Saccharopolyspora cavernae sp. nov., a novel actinomycete isolated from the Swallow Cave in Yunnan, south-west China

Gulosibacter macacae sp. nov., a novel actinobacterium isolated from Macaca mulatta faeces

A novel Gram-stain-positive, aerobic, non-spore-forming, irregular short rod-shaped actinobacterial strain, designated YIM 102482-1T, was isolated from the faeces of Macaca mulatta. Strain YIM 102482-1T grew optimally at 30–37 °C, at pH 8.0 and in the presence of 1.0–3.0% (w/v) NaCl. Similarly, analysis based on 16S rRNA gene sequences showed that strain YIM 102482-1T was a member of the genus Gulosibacter and most closely related to Gulosibacter feacalis NBRC 15706T (97.6 %), Gulosibacter bifidus NBRC 103089T (97.6 %), Gulosibacter chungangensis KCTC 13959T (96.4 %) and Gulosibacter molinativorax DSM 13485T (96.0 %), respectively. Furthermore, phylogenetic trees based on 16S rRNA gene sequences and genomic sequences demonstrated that strain YIM 102482-1T formed a distinct branch with all type strains of the genus Gulosibacter . The major whole-cell sugars and cellular fatty acids (>10.0 %) were ribose and rhamnose, and anteiso-C15 : 0, iso-C16 : 0 and C16 : 0, respectively. The predominant menaquinone was MK-9, and 2,4-diaminobutyric acid and ornithine were the diagnostic diamino acids in the cell-wall peptidoglycan. The dominant polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipid. The DNA G+C content of YIM 102482-1T was 63.0 mol%. Based on analysis results of physiological, biochemical and chemotaxonomic data, strain YIM 102482-1T represents a novel species of the genus Gulosibacter , for which the name Gulosibacter macacae sp. nov. is proposed. The type strain is YIM 102482-1T(=DSM 102156T=CCTCC AB 2016023T).

Saccharopolyspora coralli sp. nov. a novel actinobacterium isolated from the stony coral Porites

A novel Gram-stain-positive, aerobic, non-motile actinobacterium, designated strain E2A^T, was isolated from a coral sample and examined using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain E2A^T formed a distinct phyletic lineage in the genus Saccharopolyspora and was closely related to S. cavernae CCTCC AA 2012022^T (96.4 %) and S. lacisalsi CCTCC AA 2010012^T (95.3 %). The isolate grew at 15-35 °C, pH 5-12 and in the presence of 1-16 % (w/v) NaCl. The cell-wall diamino acid was meso-DAP. Major fatty acids identified were iso-C_15 : 0, iso-C_16 : 0 and C_17 : 1  ω8c. The predominant menaquinone was MK-9(H₄). The polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, one unidentified glycolipid, one unidentified phospholipid and one unidentified aminolipid. The genomic DNA G+C content was 68.6 mol%. Based on the data from the polyphasic taxonomic study reported here, strain E2A^T represents a novel species within the genus Saccharopolyspora, for which the name Saccharopolyspora coralli sp. nov. is proposed. The type strain is E2A^T=(JCM 31844^T=MCCC 1A17150^T).

Cave Actinobacteria as Producers of Bioactive Metabolites

Recently, there is an urgent need for new drugs due to the emergence of drug resistant pathogenic microorganisms and new infectious diseases. Members of phylum Actinobacteria are promising source of bioactive compounds notably antibiotics. The search for such new compounds has shifted to extreme or underexplored environments to increase the possibility of discovery. Cave ecosystems have attracted interest of the research community because of their unique characteristics and the microbiome residing inside including actinobacteria. At the time of writing, 47 species in 30 genera of actinobacteria were reported from cave and cave related habitats. Novel and promising bioactive compounds have been isolated and characterized. This mini-review focuses on the diversity of cultivable actinobacteria in cave and cave-related environments, and their bioactive metabolites from 1999 to 2018.

Saccharopolyspora spongiae sp. nov., a novel actinomycete isolated from the marine sponge Scopalina ruetzleri (Wiedenmayer, 1977)

A novel marine actinomycete, designated strain CMAA 1452T, was isolated from the sponge Scopalina ruetzleri collected from Saint Peter and Saint Paul Archipelago, in Brazil, and subjected to a polyphasic taxonomic investigation. The organism formed a distinct phyletic line in the Saccharopolyspora 16S rRNA gene tree and had chemotaxonomic and morphological properties consistent with its classification in this genus. It was found to be closely related to Saccharopolyspora dendranthemae KLBMP 1305T (99.5% 16S rRNA gene sequence similarity) and shared similarities of 99.3, 99.2 and 99.0 % with 'Saccharopolyspora endophytica' YIM 61095, Saccharopolyspora tripterygii YIM 65359T and 'Saccharopolyspora pathumthaniensis' S582, respectively. DNA-DNA relatedness values between the isolate and its closest phylogenetic neighbours, namely S. dendranthemae KLBMP 1305T, 'S. endophytica' YIM 61095 and S. tripterygii YIM 65359T, were 53.5, 25.8 and 53.2 %, respectively. Strain CMAA 1452T was also distinguished from the type strains of these species using a range of phenotypic features. On the basis of these results, it is proposed that strain CMAA 1452T (=DSM 103218T=NRRL B-65384T) merits recognition as the type strain of a novel Saccharopolyspora species, Saccharopolyspora spongiae sp. nov.

Herbihabitans rhizosphaerae gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from rhizosphere soil of the herb Limonium sinense (Girard)

The taxonomic position of an actinobacterium, designated CPCC 204279T, which was isolated from a rhizosphere soil sample of the herb Limonium sinense collected from Xinjiang Province, China, was established using a polyphasic approach. Whole-cell hydrolysates of strain CPCC 204279T contained galactose and arabinose as diagnostic sugars and meso-diaminopimelic acid as the diamino acid. The muramic acid residues in the peptidoglycan were N-acetylated. The predominant menaquinone was MK-9(H4). The phospholipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids were iso-C16 : 0, iso-C16 : 0 2-OH, C16 : 1ω9c, iso-C16 : 1 and C16 : 0. The genomic DNA G+C content was 73.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CPCC 204279T should be placed in the family Pseudonocardiaceae, in which the strain formed a distinct lineage next to the genus Actinophytocola. Signature nucleotides in the 16S rRNA gene sequence showed that the strain contained the Pseudonocardiaceae family-specific 16S rRNA signature nucleotides and a genus-specific diagnostic nucleotide signature pattern. The combination of phylogenetic analysis and phenotypic characteristics supported the conclusion that strain CPCC 204279T represents a novel species of a new genus in the family Pseudonocardiaceae, for which the name Herbihabitans rhizosphaerae gen. nov., sp. nov. is proposed. Strain CPCC 204279T (=NBRC 111774T=DSM 101727T) is the type strain of the type species.

Hamadaea flava sp. nov., isolated from a soil sample and emended description of the genus Hamadaea

A Gram-stain-positive, aerobic and non-motile actinobacterial strain, designated YIM C0533T, was isolated from a soil sample collected from Shiling county, Yunnan province, south-west China. The isolate grew at 15-37 °C, pH 6.0-8.0 and in the presence of 0-3% (w/v) NaCl. The whole-cell hydrolysates contained meso-diaminopimelic acid, xylose, galactose, mannose, ribose, arabinose, glucose and rhamnose. The acyl type of muramic acid was glycolyl. The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified phospholipid. The major cellular fatty acids were iso-C16:0, 10-methyl C17:0 and iso-C15 : 0.MK-9(H6) was the predominant menaquinone. The genomic DNA G+C content was determined to be 69.4 mol%. These chemotaxonomic data and the morphological properties were consistent with those of the genus Hamadaea. The strain showed highest sequence similarities to Hamadaea tsunoensis CGMCC 4.1403T on phylogenetic analysis of 16S rRNA gene sequences and was found to form a coherent cluster in the neighbour-joining tree. The DNA-DNA hybridization experiment indicated that the DNA-DNA relatedness value between strain YIM C0533T and H. tsunoensis CGMCC 4.1403T was 34.4±1.3 %. In addition, the results of physiological and biochemical tests allowed the isolate to be differentiated phenotypically from H. tsunoensis CGMCC 4.1403T. On the basis of data from this polyphasic study, strain YIM C0533T is characterized as a novel species of the genus Hamadaea, for which the name Hamadaea flava sp. nov. is proposed. The type strain is YIM C0533T (=CPCC 204160T=KCTC 39591T=CGMCC 4.7289T). An emended description of the genus Hamadaea is also provided.

Umezawaea endophytica sp. nov., isolated from tobacco root samples

Two Gram-staining positive, aerobic and non-motile actinomycete strains, designated YIM 2047X(T) and YIM 2047D, were isolated from tobacco root samples collected from Shiling county, Yunnan province, South-West China. The isolates grew at 15-40 °C, pH 6.0-8.0 and 0-4.5 % NaCl (w/v). The whole-cell hydrolysates contained meso-diaminopimelic acid, galactose, mannose, ribose and rhamnose. The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major cellar fatty acids identified were iso-C14:0, iso-C15:0, anteiso-C15:0, iso-C16:0, C16:0, C17:1 ω8c and C17:0. MK-9 (H4) was the predominant menaquinone. The genomic DNA G+C contents were 73.4 and 74.2 mol%, respectively. These chemotaxonomic data, together with their morphological properties, were consistent with the assignment of the two strains to the genus Umezawaea. They showed highest similarities to Umezawaea tangerina JCM 10302(T) on phylogenetic analysis of their 16S rRNA gene sequences and were found to form a coherent cluster. However, the DNA-DNA hybridization values of YIM 2047X(T) and YIM 2047D with U. tangerina JCM 10302(T) were 46.5 ± 3.1 and 57.5 ± 1.6 %, respectively; while the reassociation value between themselves was 80.4 ± 2.3 %. The results of physiological and biochemical tests allowed the two new isolates to be differentiated phenotypically from the recognized strain U. tangerina JCM 10302(T). On the basis of results from this polyphasic study, the strains were characterized as a novel species of the genus Umezawaea, for which the name Umezawaea endophytica sp. nov. is proposed. The type strain is YIM 2047X(T) (=KCTC 39538(T) = CPCC 204132(T)).

Saccharopolyspora indica sp. nov., an actinomycete isolated from the rhizosphere of Callistemon citrinus (Curtis)

A novel actinomycete strain, designated VRC122T, was isolated from a Callistemon citrinus rhizosphere sample collected from New Delhi, India, and its taxonomic status was determined by using a polyphasic approach. Strain VRC122T was a Gram-stain-positive, aerobic, non-motile, non-acid–alcohol-fast strain. Phylogenetic analysis based on 16S rRNA gene sequences showed the strain was placed in a well-separated sub-branch within the genus Saccharopolyspora . The highest levels of 16S rRNA gene sequence similarity were found with Saccharopolyspora hirsuta subsp. kobensis JCM 9109T (98.71 %), Saccharopolyspora antimicrobica I05-00074T (98.69 %) and Saccharopolyspora jiangxiensis W12T (98.66 %); 16S rRNA gene sequence similarities with type strains of all other species of the genus Saccharopolyspora were below 98 %. Chemosystematic studies revealed that it contained meso-diaminopimelic acid. Arabinose and galactose were the predominant whole-cell sugars. Diagnostic polar lipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylcholine. MK-9(H6) was the predominant menaquinone. C14 : 0, C16 : 0, iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, anteiso-C15 : 0, anteiso-C17 : 0, C17 : 0 cyclo and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) were the major cellular fatty acids. The G+C content of the genomic DNA was 69.5 mol%. The results of DNA–DNA hybridization (30 %, 22 % and 25 %, respectively) with type strains of the above-mentioned species, in combination with differences in physiological and biochemical data supported that strain VRC122T represents a novel species of the genus Saccharopolyspora , for which the name Saccharopolyspora indica sp. nov., is proposed. The type strain is VRC122T ( = KCTC 29208T = MTCC 11564T = MCC 2206T = ATCC BAA-2551T).

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send a covering letter, a copy of, or a link to the published paper and electronic copies of certificates of deposit from at least two culture collections in different countries to the IJSEM Editorial Office (ijsem@sgm.ac.uk) for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.