nov., a novel actinomycete of the family Streptosporangiaceae

An actinomycete strain K14-0274^T was isolated from the root of Arisaema thunbergii Blume subsp. urashima (H. Hara) H. Ohashi et J. Murata collected in Japan. The results of phylogenetic analysis based on the 16S rRNA gene sequence indicated thatK14-0274^T could be distinguished from the members of all known genera, although it represented a member of the family Streptosporangiaceae. K14-0274^T produced sporangium-like spherical vesicles with spores on white aerial mycelia. MK-9 (H₄) and MK-9 (H₆) were the major menaquinones. The whole-cell hydrolysates contained madurose, glucose, mannose, rhamnose and ribose. The cell-wall amino acids comprise l-alanine, d-alanine, d-glutamic acid and meso-diaminopimelic acid. The N-acyl type of muramic acid was acetyl. Mycolic acids were not detected. Phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside were detected. The predominant fatty acids were iso-C_16 : 0, 10-methyl-C_18 : 0 and C_16 : 0. The G+C content of the genomic DNA was 69.7 mol%. On the basis of morphological, phylogenetic and chemotaxonomic characteristics, strain K14-0427^T represents a novel genus in the family Streptosporangiaceae, for which the name Rhizohabitans arisaemae gen. nov., sp. nov. is proposed. The type strain is K14-0247^T (=NBRC 114594^T =TBRC 12948^T).

Antifungal Activities of Compounds Produced by Newly Isolated Acrocarpospora Strains

In our continued search for bioactive metabolites from cultures of rare Actinobacteria resources from all over Taiwan and various natural ecological environments, an active antimicrobial strain of Acrocarpospora punica 04107M was collected in Taitung County in Taiwan and prepared from soil. The bioassay-guided fractionation of the BuOH extract of a culture broth from A. punica 04107M led to the isolation of five previously undescribed compounds: Acrocarposporins A−E (Compounds 1−5). All the constituents were confirmed by HRESIMS and 1D- and 2D-NMR spectroscopy. Their antifungal activity was also evaluated. Our results showed that four constituents (Compounds 1, 2, 4, and 5) possessed mild antifungal activity against Aspergillus niger, Penicillium italicum, Candida albicans, and Saccharomyces cerevisiae. It is worth mentioning that the chemical composition of Acrocarpospora punica 04107M has never been studied. This is the first report on diterpenoid metabolites from the genus Acrocarpospora.

Undescribed Metabolites from an Actinobacteria Acrocarpospora punica and Their Anti-Inflammatory Activity

In an effort to explore bioactive anti-inflammatory compounds from natural Actinobacteria resources from all over Taiwan and various ecological environments, an active strain of Acrocarpospora punica was collected at Taitung County in Taiwan, prepared from soil origin. A bioassay-guided fractionation of the BuOH extract of a culture broth of a new strain of the actinomycete Acrocarpospora punica led to the isolation of five previously undescribed compounds: acrocarpunicains A-F (1-6). The structures were elucidated by 1D and 2D Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry. Furthermore, the isolated compounds were subjected to in vitro testing to evaluate their anti-inflammatory activity. Of these isolates, acrocarpunicains A (1), B (2), C (3) and F (6) showed NO inhibitory activity with IC₅₀ values of 9.36 ± 0.25, 10.11 ± 0.47, 5.15 ± 0.18, and 27.17 ± 1.87 μM, stronger than the positive control, quercetin (IC₅₀ = 35.95 ± 2.34 μM). To the best of our knowledge, this is the first report on azaphilone and phenanthrene-type metabolites from the genus Acrocarpospora.

Secondary Metabolites with Antimycobacterial Activities from One Actinobacteria: Herbidospora yilanensis

The cultivation of one actinobacteria strain, Herbidospora yilanensis, was isolated from sediment samples collected from Yilan County City in Taiwan, resulting in the isolation of five previously undescribed compounds: herbidosporayilanensins A-E (1-5), and four compounds isolated from nature for the first time: herbidosporayilanensins F-I (6-9). Their structures were elucidated by spectroscopic analyses, including 1D- and 2D-NMR experiments with those of known analogues, and on the basis of HR-EI-MS mass spectrometry, their antimycobacterial activities were also evaluated.

Nonomuraea montanisoli sp. nov., isolated from mountain forest soil

A novel actinomycete, strain SMC 257^T, was isolated from a soil sample collected from mountain forest, Nan Province, Thailand. Strain SMC 257^T formed tightly closed spiral spore chains on aerial mycelia. A polyphasic approach was used for the taxonomic study of this strain. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SMC 257^T belonged to the genus Nonomuraea, and the closest phylogenetically related species were Nonomuraea roseoviolacea subsp. carminata JCM 9946^T (98.9 % 16S rRNA gene sequence similarity), Nonomuraea rhodomycinica TBRC 6557^T (98.4 %), and Nonomuraea roseoviolacea subsp. roseoviolacea JCM 3145^T (98.3 %). Genome sequencing revealed a genome size of 9.76 Mbp and a G+C content of 72.3 mol%. The genome average nucleotide identity (ANI) and the digital DNA-DNA hybridization (dDDH) values that distinguished this novel strain from its closest related species were species boundary of 95-96 % and 70 %, respectively. The cell wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars were glucose, ribose, madurose and mannose. The major menaquinone was MK-9(H₄). The polar lipid profile consisted of phosphatidylethanolamine, hydroxyphosphatidylethanolamine, lysophosphatidylethanolamine, diphosphatidylglycerol, N-phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The predominant cellular fatty acids were C_17 : 0 10-methyl and iso-C_16 : 0. Based on comparative analysis of phenotypic, chemotaxonomic and genotypic data, strain SMC 257^T is considered to represent a novel species of the genus Nonomuraea, for which the name Nonomuraea montanisoli is proposed. The type strain is SMC 257^T (=TBRC 13065^T=NBRC 114772^T).

and a taxonomic home for the genus Sinosporangium in the family Streptosporangiaceae

In recent years, the results of genome-based phylogenetic analyses have contributed to microbial systematics by increasing the availability of sequenced microbial genomes. Therefore, phylogenomic analysis within large taxa in the phylum Actinobacteria has appeared as a useful tool to clarify the taxonomic positions of ambiguous groups. In this study, we provide a revision of the actinobacterial family Streptosporangiaceae using a large collection of genome data and phylogenomics approaches. The phylogenomic analyses included the publicly available genome data of the members of the family Streptosporangiaceae and the state-of-the-art tools are used to infer the taxonomic affiliation of these species within the family. By comparing genome-based and 16S rRNA gene-based trees, as well as pairwise genome comparisons, the recently described genera Spongiactinospora and Desertactinospora are combined in the genus Spongiactinospora. In conclusion, a comprehensive phylogenomic revision of the family Streptosporangiaceae is proposed.

Nonomuraea phyllanthi sp. nov., an endophytic actinomycete isolated from the leaf of Phyllanthus amarus

A novel actinomycete, strain PA1-10^T, isolated from the leaf of Phyllanthus amarus collected from Bangkok, Thailand, was characterized taxonomically using a polyphasic approach. This strain contained the characteristics consistent with those of members of the genus Nonomuraea. It formed short rugose spore chain on aerial mycelium. The diamino acid in cell wall peptidoglycan was meso-diaminopimelic acid. Galactose, glucose, madurose, mannose, and ribose were found in whole-cell hydrolysates. Predominant menaquinones were MK-9 (H₂), MK-9 (H₄), and MK-9 (H₆). Major cellular fatty acids were iso-C_16:0 and C_17:0 10-methyl. Phospholipid profiles were composed of phosphatidylinositol mannoside (PIM), lyso-phosphatidylethanolamine (lyso-PE), phosphatidylethanolamine (PE), methylphosphatidylethanolamine (PME), diphosphatidylglycerol (DPG), and phosphatidylglycerol (PG). The G + C content of DNA was 71.2 mol%. Strain PA1-10^T showed the highest 16S rRNA gene sequence similarity with Nonomuraea candida JCM 15928^T (98.35%) and shared the same node with Nonomuraea maritima JCM 18321^T in the phylogenetic tree analysis. Based on the phenotypic characteristics, DNA-DNA relatedness, and average nucleotide identity (ANI), the strain is considered to represent a novel species of the genus Nonomuraea, for which the name Nonomuraea phyllanthi is proposed. The type strain is PA1-10^T (= JCM 33073^T = NBRC 112774^T = TISTR 2497^T).

nov., a new member of the family Streptosporangiaceae

A novel aerobic, spore-forming, marine actinomycete, designated strain LHW63015^T, was isolated from a Craniella marine sponge collected in the South China Sea. The strain formed extensively branched substrate and aerial mycelia which carried long and crooked spore chains composed of ridged spores and spherical pseudosporangia. Strain LHW63015^T contained meso-diaminopimelic acid as the diagnostic diamino acid. Glucose, ribose, mannose, galactose and madurose occured in whole-cell hydrolysates. The predominant polar lipids were hydroxyl-phosphatidylethanolamine, phosphoglycolipid and ninhydrin-positive phosphoglycolipid. MK-10(H4) and MK-10(H6) were the predominant menaquinones. The major fatty acids were 10-methyl C17 : 0 and C17 : 1ω8c. The G+C content of the genomic DNA was 70.8 mol%. In phylogenetic analysis based on 16S rRNA gene sequences, strain LHW63015^T fell within the family Streptosporangiaceae and formed a distinct monophyletic lineage adjacent to the genus Sphaerisporangium, and shared the highest 16S rRNA gene sequence similarity of 96.2 % with Sphaerisporangium album YIM 48782^T. On the basis of the polyphasic evidence, a novel genus and species of the family Streptosporangiaceae, for which the name Spongiactinospora rosea gen. nov., sp. nov., is proposed, with the type strain LHW63015^T (=DSM 106635^T=CCTCC AA 2018019^T).

Gyrase subunit B amino acid signatures for the actinobacterial family Streptosporangiaceae

Higher order taxonomic assignments (family level and above) in the phylum Actinobacteria are currently based only on 16S-rRNA gene sequence analyses. Additional molecular markers need to be identified to increase the number of reference points for defining actinobacterial families and other higher taxa. Furthermore, since most novel actinobacterial taxa are defined at the level of species and genera, it is necessary to define molecular signatures at the genus level to enhance the robustness of genus descriptions. The current use of chemotaxonomic markers to define genera could be improved by the identification of genus-specific molecular signatures. In this study, GyrB amino acid sequences for members of the family Streptosporangiaceae were analysed for molecular signatures. Phylogenetic analyses showed that the gyrB gene tree supported the composition of the currently recognised genera in this family. The catalytically important amino acids were identified in the GyrB sequences, as were the GHKL superfamily motifs. Examination of GyrB protein sequence alignments revealed that there are genus-specific sequences for most of the multi-species genera and genus-defining amino acid insertions for the genera Herbidospora and Microbispora. Furthermore, there are GyrB signature amino acids which distinguish the family Streptosporangiaceae from the family Nocardiopsaceae.

Complete genome sequence of Streptosporangium roseum type strain (NI 9100)

Streptosporangium roseum Crauch 1955 is the type strain of the species which is the type species of the genus Streptosporangium. The 'pinkish coiled Streptomyces-like organism with a spore case' was isolated from vegetable garden soil in 1955. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Streptosporangiaceae, and the second largest microbial genome sequence ever deciphered. The 10,369,518 bp long genome with its 9421 protein-coding and 80 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.