Shinji Miyadoh

Herbidospora gen. nov., a New Genus of the Family Streptosporangiaceae Goodfellow et al. 1990

Eight actinomycete strains originally isolated from soil and plant samples were studied to determine their taxonomic status. All isolates produced branching substrate mycelia, but no distinct aerial hyphae. Relatively short chains of nonmotile spores (10 to 30 spores per chain) were borne on the tips of sporophores arising directly from the agar surface. The chemotaxonomic characteristics of the isolates, with the exception of the menaquinone profile, coincided with those of members of the family Streptosporangiaceae Goodfellow, Stanton, Simpson, and Minnikin 1990. Furthermore, the results of a phylogenetic analysis performed with 5S rRNA support the conclusion that the isolates should be classified in this family. The isolates differed from members of the constituent genera of the Streptosporangiaceae in morphological characteristics and menaquinone composition. Therefore, we propose a new genus for the strains, Herbidospora. The type species and type strain are Herbidospora cretacea sp. nov. and strain K-319 (= JCM 8553), respectively.

A taxonomic review of the genus microbispora and a proposal to transfer two species to the genus Actinomadura and to combine ten species into Microbispora rosea

We conducted a taxonomic review of the genus Microbispora using chemotaxonomic and DNA-DNA hybridization techniques, and reached the following conclusions: Microbispora viridis should be transferred to the genus Actinomadura as Actinomadura rugatobispora comb. nov., nom. nov. (type strain SF2240 = IFO 14382 = JCM 3366) and Microbispora echinospora should be transferred to the genus Actinomadura as Actinomadura echinospora comb. nov. (type strain JCM 3148 = ATCC 27300). We also propose that Microbispora rosea, Microbispora amethystogenes, Microbispora chromogenes, Microbispora diastatica, Microbispora indica, Microbispora karnatakensis and Microbispora parva should be combined into the species Microbispora rosea subsp. rosea (type strain JCM 3006 = ATCC 12950), and that Microbispora aerata, Microbispora thermodiastatica and Microbispora thermorosea should be combined and transferred to the new subspecies Microbispora rosea subsp. aerata comb. nov. (type strain IFO 12581 = ATCC 15448). Microbispora bispora clearly differs from these ten strains at the species level.

Polyacrylamide Gel Electrophoresis Analysis of Ribosomal Protein AT-L30 as a Novel Approach to Actinomycete Taxonomy: Application to the Genera Actinomadura and Microtetraspora

Actinomycete ribosomal protein AT-L30 exhibits electrophoretic mobility that is specific for each genus. On the basis of this fact, we analyzed ribosomal AT-L30 proteins from 26 type strains of species belonging to the genera Actinomadura and Microtetraspora. The electrophoretic mobilities of AT-L30 preparations from these strains, as determined by two-dimensional polyacrylamide gel electrophoresis, revealed that they could be divided into two groups, one group with relative electrophoretic mobilities of 14.0 to 41.5 and another group with relative electrophoretic mobilities of -6.5 to 0. The first group corresponded to the genus Actinomadura, and the second group corresponded to the genus Microtetraspora. Partial amino acid sequencing of AT-L30 preparations from several strains proved that we were indeed dealing with the specified protein homologous to ribosomal protein L30 of Escherichia coli. Our results strongly supported the conclusions of previous work and thus proved the efficacy of ribosomal protein analysis as a novel approach for taxonomy of actinomycetes.

Taxonomic and ecological studies of actinomycetes from Vietnam: isolation and genus-level diversity

Actinomycetes were isolated from 109 soil and 93 leaf-litter samples collected at five sites in Vietnam between 2005 and 2008 using the rehydration-centrifugation (RC) method, sodium dodecyl sulfate-yeast extract dilution method, dry-heating method and oil-separation method in conjunction with humic acid-vitamin agar as an isolation medium. A total of 1882 strains were identified as Vietnamese (VN)-actinomycetes including 1080 (57%) streptomycetes (the genus Streptomyces isolates) and 802 (43%) non-streptomycetes. The 16S ribosomal RNA gene sequences of the VN-actinomycetes were analyzed using BLAST searches. The results showed that these isolates belonged to 53 genera distributed among 21 families. Approximately 90% of these strains were members of three families: Streptomycetaceae (1087 strains, 58%); Micromonosporaceae (516 strains, 27%); and Streptosporangiaceae (89 strains, 5%). Motile actinomycetes of the genera Actinoplanes, Kineosporia and Cryptosporangium, which have quite common morphological characteristics, were frequently isolated from leaf-litter samples using the RC method. It is possible that these three genera acquired common properties during a process of convergent evolution. By contrast, strains belonging to the suborder Streptosporangineae were exclusively isolated from soils. A comparison of the sampling sites revealed no significant difference in taxonomic diversity between these sites. Among the non-streptomycetes, 156 strains (19%) were considered as new taxa distributed into 21 genera belonging to 12 families. Interestingly, the isolation of actinomycetes from leaf-litter samples using the RC method proved to be the most efficient way to isolate new actinomycetes in Vietnam, especially the Micromonosporaceae species.

Actinomadura malachitica, and Microtetraspora viridis are synonyms and should be transferred as Actinomadura viridis comb. nov

We compared strain SF2461, Microtetraspora viridis JCM 3112T (T = type strain), Microtetraspora viridis subsp. intermedia JCM 3113T, and Actinomadura malachitica JCM 3297T by using morphological, cultural, physiological, and chemotaxonomic characteristics, as well as deoxyribonucleic acid homology. All of our results indicated that these four strains belong to the same species and that they are far from the other type strains of Microtetraspora species. Therefore, we propose that Actinomadura malachitica is a synonym of Microtetraspora viridis and that Microtetraspora viridis should be transferred to the genus Actinomadura as Actinomadura viridis comb. nov., with strain JCM 3112 (= ATCC 27103) as the type strain.

Proposal to transfer Actinomadura carminata to a new subspecies of the genus nonomuraea as nonomuraea roseoviolacea subsp. carminata comb, nov.

An anthracycline-producing actinomycete (strain SF2303) was compared with two other anthracycline producers, Actinomadura carminata IFO 15903T and Nonomuraea roseoviolacea IFO 14098T, using morphological, physiological, chemotaxonomic and molecular-genetic criteria. The morphological and cultural characteristics of these three strains are similar. The physiological properties of strain SF2303 and N. roseoviolacea IFO 14098T are very similar, but are different from those of A. carminata IFO 15903T in the utilization of some sugars and the reduction of nitrate. Their chemotaxonomic properties [cell wall chemotype, IIIB; major menaquinone, MK-9 (III, VIIl-H4); phospholipid type, PIV; cellular fatty acids 10M-17:0/17:1 and iso-16:0 as major components and 2-hydroxy fatty acids as minor components; mycolic acid, absent] were identical and indicated that these three strains belong to the family Streptosporangiaceae. On the basis of 16S rDNA sequences and phylogenetic analysis, they were all included in the cluster formed by species of Nonomuraea. The levels of DNA relatedness between strain SF2303 and N. roseoviolacea IFO 14098T ranged from 71 to 78%; however, the levels of relatedness between the two strains and A. carminata IFO 15903T were lower (49-60%). Therefore, strain SF2303 was identified as a member of the species N. roseoviolacea and it is proposed that Actinomadura carminata Gauze et al. 1973 should be transferred to a new subspecies of the genus Nonomuraea Zhang et al. 1998 as N. roseoviolacea subsp. carminata comb. nov.

SF2446, NEW BENZO[α]NAPHTHACENE QUINONE ANTIBIOTICS

New antibiotics SF2446A1, A2, A3, B1 and B2 have been isolated from the culture of Streptomyces sp. SF2446 and antibiotic SF2446B3 has been obtained by methanolysis of SF2446B1 or B2. SF2446A1, A2 and B1 showed strong inhibitory activities against mycoplasmas and Gram-positive bacteria. Empirical molecular formulae of antibiotics SF2446-A1, A2, A3, B1, B2 and B3 were determined to be C34H35NO15, C26H21NO11, C34H35NO14, C34H35NO14 and C26H21NO10, respectively.

Taxonomic distribution of Streptomyces species capable of producing bioactive compounds among strains preserved at NITE/NBRC

The taxonomic distribution of Streptomyces species capable of producing bioactive compounds was investigated. Nine hundred and six strains were tested for the following four biological activities: antimicrobial, anti-tyrosinase, antioxidant, and hemolytic. Approximately 30% of strains tested showed antimicrobial activities, except for anti-Escherichia coli activity, which was present in only a few strains, while the rates of positivity for the anti-tyrosinase, antioxidant, and hemolytic activities were much lower. The distribution of Streptomyces strains capable of producing bioactive compounds was analyzed by the taxonomy based on 16S rRNA gene sequences. Moreover, the strains of Streptomyces hygroscopicus tested were divided into two clades in the phylogenetic tree, and all of the strains belonging to one clade showed antibacterial and antifungal activities. For detection of polyenes, the UV–visible spectra of metabolic extracts in the strains showing antifungal activities were measured. It was suggested that Streptomyces strains produce universal active compounds under different growth conditions. Further information on the relationship between the microbial taxonomy and the bioactive compounds produced would be useful for the utilization of industrial microorganisms.

Polyacrylamide gel electrophoresis analysis of ribosomal protein AT-L30 from an actinomycete genus, Streptosporangium.

We analyzed the ribosomal AT-L30 proteins from 11 type strains of species belonging to the genus Streptosporangium. The electrophoretic mobilities of the AT-L30 preparations from these strains, as determined by two-dimensional polyacrylamide gel electrophoresis, revealed that they could be divided into three groups. The first group contained Streptosporangium viridogriseum, S. viridogriseum subsp. kofuense, and S. albidum, while the second group contained S. roseum, S. album, S. vulgare, S. nondiastaticum, S. fragile, S. violaceochromogenes, and S. amethystogenes. S. corrugatum was a member of the third group. These groups were completely consistent with Nonomuras previous classification, which was based on morphological criteria. The results of partial amino acid sequencing of AT-L30 preparations from several representative strains strongly supported the hypothesis that each of the three groups of the genus Streptosporangium merits separate generic status.

Kineosporia babensis sp. nov., isolated from plant litter in Vietnam

Three actinomycetes, designated strains VN05A0342, VN05A0351 and VN05A0415(T), were isolated from plant-litter samples collected in the north of Vietnam and examined in a polyphasic taxonomic study. Phylogenetic analysis based on the 16S rRNA gene sequences showed that these isolates were most closely related to the type strain of Kineosporia mikuniensis (98.5 % sequence similarity). Morphological properties (the formation of spore domes and motile spores) and chemotaxonomic data supported the assignment of the three isolates to the genus Kineosporia. The isolates all contained the following: meso-diaminopimelic acid in the peptidoglycan (with small amounts of the ll isomer); ribose, mannose, galactose and glucose as the whole-cell sugars; MK-9(H(4)) as the predominant isoprenoid quinone; C(18 : 1) and C(16 : 0) as the major cellular fatty acids; and phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol as the phospholipids. The high DNA-DNA relatedness (>71 %) among the three isolates showed that they represented a single species. On the other hand, the DNA-DNA relatedness between the novel isolates and all type strains of Kineosporia species was less than 46 %. The physiological properties of our isolates were distinct from those of all of the Kineosporia species with validly published names, e.g. decomposition of l-tyrosine and aesculin and the utilization of raffinose and d-arabitol. Therefore, strains VN05A0342, VN05A0351 and VN05A0415(T) represent a novel species of the genus Kineosporia, for which the name Kineosporia babensis sp. nov. is proposed. The type strain is VN05A0415(T) (=VTCC-A-0961(T) =NBRC 104154(T)).