Actinoplanes pyxinae sp. nov., a new lichen-derived rare actinobacterium exhibiting antimicrobial and anticancer activity

A novel lichen-derived actinobacterium, designated Pm04-4T, was isolated from Pyxine cocoes (Sw.) Nyl. lichen collected from Chaiyaphum, Thailand. A polyphasic approach was used to describe the taxonomic position of the strain. The strain had morphological and chemotaxonomic properties similar to members of the genus Actinoplanes. It produced sporangia on the substrate mycelia. Meso-diaminopimelic acid, galactose, glucose and mannose were detected in the whole-cell hydrolysate of the strain. The major menaquinone was MK-9(H4). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Strain Pm04-4T showed the highest 16S rRNA gene sequence similarity to Actinoplanes akusuensis TRM 8003T (99.0 %). In the phylogenomic tree, strain Pm04-4T was positioned close to A. aksuensis TRM88003T, A. maris M416T, A. polyasparticus TRM66264T, A. hotanensis TRM88002T, A. abujensis DSM 45518T, A. bogorensis NBRC 110975T, A. brasiliensis DSM 43805T, A. lichenicola LDG1-01T and A. ovalisporus LDG1-06T. The average nucleotide identity and digital DNA-DNA hybridization values between strain Pm04-4T and its closely related neighbours were below the threshold values for describing new species. Moreover, the strain could be distinguished from its closely related type strains by phenotypic properties. Based on genotypic and phenotypic evidence, it can be concluded that strain Pm04-4T is a representative of a new Actinoplanes species for which the name Actinoplanes pyxinae sp. nov. is proposed. The type strain is Pm04-4T (=TBRC 16207T=NBRC 115836T). The type strain exhibited activity against Staphylococcus aureus ATCC 25923 as well as four yeast strains, namely Candida albicans TISTR 5554, Candida glabrata TISTR 5006, Candida krusei TISTR 5351 and Candida parapsilosis TISTR 5007. It also showed cytotoxicity against Caco-2, MNT-1 and MCF-7 cancer cells.

Streptomyces rugosispiralis sp. nov., a Novel Actinobacterium Isolated from Peat Swamp Forest Soil That Produces Ansamycin Derivatives and Nocardamines

Actinomycetes, especially the genus Streptomyces, are one of the most promising sources of bioactive natural products. In this study, a novel Streptomyces strain, RCU-064T, was isolated from a soil sample collected from a peat swamp forest in Thailand. Strain RCU-064T showed the highest 16S rRNA gene sequence similarity (99.06%) with Streptomyces malaysiensis NBRC 16446T. Based on a polyphasic approach, strain RCU-064T represents a novel species of the genus Streptomyces, for which the name Streptomyces rugosispiralis sp. nov. is proposed. The chemical isolation of the crude ethyl acetate extracts of the strain led to the isolation of six compounds: (1) geldanamycin, (2) 17-O-demethylgeldanamycin, (3) reblastatin, (4) 17-demethoxyreblastatin, (5) nocardamine, and (6) dehydroxynocardamine. These compounds were evaluated for their biological activities. All compounds showed no antimicrobial activity against tested microorganisms used in this study. Compounds (1)-(4) displayed cytotoxic activity against the NCI-H187 cell line, with IC50 values ranging from 0.045-4.250 µg/mL. Cytotoxicity against the MCF-7 cell line was found in compounds (1) and (3) with IC50 values of 3.51 and 1.27 µg/mL, respectively. Compounds (5) and (6) exhibited cytotoxicity only against Vero cells (IC50 of 16.57 µg/mL) and NCI-H187 cells (IC50 of 13.96 µg/mL), respectively. These results indicate that peat swamp forest soil remains a promising reservoir of novel actinomycetes capable of producing bioactive natural products.

Streptomyces cylindrosporus sp. nov. and Streptomyces spinosisporus sp. nov.: two new endophytic actinobacteria isolated from the roots of Barleria lupulina Lindl

Two endophytic actinobacteria, designated as strains 7R015^T and 7R016^T, were isolated from the roots of Barleria lupulina collected in Thailand. The morphological characteristics and results of chemotaxonomic studies and 16S rRNA gene analysis indicated that both strains represented members of the genus Streptomyces. They contained ll-diaminopimelic acid in the peptidoglycan. Ribose and glucose were detected as the whole-cell sugars. MK-9(H₄), MK-9(H₆) and MK-9(H₈), were found as the membrane menaquinone. The predominant cellular fatty acids detected were iso-C_16 : 0 and anteiso-C_15 : 0. The genomes of both strains harboured biosynthetic gene clusters for melanin, terpene, lanthipeptide, polyketides, non-ribosomal peptide synthetase, siderophore and ectoine. The 16S rRNA gene sequence of 7R015^T showed the highest similarity to that of Streptomyces pseudovenezuelae DSM 40212^T (98.6 %), Streptomyces cyaneus NRRL B2296^T (98.6 %) and Streptomyces curacoi DSM 40107^T (98.6 %). Strain 7R016^T showed the highest 16S rRNA gene sequence similarity to Streptomyces gilvifuscus NBRC 110904^T (98.2 %), which is lower than the threshold value for 16S rRNA gene sequence similarity for differentiation at the species level (98.65 %). Comparative genome analysis revealed that the genomes of 7R015^T, 7R016^T and the closely related type strains had an average nucleotide identity (ANI) of less than 95 % and a digital DNA-DNA hybridisation (dDDH) of less than 70 %, the thresholds for species demarcation. On the basis of the results of the polyphasic study, strains 7R015^T and 7R016^T represent novel species of the genus Streptomyces and are named herein as Streptomyces cylindrosporus sp. nov. (=NBRC 115200^T = TBRC 14542^T) for strain 7R015^T and Streptomyces spinosisporus sp. nov. (=NBRC 115201^T = TBRC 14543^T) for strain 7R016^T.

Streptomyces macrolidinus sp. nov., a novel soil actinobacterium with potential anticancer and antimalarial activity

A novel actinomycete, strain RY43-2^T, belonging to the genus Streptomyces, was isolated from a peat swamp forest soil collected from Rayong Province, Thailand. The strain was characterized by using a polyphasic approach. The cell-wall peptidoglycan contained ll-diaminopimelic. Ribose and glucose were detected in its whole-cell hydrolysates. The strain contained anteiso-C_15:0, iso-C_14:0 and iso-C_16:0 as the predominant fatty acids, and MK-9(H₄), MK-9(H₆) and MK-9(H₈) as the major menaquinones. The phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, three unidentified ninhydrin-positive phospholipids and two unidentified phospholipids. Strain RY43-2^T showed the highest 16S rRNA gene similarity to Streptomyces misionensis JCM 4497^T (98.9 %) and Streptomyces lichenis LCR6-01^T (98.9 %). The draft genome of RY43-2^T was 6.7 Mb with 6078 coding sequences with an average G+C content of 70.8 mol%. Genomic analysis revealed that the average nucleotide identity (ANI) values based on blast (ANIb) and MUMmer (ANIm) between strain RY43-2^T and S. misionensis JCM 4497^T were 80.1 and 86.1%, respectively. The ANIb and ANIm values between strain RY43-2^T and S. lichenis LCR6-01^T were 77.0 and 85.5%, respectively. The digital DNA-DNA hybridization values were 25.2 and 23.0% in comparison with the draft genomes of S. misionensis JCM 4497^T and S. lichenis LCR6-01^T, respectively. The results of taxonomic analysis suggested that strain RY43-2^T represented a novel species of the genus Streptomyces for which the name Streptomyces macrolidinus sp. nov. is proposed. The type strain is RY43-2^T (=TBRC 7286^T=NBRC 115640^T). Strain RY43-2^T exhibited antimicrobial activity against Enterococcus faecium ATCC 51559, Colletotrichum capsici BMGC 106 and Colletotrichum gloeosporioides BMGC 107 with the minimum inhibitory concentration values of 25.0, 12.5, and 6.25 µg ml^-1. It also exhibited potent antimalarial activity against Plasmodium falciparum K1 with IC₅₀ of 0.0031 µg ml^-1. In addition, it showed cytotoxicity against Vero, KB, MCF-7 and NCI-H187 with IC₅₀ values of 0.0347, 6.15, 3.36 and 0.0352 µg ml^-1, respectively.

Saccharothrix obliqua sp. nov., isolated from soil of Sichang Island, Thailand

During an investigation of rare actinobacteria, isolate SC076T was isolated from a soil sample collected from Sichang Island, Chonburi Province, Thailand. The strain showed the highest 16S rRNA gene similarity to Saccharothrix australiensis DSM 43800T (98.6%) and Saccharothrix espanaensis DSM 44229T (98.6%). The zigzag morphology of the spore chain was observed on the aerial mycelia. meso-Diaminopimelic acid was detected in the peptidoglycan. Whole-cell sugars contained rhamnose, ribose, mannose glucose and galactose. Polar lipids were phosphatidylethanolamine, hydroxyphosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol, unidentified ninhydrin-positive glycolipid, unidentified glycolipid and four unidentified lipids. The menaquinones were MK-9(H8), MK-9(H4), MK-9(H2) and MK-9(H0). The predominant fatty acids were iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 0. The draft genome of SC076T was 8040245 bp with a G+C content of 72.5 mol%. The results of genomic analysis between strain SC076T and the related type strains showed that the digital DNA–DNA hybridization and average nucleotide identity values among the strains were 23.6-32.8% and 77.7–86.8 %, respectively, which are lower than the thresholds used to distinguish strains from others of the same species. Based on the taxonomic evidence, strain SC076T represents a novel species of the genus Saccharothrix for which the name Saccharothrix obliqua sp. nov. is proposed. The type strain is SC076T (=TBRC 14540T=NBRC 115117T).

Streptomyces corallincola and Kineosporia corallincola sp. nov., two new coral-derived marine actinobacteria

Two new marine actinobacteria, designated as J2-1^T and J2-2^T, were isolated from a coral, Favites pentagona, collected from Rayong Province, Thailand. The taxonomic positions of the two strains were identified based on polyphasic taxonomy. Based on morphological characteristics and chemotaxonomy, strains J2-1^T and J2-2^T were identified as members of the genus Streptomyces and Kineosporia, respectively. Strains J2-1^T and J2-2^T showed the highest 16S rRNA gene sequence similarity to Streptomyces broussonetiae T44^T (98.62 %) and Kineosporia babensis VN05A0415^T (98.08 %), respectively. Strain J2-1^T had chemotaxonomic properties resembling members of the genus Streptomyces. ll-Diaminopimelic acid, glucose and ribose were detected in the whole-cell hydrolysate. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositolmannoside, unidentified aminolipid and five unidentified phospholipids were detected as the polar lipids. The major cellular fatty acids were C_16 : 0 iso, C_15 : 0 anteiso, C_15 : 0 iso, C_16 : 0, C_17 : 0 anteiso, C_14 : 0 iso and C_17 : 0 iso. Strain J2-2^T a showed similar cell composition to members of the genus Kineosporia. Both isomers of ll- and meso-diaminopimelic acid were detected in the peptidoglycan. Arabinose, galactose, madurose and xylose were observed in the whole-cell hydrolysate. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, phosphatidylcholine, an unidentified phospholipid and an unidentified glycolipid. The major cellular fatty acids were C_16 : 0, C_18 : 1 ω9c, C_18 : 0 10-methyl, tuberculostearic acid, C_18 : 0 and C_17 : 0. Both strains could be distinguished from their closely related type strains according to their phenotypic characteristics. Comparative genome analysis indicated the delineation of two novel species based on digital DNA-DNA hybridization and average nucleotide identity values, which were below 70 and 95 %, respectively. The names proposed are Streptomyces corallincola sp. nov. (J2-1^T=TBRC 13503^T=NBRC 115066^T) and Kineosporia corallincola sp. nov. (J2-2^T=TBRC 13504^T=NBRC 114885^T).

Potential antibiotic production of Streptomyces justiciae sp. nov., isolated from the root of Justicia subcoriacea

Endophytic actinobacterial strain 3R004^T was isolated from a root of Justicia subcoriacea collected in Thailand. In this report, the taxonomic position of this strain is described using a polyphasic approach. Based on the morphological characteristics and chemical composition of its cells, strain 3R004^T was identified as a member of the genus Streptomyces. It produced a long chain of cylindrical spores on aerial mycelia. ll-Diaminopimelic acid was detected in the cell wall peptidoglycan. The menaquinones were MK-9(H₄), MK-9(H₆) and MK-9(H₈). C_16 : 0, iso-C_16 : 0, anteiso-C_15 : 0 and iso-C_15 : 0 were detected as the major cellular fatty acids. Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and one unidentified lipid. Strain 3R004^T showed the highest 16S rRNA gene similarity of 99.45 % to Streptomyces cyaneochromogenes MK-45^T. The phylogenomic results indicated that strain 3R004^T was close to Streptomyces aquilus GGCR-6^T and Streptomyces antibioticus DSM 40234^T. The DNA-DNA hybridization and average nucleotide identity values among strain 3R004^T and closely related Streptomyces species were 35.5-63.1 % and 82.7-94.3 %, respectively. The type strain produced actinomycin D antibiotic as the major secondary metabolite. The maximum productivity of the actinomycin D (378 mg l^-1) was observed when the strain was grown in 301 broth at 30 °C, 180 r.p.m. for 12 days. On the basis of phenotypic and genotypic evidence, strain 3R004^T represents a novel species of the genus Streptomyces, for which the name Streptomyces justiciae is proposed. The type strain is 3R004^T (=LMG 32138^T=TBRC 13128^T=NBRC 115065^T).

Potential antimicrobial properties of streptomyces isolated from Sammuk Mountain soil, Chonburi Province, Thailand

An infection of pathogenic microorganisms can create a big problem for human health. This has triggered the need for discovery and development of antibiotic drugs with altered modes of action. Approximately 45% of antibiotic drugs are derived from Streptomyces, which are the most commonly isolated actinomycete genera. The present investigation aimed to search for and study antimicrobial-producing actinomycetes isolated from soil samples from Sammuk Mountain, Chonburi province, Thailand. A total of 50 isolates from six soil samples were obtained and their actinomycetes were better isolated using humic acid-vitamin agar medium (64.0%) than starch casein nitrate agar medium (36.0%). In addition, the secondary metabolites produced from 13 isolates (26.0%) exhibited a broad spectrum of antimicrobial activity against Gram-positive bacteria and yeast. Thus, Sammuk Mountain soil is an important source of antibiotic-producing actinomycetes.

Antimicrobial substances from the rare actinomycete Nonomuraea rhodomycinica NR4-ASC07T

Nonomuraea rhodomycinica NR4-ASC07^T is a rare actinomycete isolated from soil in Sirindhorn peat swamp forest. The crude extract of its culture broth exhibited antimicrobial and anticancer against diverse human pathogens and cancer cells. The chemical investigation of the crude extract led to the isolation of two new metabolites named nonomuric acid (1) and 3-hydroxy deoxydaunorubicinol aglycone (2), along with two known bioactive compounds [ε-rhodomycinone (3) and 7-deoxy-13-dihydrocarminomycinone (4)]. Compounds 1 and 3 showed antimalarial activity with the half maximal inhibitory concentration (IC₅₀) of 8.00 and 8.88 μg mL^-1, respectively. Compound 4 inhibited growth of Mycobacterium tuberculosis and Bacillus cereus at the minimum inhibitory concentrations of 50.0 and 12.50 μg mL^-1, respectively. Every compound exhibited cytotoxicity against cancer cells tested at IC₅₀ ≥ 6.34 μg mL^-1. These finding are the first report of bioactive metabolites produced by strain NR4-ASC07^T, suggesting that rare actinomycetes are yet promising sources for novel drug discovery.

Streptomyces krungchingensis sp. nov., isolated from soil

A novel actinomycete, designated strain KC-035T, was isolated from soil collected from Krung Ching Waterfall National Park, Nakhon Si Thammarat Province, Thailand. Its taxonomic position was determined using a polyphasic approach. The strain had morphological and chemotaxonomic properties typical of members of the genus Streptomyces: flexuous spore chain; ll-diaminopimelic acid in the cell-wall peptidoglycan; MK-9(H8), MK-9(H6) and MK-9(H4) as menaquinones; diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside as phospholipids; anteiso-C15 : 0, C16 : 0, iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0 as major cellular fatty acids; and DNA G+C content of 72 mol%. 16S rRNA gene sequence analysis revealed that strain KC-035T showed high similarity to Streptomyces albiflavescens n20T (99.16 %) and Streptomyces siamensis KC-038T (98.43 %) as well as formed a monophyletic clade with them in the phylogenetic tree. On the basis of comparison of phenotypic properties and the low level of DNA-DNA relatedness, strain KC-035T could be distinguished from its closely related Streptomyces species and is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces krungchingensis sp. nov. is proposed. The type strain is KC-035T (=NBRC 110087T=KCTC 29503T=TISTR 2402T).

Streptomyces andamanensis sp. nov., isolated from soil

A novel actinomycete, strain KC-112T, was isolated from soil collected from Similan Islands, Phang-Nga Province, Thailand. The strain exhibited morphological and chemotaxonomic characteristics consistent with those of members of the genus Streptomyces. The formation of smooth spiral spore chains was observed on aerial mycelia. ll-Diaminopimelic acid was detected in whole-cell hydrolysates, but no diagnostic sugars were detected and the strain lacked mycolic acids. The N-acyl type of muramic acid was acetyl. The major menaquinones were MK-9(H8), MK-9(H6) and MK-9(H2). The predominant cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unknown phospholipid, an unknown aminolipid, unknown lipids and an unknown glycolipid. The DNA G+C content was 73 mol%. On the basis of 16S rRNA gene sequence analysis, strain KC-112T was closely related to Streptomyces fumanus NBRC 13042T (98.8 % 16S rRNA gene sequence similarity), Streptomyces anandii NBRC 13438T (98.8 %) and Streptomyces capillispiralis NBRC 14222T (98.8 %). DNA-DNA relatedness values among strain KC-112T and type strains of closely related species were lower than 70 %. On the basis of evidence from this taxonomic study using a polyphasic approach, strain KC-112T represents a novel species of the genus Streptomyces, namely Streptomyces andamanensis sp. nov. The type strain is KC-112T ( = KCTC 29502T = NBRC 110085T = PCU 347T = TISTR 2401T).

Identification and antimicrobial activity of actinobacteria from soils in southern Thailand

The aim of this research was to study on the identification and antimicrobial activity of actinobacteria from six soil samples collected around Krung Ching waterfall, Nakhon Si Thammarat province, the southern part of Thailand. Thirty-one isolates of actinobacteria were isolated using the dilution plating method on modified starch casein nitrate agar plates and potato starch-glycerol agar plates. On the primary screening, 9 isolates exhibited the antimicrobial activity against Bacillus subtilis, 8 isolates against Kocuria rhizophila, 6 isolates against Mucor racemosus, 2 isolates against Escherichia coli and Candida albicans and 5 isolates against Xanthomonas campestris pv. oryzae. All the isolates were identified based on their morphological and cultural characteristics including the 16S rRNA gene sequence analysis. Eighteen isolates were identified as Streptomyces, 8 isolates as Nocardia, 2 isolates as Kitasatospora, one of each isolate as Amycolatopsis, Rhodococcus and Gordonia.