical-scavenger

Surugapyrone A, a novel 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical-scavenging 2-pyrone, was isolated from the culture filtrate of an actinomycete strain USF-6280. This strain was assigned to the genus Streptomyces owing to its morphological and chemotaxonomic characteristics. Phylogenetic analysis based on 16S ribosomal RNA gene sequences supported the classification of the producing strain as a member of the genus Streptomyces and indicated that it was closely related to Streptomyces coelicoflavus. As the morphological, physiological and biochemical characteristics of the producing strain were in agreement with those of the type strain of S. coelicoflavus, we concluded that strain USF-6280 should be identified as a member of S. coelicoflavus. The structure of surugapyrone A was determined to be 4-hydroxy-6-isopropyl-3-methyl-2-pyrone on the basis of the spectroscopic data. The results of feeding experiments with 13C-labeled compounds indicated that surugapyrone A was biosynthesized through a polyketide pathway involving isobutyrate, acetate and propionate.

Micromonospora fluostatini sp. nov., isolated from marine sediment

The novel actinomycete strain PWB-003T, which produced fluostatins B and C antibiotics, was isolated from nearshore sediment collected from Panwa Cape, Phuket Province, Thailand. Data from the present polyphasic study indicated that strain PWB-003T represented a member of the genus Micromonospora. It produced single spores on substrate mycelia and contained meso-diaminopimelic acid in the cell-wall peptidoglycan. Whole-cell hydrolysate contained ribose, xylose, arabinose, mannose and glucose. The predominant menaquinone was MK-10 (H4). Cellular fatty acids comprised C18 : 1ω9c, iso-C16 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C17 : 0. On the basis of 16S rRNA gene sequence similarity analysis, the novel strain was closely related to Micromonospora eburnea LK2-10T (99.38 %), Micromonospora chaiyaphumensis MC5-1T (99.16 %), Micromonospora yangpuensis FXJ6.011T (98.97 %), Micromonospora echinaurantiaca DSM 43904T (98.97 %), Micromonospora pallida DSM 43817T (98.97 %), Micromonospora sagamiensis DSM 43912T and Micromonospora auratinigra JCM 12357T (both 98.97 %). The G+C content of the DNA was 74.5 mol%. DNA-DNA relatedness values among strain PWB-003T and related type strains ranged from 11.3 ± 1.3 to 38.8 ± 1.1 %. On the basis of these observations, strain PWB-003T could be distinguished from its closely related type strains and is considered to represent a novel species of the genus Micromonospora, for which the name Micromonospora fluostatini sp. nov. (type strain PWB-003T = JCM 30529T = PCU 341T = TISTR 2345T) is proposed.

Nonomuraea rhodomycinica sp. nov., isolated from peat swamp forest soil

The taxonomic position of an actinomycete, strain NR4-ASC07T, isolated from a soil sample collected from Sirindhorn peat swamp forest, Narathiwat Province, Thailand, was clarified using a polyphasic approach. On the basis of morphological and chemotaxonomic characteristics, it was classified among the members of the genus Nonomuraea. It produced tightly closed spiral spore chains on aerial mycelium as well as forming a pseudosporangium. Whole-cell hydrolysates contained meso-diaminopimelic acid, glucose, ribose, madurose and mannose. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides, unknown ninhydrin-positive phosphoglycolipids and unknown glycolipid. Menaquiones were MK-9(H4), MK-9(H0), MK-9(H2), MK-10(H4) and MK-9(H6). Predominant cellular fatty acids were iso-C16 : 0, C17 : 0 10-methyl, C16 : 0, C17 : 1ω8c, C16 : 0 2-OH and iso-C15 : 0. The phylogenetic tree reconstructed on the basis of 16S rRNA gene sequences showed that the strain fell within the clade containing Nonomuraea muscovyensis FMN03T, Nonomuraea roseoviolacea subsp. roseoviolaceaNBRC 14098T and Nonomuraea roseoviolacea subsp. carminataNBRC 15903T. The DNA-DNA relatedness and phenotypic data supported that strain NR4-ASC07T was clearly distinguished from the closely related species and represents a novel species of the genus Nonomuraea for which the name Nonomuraea rhodomycinica sp. nov. is proposed. The type strain is NR4-ASC07T (=NBRC 112327T=TISTR 2465T).

Actinomadura montaniterrae sp. nov., isolated from mountain soil.

The taxonomic position of the mountain soil actinomycete, strain CYP1-1BT, was clarified by a polyphasic study. The strain produced a single spore, or occasionally a chain of spores, on aerial mycelium. Chemotaxonomic data supported the classification of CYP1-1BT as representing a member of the genus Actinomadura on the basis of the presence of meso-diaminopimelic acid in the peptidoglycan; galactose, glucose, madurose and ribose as whole cell sugars; MK-9(H6), MK-9(H8) and MK-9(H4) as dominant menaquinones; C16 : 0, 10-methylated C18 : 0 and C18 : 1ω9c as the major cellular fatty acids; and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol manosides as the predominant phospholipids. The DNA G+C content was 74.3 mol%. On the basis of the combination of morphological and chemotaxonomic characteristics, CYP1-1BT was identified as representing a member of the genus Actinomadura. On the basis of the results of 16S rRNA gene analysis, CYP1-1BT, was shown to be closely related to Actinomadura nitritigenes DSM 44137T (98.9 %). Phenotypic, genotypic and DNA-DNA hybridization data supported the hypothesis that CYP1-1BT represents a novel species of the genus Actinomadura for which the name Actinomadura montaniterrae sp. nov. is proposed. The type strain is CYP1-1BT (=JCM 16995T=KCTC 39784T=PCU 349T=TISTR 2400T).

Actinomadura rayongensis sp. nov., isolated from peat swamp forest soil.

A novel actinomycete strain RY35-68(T), isolated from a peat swamp forest soil sample in Rayong Province, Thailand, was characterized using a polyphasic approach. The strain belonged to the genus Actinomadura based on morphological and chemotaxonomic characteristics. Cell-wall analysis revealed the presence of meso-diaminopimelic acid and N-acetylmuramic acid in the peptidoglycan layer. The diagnostic sugar in whole-cell hydrolysates was identified as madurose. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The major cellular fatty acids were C16 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The genomic DNA G+C content was 73.7 mol%. On the basis of 16S rRNA gene sequence similarity analysis, strain RY35-68(T) was closely related to the species Actinomadura atramentaria JCM 6250(T) (97.5 %). The value of DNA-DNA relatedness between strain RY35-68(T) and A. atramentaria JCM 6250(T) was 37.6-42.6 %. On the basis of its phenotypic characteristics and these results mentioned, this strain could be distinguished from the closely related type strain and represents a novel species of the genus Actinomadura, for which the name Actinomadura rayongensis sp. nov. (type strain RY35-68(T) = JCM 19830(T) = TISTR 2211(T) = PCU 332(T)) is proposed.

Nocardia rayongensis sp. nov., isolated from Thai peat swamp forest soil.

An actinomycete strain, RY45-3T, isolated from a peat swamp forest soil in Rayong Province, Thailand, was characterized using a polyphasic approach. The strain belonged to the genus Nocardia on the basis of morphological, physiological, biochemical and chemotaxonomic properties. Cell-wall peptidoglycan contained meso-diaminopimelic acid. The N-acyl group of muramic acid in the cell wall was glycolyl type. The diagnostic sugars in whole-cell hydrolysates were galactose and arabinose. MK-8 (H4ω-cycl) was the major menaquinone. The major fatty acids were C16 : 0 and C18 : 1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The genomic DNA G+C content was 71 mol%. On the basis of 16S rRNA gene sequence similarity analysis, strain RY45-3T was closely related to Nocardia jiangxiensis JCM 12861T (98.9 %), Nocardia nova JCM 6044T (98.8 %) and Nocardia pseudobrasiliensis JCM 9894T (98.6 %). The strain showed low levels of DNA-DNA relatedness with N. jiangxiensis JCM 12861T, N. nova JCM 6044T and N. pseudobrasiliensis JCM 9894T (range from 3.6 to 55.3 %). On the basis of the phenotypic characteristics and the results mentioned, this strain could be differentiated from closely related type strains and represents a novel species of the genus Nocardia, for which the name Nocardia rayongensis sp. nov. (type strain RY45-3T = JCM 19832T = TISTR 2213T = PCU 334T) is proposed.

Virgibacillus kapii sp. nov., isolated from Thai shrimp paste (Ka-pi).

A Gram-reaction-positive and rod-shaped bacterium, designated KN3-8-4T, was isolated from shrimp paste collected from a market in Nakhon Sri Thammarat province, Thailand. Strain KN3-8-4T was a strictly aerobic, motile bacterium that produced ellipsoidal endospores at a terminal position. The isolate grew at pH 4.5-10 (optimum pH 7.5), at 11-42 °C (optimum 37 °C) and in the presence of 0-15% (w/v) NaCl (optimum 1-5%). On the basis of 16S rRNA gene sequences, strain KN3-8-4T belonged to the genus Virgibacillus and showed highest similarity with Virgibacillus olivae JCM 30551T (97.85% 16S rRNA gene sequence similarity). The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid and the major isoprenoid quinone was MK-7. Strain KN3-8-4T contained anteiso-C15:0 and anteiso-C17:0 as major cellular fatty acids and had phosphatidylglycerol, diphosphatidylglycerol, two unknown phospholipids and one glycolipid as polar lipids. The DNA G+C content was 43.5 mol%. Strain KN3-8-4T showed low DNA-DNA relatedness (20.44%) with V. olivae JCM 30551T. On the basis of phenotypic and chemotaxonomic data and phylogenetic analyses, strain KN3-8-4T represents a novel species of the genus Virgibacillus for which the name Virgibacillus kapii sp. nov. is proposed. The type strain is KN3-8-4T (=JCM 30071T=LMG 28282T=TISTR 2279T=PCU 345T).

Pseudonocardia thailandensis sp. nov., an actinomycete isolated from a subterranean termite nest

A novel Gram-stain-positive bacterium designated CMU-NKS-70T was isolated from a subterranean termite nest and characterized using a polyphasic approach. The strain exhibited branching, pinkish-cream aerial mycelium and cream-brown substrate mycelium, and formed chains of rod-like spores. The 16S rRNA gene sequence analyses indicated that strain CMU-NKS-70T belonged to the genus Pseudonocardia, showing high similarity with Pseudonocardia oroxyli D10T (98.9 % 16S rRNA gene sequence similarity), Pseudonocardia xishanensis YIM 63638T (98.9 %) and Pseudonocardia kujensis A4038T (98.5 %). However, DNA-DNA relatedness values between strains CMU-NKS-70T and the closest phylogenetically related species ranged from 40.5±2.9 to 48.6±0.7 %. Whole-cell hydrolysates of strain CMU-NKS-70T consisted of meso-diaminopimelic acid, glucose, galactose, arabinose, mannose, ribose and rhamnose. The predominant menaquinone was MK-8(H4). The major cellular fatty acids (>10 %) were iso-C16 : 0, C16 : 0, C16 : 1ω7c and/or iso-C15 : 0 2-OH and 10-methyl C16 : 0. The polar lipids detected were phosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, three unidentified glycolipids and two unidentified phospholipids. The G+C content of genomic DNA was 71.9 mol%. The physiological and biochemical properties also supported the phenotypic distinction of strain CMU-NKS-70T from its closely related species. On the basis of evidence from this study using a polyphasic approach, strain CMU-NKS-70T represents a novel species of the genus Pseudonocardia for which the name Pseudonocardia thailandensis sp. nov. is proposed. The type strain is CMU-NKS-70T (=JCM 31292T=TBRC 2000T).

Bacillus piscicola sp. nov., isolated from Thai fish sauce (Nam-pla)

A Gram-reaction-positive, spore-forming, rod-shaped bacterium, designated NR1-3-2T, was isolated from fish sauce collected from a factory in Chonburi province, Thailand. Strain NR1-3-2T grew at pH 5-10 (optimum 7.5), at 21-48 °C (optimum 37 °C) and with 0-15 % (w/v) NaCl (optimum 1-3 %). The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Menaquinone with seven isoprene units (MK-7) was the major isoprenoid quinone. The strain contained anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 as major cellular fatty acids. Diphosphatidylglycerol, phosphatidyl glycerol and one unknown glycolipid were detected as major polar lipids. On the basis of 16S rRNA gene sequence analysis, strain NR1-3-2T belonged to the genus Bacillus and was closely related to Bacillus iranensis DSM 23995T (97.4 % similarity). Strain NR1-3-2T exhibited low DNA-DNA relatedness (31.2-39.8 %) with B. iranensis DSM 23995T. The DNA G+C content was 44.2 mol%. On the basis of phenotypic characteristics, DNA-DNA relatedness and phylogenetic analyses, the strain is considered to represent a novel species of the genus Bacillus and the name Bacillus piscicola sp. nov. is proposed. The type strain is NR1-3-2T ( = JCM 19598T = LMG 28281T = PCU 340T = TISTR 2295T).

Dactylosporangium sucinum sp. nov., isolated from Thai peat swamp forest soil

The actinomycete strain RY35-23T was isolated from peat swamp forest soil in Thailand. The taxonomic position of this strain was determined using polyphasic approach. Strain RY35-23T showed typical morphology and chemical properties similar to the members in the genus Dactylosporangium. On the basis of 16S ribosomal RNA gene analysis, this strain was closely related to Dactylosporangium fulvum JCM 5631T (98.94%), D. roseum JCM 3364T (98.87%) and D. darangshiense JCM 17441T (98.86%). The DNA–DNA relatedness between strain RY35-23T and its closely related species was lower than 70%, the cutoff level for assigning strains to the same species. On the basis of these results mentioned, the strain RY35-23T could be distinguished from its closely related type strains and represents a novel species of the genus Dactylosporangium, for which the name Dactylosporangium sucinum (type strain RY35-23T=JCM 19831T=TISTR 2212T=PCU 333T) is proposed.