- Volume 59, Issue 6, 2009

As part of an antibiotic-screening programme, an actinomycete, designated strain SPRT, was isolated from soil collected from the banks of the Umgeni River, KwaZulu-Natal Province, South Africa. The isolate produced branching vegetative mycelia with sporangiophores bearing sporangia developing at a late stage of growth. The sporangia contained smooth, almond-shaped, non-motile spores. Strain SPRT exhibited antibiosis against various Gram-positive and Gram-negative bacteria, including Enterococcus faecium VanA (a vancomycin-resistant strain), Mycobacterium aurum A+ and Escherichia coli ATCC 25922. The chemotaxonomic characteristics of the strain, with the exception of the phospholipid pattern, corresponded with those of the members of the family Streptomycetaceae Waksman and Henrici 1943. Furthermore, phylogenetic analysis based on 16S rRNA genes showed that the strain was closely related to members of the genus Streptomyces, which supports its classification in the family Streptomycetaceae. Thus strain SPRT represents a novel species of the genus Streptomyces, for which the name Streptomyces polyantibioticus sp. nov. is proposed. The type strain is SPRT (=DSM 44925T=NRRL B-24448T).

A Gram-positive actinobacterium, designated strain YIM 90716T, was isolated from a saline soil sample collected from Ganjiahu Suosuo Forest National Nature Reserve in Xinjiang Province, north-west China. The new isolate contained lysine, glutamic acid and alanine with peptidoglycan type Lys–Ala3 (variation A3α). The major phospholipids were phosphatidylglycerol and diphosphatidylglycerol. The predominant menaqinone was MK-7(H2). The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The DNA G+C content of strain YIM 90716T was 68.0 mol%. Chemotaxonomic properties supported the affiliation of strain YIM 90716T to the genus Kocuria. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism was related most closely to Kocuria kristinae DSM 20032T (96.8 % similarity) and showed lower levels of 16S rRNA gene similarity (<96.5 %) with the type strains of other species of the genus Kocuria. The results of fatty acid analysis and physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain YIM 90716T from its closest relatives. On the basis of data from the present polyphasic study, strain YIM 90716T is considered to represent a novel species of the genus Kocuria, for which the name Kocuria halotolerans sp. nov. is proposed. The type strain is YIM 90716T (=DSM 18442T=KCTC 19172T=CCTCC AB 206069T).

The taxonomic position of an actinomycete isolated from a lead-polluted soil in Gansu province, north-west China, was determined by using a polyphasic approach. Chemical and morphological properties of the isolate, designated strain CCNWHX 13-160T, were similar to those of streptomycetes. Analysis of the almost complete 16S rRNA gene sequence placed strain CCNWHX 13-160T in the genus Streptomyces where it formed a distinct phyletic line with recognized Streptomyces species. The strain was most similar to Streptomyces pseudovenezuelae NBRC 12904T (98.9 %) and Streptomyces resistomycificus NBRC 12814T (98.8 %). Furthermore, DNA–DNA hybridization studies between the novel isolate and these two strains showed relatedness values of 49.7±0.8 and 43.2±1.1 %, respectively. It is proposed that strain CCNWHX 13-160T (=ACCC 41207T=HAMBI 2991T) be classified as the type strain of a novel species in the genus Streptomyces, Streptomyces plumbiresistens sp. nov. The MIC of Pb2+ for growth of strain CCNWHX 13-160T was 4.0 mM.

A novel, non-pigmented, slow-growing mycobacterium was identified on the basis of biochemical and nucleic acid analyses, as well as growth characteristics. Three isolates were cultured from clinical samples (two from sputum and one from pus in lymph nodes) obtained from three immunocompetent patients with infections. Bacterial growth occurred at 28–42 °C on Middlebrook 7H11-OADC agar. The isolates showed negative results for Tween hydrolysis, nitrate reductase, semiquantitative catalase, urease activity, 3 day arylsulfatase activity, pyrazinamidase, tellurite reduction and niacin accumulation tests, but positive results for 14 day arylsulfatase activity and heat-stable catalase tests. The isolates contained α-, keto-, and dicarboxymycolates in their cell walls. Sequence analysis revealed that all isolates had identical, unique 16S rRNA sequences. Phylogenetic analysis of the 16S rRNA, rpoB, hsp65 and sodA gene sequences confirmed that these isolates are unique but closely related to Mycobacterium celatum. DNA–DNA hybridization of the isolates demonstrated less than 50 % reassociation with M. celatum and Mycobacterium branderi. On the basis of these findings, a novel species designated Mycobacterium kyorinense sp. nov. is proposed. The type strain is KUM 060204T (=JCM 15038T=DSM 45166T).

Strains KFC-22T and SPC-20T are yellow-pigmented, Gram-positive, aerobic, non-motile, rod-shaped bacteria that were isolated from a soil sample near the Kafni glacier in the Himalayan mountain ranges in India, and from a spade core sediment sample from the Antarctic Ocean at Larsemann Hill, respectively. In both cases, the cell-wall peptidoglycan contained 2,4-diaminobutyric acid as the diamino acid, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 were the predominant fatty acids and MK-11 was the major isoprenoid quinone in the cell membrane. On the basis of the above-mentioned characteristics, both strains can be assigned to the genus Leifsonia. The strains share 16S rRNA gene sequence similarity of 97.7 % and DNA relatedness of only 10 %, indicating that they represent different species. A blast analysis indicated that Leifsonia pindariensis PON10T was the closest phylogenetic neighbour of strains SPC-20T and KFC-22T, showing 16S rRNA gene sequence similarities of 97.3 and 97.7 %, respectively. However, at the whole-genome level, strains KFC-22T and SPC-20T shared 42 and 11 % DNA–DNA relatedness, respectively, with L. pindariensis PON10T. In addition, both strains exhibited several phenotypic differences with respect to L. pindariensis PON10T. Thus, on the basis of the differences that the two strains exhibited with respect to L. pindariensis, both were identified as representing novel species of the genus Leifsonia, for which the names Leifsonia kafniensis sp. nov. (type strain KFC-22T =NCCB 100216T =LMG 24362T) and Leifsonia antarctica sp. nov. (type strain SPC-20T =NCCB 100227T =LMG 24541T) are proposed.

A novel actinomycete, designated strain RP-AC36T, was isolated from a cliff-associated plant (Peucedanum japonicum Thunb.) in the Republic of Korea and its taxonomic status was determined by using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequence analysis showed that the organism formed a distinct clade within the radiation of the genus Amycolatopsis. The chemotaxonomic properties supported the assignment of the isolate to the genus Amycolatopsis. High levels of 16S rRNA gene sequence similarity were found with Amycolatopsis sulphurea (98.2 %), Amycolatopsis halotolerans (97.5 %) and Amycolatopsis jejuensis (97.1 %). DNA–DNA relatedness data, together with phenotypic differences, clearly distinguished the isolate from its closest relative A. sulphurea. Based on the phenotypic and genotypic evidence, it is suggested that the organism be assigned as representing a novel species of the genus Amycolatopsis, for which the name Amycolatopsis ultiminotia sp. nov. is proposed. The type strain is RP-AC36T (=NRRL B-24662T=DSM 45180T).

A strictly anaerobic, Gram-positive, short-rod/coccobacillus-shaped bacterial strain, designated 7-10-1-bT, was isolated from the colon of a patient suffering from acute Crohn's disease. The isolate formed small, pale-white, semi-translucent colonies on solid cultivation media. The strain was catalase-positive and metabolized only a small number of carbon sources. Whole-cell fatty acids consisted predominantly of saturated fatty acids (89 %), of which 15 : 0 anteiso was the major component. The polar lipids phosphatidylglycerol and diphosphatidylglycerol as well as four glycolipids were identified. 16S rRNA gene sequence analysis revealed that the isolate represents a distinct lineage within the family Coriobacteriaceae and has 94.6 % identity to the type strain of [Eggerthella] hongkongensis, the phylogenetically closest bacterial species. On the basis of the analyses performed, the new genus and species Gordonibacter pamelaeae gen. nov., sp. nov. is described, with strain 7-10-1-bT (=DSM 19378T =CCUG 55131T) as the type and only strain of Gordonibacter pamelaeae. Also, based on the chemotaxonomic data obtained for all type strains of the neighbouring genus Eggerthella, we propose that Eggerthella hongkongensis Lau et al. 2006 be transferred to a new genus as Paraeggerthella hongkongensis gen. nov., comb. nov.; the type strain of Paraeggerthella hongkongensis is HKU10T (=DSM 16106T =CCUG 49250T).

An actinomycete strain, isolated from the marine sponge Axinella polypoides collected from Banyuls-sur-Mer, France, was characterized using a polyphasic approach. Based on its chemotaxonomic and morphological characteristics, strain Pol001T belongs to the genus Streptomyces. The strain is characterized by ll-diaminopimelic acid in the cell wall, menaquinones MK-9(H4, H6, H8) and a DNA G+C content of 71.0 mol%. It forms a separate phyletic line based on phylogenetic analyses of the nearly complete 16S rRNA gene sequence. Strain Pol001T could be differentiated from other closely related Streptomyces species with validly published names by phenotypic and genotypic analysis. DNA–DNA hybridization between strain Pol001T and closely related reference strains further confirmed that strain Pol001T represents a novel taxon of the genus Streptomyces. Therefore, it is proposed that strain Pol001T represents a novel species in the genus Streptomyces, Streptomyces axinellae sp. nov.; the type strain is Pol001T (=DSM 41948T =CIP 109838T).

A Gram-positive, short diphtheroid-shaped organism was isolated from a sow's placenta of an abortion. This novel isolate, strain MurakamiT, was examined physiologically, chemotaxonomically and phylogenetically. Cells had an irregular V-shaped or palisade arrangement. Colonies appeared translucent on TMVL agar. Cells were strictly anaerobic, negative for catalase and gelatin decomposition and positive for nitrate reduction and soluble starch hydrolysis. Fourteen sugars including glucose were utilized as carbon sources for growth, but 15 sugars including arabinose were not. α-Galactosidase, β-galactosidase, α-glucosidase and leucine arylamidase were produced, but β-glucosidase was not. Fermentation products were lactic, succinic and acetic acids. Sugars of whole cells consisted of rhamnose and ribose. The amino-acid composition of the peptidoglycan was glutamic acid, alanine and lysine in the molar ratio of 1 : 2 : 1. The main fatty acid components of whole cells were C14 : 0, C16 : 0, C16 : 1 ω7 and C18 : 1 ω9. The bacterial menaquinone was MK-10(H4). The polar lipids were phosphatidylethanolamine and two unknown phosphatidylinositol mannosides. The G+C content of the genomic DNA of strain MurakamiT was 63.8 mol%. Phylogenetic analysis of 16S rRNA gene sequences from strain MurakamiT and other members of the genus Arcanobacterium supported the phenotypic findings that strain MurakamiT represents a novel species, for which the name Arcanobacterium abortisuis sp. nov. is proposed. The type strain is MurakamiT (=ATCC BAA-1522T =DSM 19515T =JCM 14813T).

A novel Gram-positive-staining actinomycete designated strain GMKU095T was isolated from surface-sterilized roots of Acacia auriculiformis A. Cunn. ex Benth. (earpod wattle). The organism produced branching mycelium. The spores were non-motile and had a spiny surface. Growth of strain GMKU095T occurred at 18–42 °C, pH 5.0–8.0 and at NaCl concentrations up to 5 %. Whole-cell hydrolysates contained arabinose and galactose as major characteristic sugars. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The glycan moiety of the murein contained acetyl residues. The menaquinone was MK-8(H4); mycolic acids were not detected. The G+C content of the DNA was 71.6 mol%. iso-C16 : 0 was detected as the major cellular fatty acid. Comparative studies of 16S rRNA gene sequences indicated that the strain was phylogenetically related to members of the genus Pseudonocardia. The most closely related type strain is Pseudonocardia spinosispora IMSNU 50581T, which is 96.2 % similar in 16S rRNA gene sequence. On the basis of the genotypic and phenotypic properties presented, a novel species of the genus Pseudonocardia is proposed, Pseudonocardia acaciae sp. nov. The type strain is strain GMKU095T (=NRRL B-24609T =BCC 28481T =TISTR 1862T =NBRC 104274T).

An endophytic actinomycete, strain YIM 65188T, was isolated from surface-sterilized tissue of Sedum sp. collected from Yunnan province, south-west China, and characterized by using a polyphasic approach. Analysis of the 16S rRNA gene sequence showed that strain YIM 65188T is a member of the genus Streptomyces and exhibited 97.5 and 96.3 % gene sequence similarities to Streptomyces specialis GW41-1564T and Streptomyces hainanensis YIM 47672T, respectively, whereas low sequence similarity values (<95.2 %) distinguished strain YIM 65188T from all other Streptomyces species with validly published names. Strain YIM 65188T had a unique menaquinone composition, with the predominant quinones being MK-11(H6) and MK-10(H6), with moderate amounts of MK-10(H8), MK-11(H8), MK-9(H8), MK-11(H4), MK-9(H6) and MK-10(H4). Similarly, the closest phylogenetic relative, S. specialis GW41-1564T, also had an unusual quinone composition, with the predominant menaquinones MK-10(H4) and MK-10(H6) and minor amounts of MK-9(H4) and MK-9(H6). The DNA–DNA hybridization value between strain YIM 65188T and S. specialis GW41-1564T was 42.7 %. On the basis of phenotypic and phylogenetic characteristics, strain YIM 65188T was identified as a novel species of the genus Streptomyces for which the name Streptomyces sedi sp. nov. is proposed, with YIM 65188T (=CCTCC AA 208020T =DSM 41942T) as the type strain.

Two strains of nocardioform actinomycetes, isolated from soil and plant litter in Yamanashi prefecture, Japan, showed substrate mycelium with purple to dark-red colours. 16S rRNA gene sequence analysis indicated that the organisms belonged to the family Actinosynnemataceae and were related closely to Saccharothrix strains (96.7–98.0 % sequence similarity). The isolates contained MK-9(H4) as the predominant menaquinone, meso-diaminopimelic acid, galactose as the diagnostic whole-cell sugar and phosphatidylethanolamine as the predominant polar lipid. Based on a combination of cultural, physiological and chemotaxonomic properties, in addition to the phylogenetic analysis and DNA–DNA hybridization data, we propose a novel species, Saccharothrix violaceirubra sp. nov., for these strains, with the type strain YU 692-1T (=NBRC 102064T =KCTC 19326T).

Five independent strains, isolated from clinical samples but probably not responsible for disease, revealed phenotypic and genotypic features that appeared to exclude their belonging to any of the recognized Mycobacterium species. The strains, which are non-pigmented rapid growers, presented a cell-wall lipid pattern resembling those of Mycobacterium brumae and Mycobacterium fallax. Sequencing of the 16S rRNA, hsp65 and rpoB genes and the 16S–23S rRNA gene internal transcribed spacer (ITS) revealed that the strains are clearly distinct from every other Mycobacterium species. While the 16S rRNA and rpoB genes were characterized by a single sequevar, two sequevars were detected in hsp65 and three in the ITS. The divergence shown in the latter region was striking, in which only two short regions (less than 150 bp in all) were comparable with other mycobacteria, apart from Mycobacterium monacense and Mycobacterium gilvum. The PCR restriction analysis pattern of the novel strains also differs from any reported to date. The name Mycobacterium insubricum sp. nov. is proposed for the novel species; the type strain is FI-06250T (=DSM 45132T =CIP 109609T).

Two novel micro-organisms, designated strains YIT 10443T and YIT 10738, were isolated from airag, a traditional fermented mare's milk from Mongolia. The two strains were Gram-positive-staining, non-motile, asporogenous, catalase-negative, facultatively anaerobic rods of various shapes. Comparative analyses of 16S rRNA and ClpC ATPase (clpC) gene sequences and the presence of fructose-6-phosphate phosphoketolase (F6PPK) demonstrated that the novel strains were members of the genus Bifidobacterium. On the basis of 16S rRNA gene sequence similarity, the type strains of Bifidobacterium minimum (96.6 %) and Bifidobacterium psychraerophilum (95.7 %) were the closest neighbours of the novel strains, and DNA–DNA reassociation values with these strains were found to be lower than 15 %. The phenotypic and genotypic features demonstrated that the two strains represent a single, novel Bifidobacterium species, for which the name Bifidobacterium mongoliense sp. nov. is proposed. The type strain is YIT 10443T (=JCM 15461T =DSM 21395T).

A Gram-positive, slightly acid–alcohol-fast, carbon monoxide-oxidizing bacterium, strain Y2T, was isolated from a soil sample collected from a roadside in Seoul, Korea. On the basis of 16S rRNA gene sequence comparative analyses, strain Y2T was shown to belong to the genus Tsukamurella and was most closely related to Tsukamurella tyrosinosolvens DSM 44234T (GenBank accession no. AY238514; 99.8 %). The predominant fatty acids were C18 : 1 ω9c and C16 : 0. The cell-wall peptidoglycan of strain Y2T contained meso-diaminopimelic acid as the diagnostic diamino acid. Strain Y2T contained galactose and arabinose as the whole cell sugars. The DNA G+C content was 77 mol%. The DNA–DNA relatedness value between strain Y2T and T. tyrosinosolvens DSM 44234T was 62.7 %. Based on the combination of the carbon source utilization pattern, fatty acid profile, cell-wall chemotype, DNA G+C content and DNA–DNA hybridization experiments, it is proposed that strain Y2T (=KCCM 42885T=JCM 15482T) represents the type strain of a novel species, Tsukamurella carboxydivorans sp. nov.

A Gram-positive-staining, coccoid-shaped, oxidase-negative, non-spore-forming, non-motile bacterium, strain KSS-17SeT, was isolated from a metalworking fluid. On the basis of its major fatty acid (ai-C15 : 0) and 16S rRNA gene sequence similarity, the strain grouped with Tessaracoccus bendigoensis and Tessaracoccus flavescens, sharing 95.3 and 97.4 % 16S rRNA gene sequence similarity with the respective type strains. Similarities with other established species of the genera Luteococcus, Propioniferax and Granulicoccus were lower than 95.5 %. The quinone system was characterized by the major menaquinone MK-9(H4). In the polar lipid profile, diphosphatidylglycerol, phosphatidylglycerol, an unknown glycolipid and an unknown polar lipid were detected as major compounds. Additionally, three unknown glycolipids and minor amounts of phosphatidylethanolamine, two unknown aminolipids and two unknown polar lipids were detected. Phosphatidylinositol was present only in trace amounts. Predominant polyamines were spermine and spermidine. ll-Diaminopimelic acid was identified as the diagnostic diamino acid in the cell wall. The strain showed clear differences in phenotype (including chemotaxonomic features) from both Tessaracoccus species and members of the other above-mentioned genera. DNA–DNA hybridization between KSS-17SeT and T. bendigoensis Ben-106T and T. flavescens SST-39T yielded similarities of 15.1 and 21.0 %, respectively. It is evident that the organism represents a novel species, for which the name Tessaracoccus lubricantis sp. nov. is proposed. The type strain is KSS-17SeT (=DSM 19926T =CCUG 55516T).

Two yellow-coloured bacterial strains, designated JS13-10T and JS16-4T, were isolated from soil from Jeju Island, Republic of Korea. On the basis of 16S rRNA gene sequence analysis, the strains were found to be affiliated with members of the genus Chitinophaga. Phenotypically, the novel strains were identified as being different from each other and from recognized species of the genus Chitinophaga. DNA–DNA hybridization tests between the two novel strains and closely related Chitinophaga reference strains produced DNA relatedness values that were significantly lower (<36 %) than those generally accepted as the highest threshold for the phylogenetic definition of a species. On the basis of their distinct taxonomic characteristics, these strains represent two novel species of the genus Chitinophaga, for which the names Chitinophaga niabensis sp. nov. (type strain JS13-10T=KACC 12952T=JCM 15440T) and Chitinophaga niastensis sp. nov. (type strain JS16-4T=KACC 12954T=JCM 15441T) are proposed.

The taxonomic status of a yellow- to light orange-coloured strain isolated from soil of a Korean ginseng field was established based on a polyphasic investigation. The novel isolate, strain GR10-1T, was an obligately aerobic, Gram-staining-negative, non-motile, flexirubin-pigment-producing, short rod-shaped bacterium. The strain grew optimally at 28–30 °C, at pH 7.0 and in the presence of 0–1 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that the new isolate showed the highest sequence similarities with Niabella aurantiaca R2A15-11T (95.1 %) and Niabella soli JS13-8T (94.6 %). The DNA G+C content of strain GR10-1T was 43 mol%. It contained iso-C15 : 1 G (36.4 %) and iso-C15 : 0 (32.8 %) as the major fatty acids (>10 %) and MK-7 as the major isoprenoid quinone. On the basis of evidence from our polyphasic taxonomic study, it was concluded that strain GR10-1T should be classified within a novel species of the genus Niabella, for which the name Niabella ginsengisoli sp. nov. is proposed. The type strain is GR10-1T (=KACC 13021T =JCM 15444T).