- Volume 60, Issue 7, 2010

A novel streptomycete, designated strain HM 35T, was isolated from soil in Isfahan city, Iran. Strain HM 35T produced a branched substrate mycelium and aerial hyphae that developed into short, compact, spiral spore chains with grey rugose spores at the tips of the aerial hyphae. On some media, these spirals coalesced into dark masses of spores with age. Whole-cell hydrolysates of strain HM 35T contained ll-diaminopimelic acid, glucose and ribose. Phospholipids detected were phosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine, phosphatidylinositol mannosides, hydroxy-phosphatidylethanolamine, lyso-phosphatidylethanolamine and hydroxy-lyso-phosphatidylethanolamine. MK-9(H4), MK-9(H6) and MK-9(H8) were the predominant menaquinones. The major fatty acids were iso- and anteiso-branched components. The chemotaxonomic characteristics of the novel isolate matched those described for members of the genus Streptomyces. Based on 16S rRNA gene sequence analysis, strain HM 35T showed highest similarity to Streptomyces rapamycinicus NRRL 5491T (99.2 %), Streptomyces violaceusniger DSM 40563T (99.1 %), Streptomyces javensis DSM 41764T (99.1 %) and Streptomyces yogyakartensis DSM 41766T (99.1 %). The novel strain formed a distinct monophyletic line within the 16S rRNA gene sequence tree. The level of DNA–DNA relatedness between strain HM 35T and the type strain of S. rapamycinicus was 72.7 %. Strain HM 35T showed the typical morphology found among members of the S. violaceusniger/Streptomyces hygroscopicus group but could be clearly differentiated from closely related species based on other phenotypic markers. Phenotypic and genotypic data thus indicate that strain HM 35T represents a novel species of the genus Streptomyces, for which the name Streptomyces iranensis is proposed. The type strain is HM 35T (=DSM 41954T=CCUG 57623T).

A Gram-positive, aerobic, non-motile, rod-shaped actinomycete, designated strain DSW-2T, was isolated from a seaweed sample collected around Mara Island, Jeju, Republic of Korea. Comparative 16S rRNA gene sequence analysis showed that strain DSW-2T belongs to the suborder Micrococcineae and forms a distinct clade separated from representatives of the several families of this order. Levels of 16S rRNA gene sequence similarity between the novel strain and members of this suborder were lower than 96.4 %. The peptidoglycan type is A3α with Lys–Ser as the interpeptide bridge. Whole-cell sugars are glucose and galactose. The major menaquinone is MK-9(H4). The predominant fatty acid is ai-C15 : 0. The polar lipids are phosphatidylglycerol and phosphatidylinositol. The DNA G+C content was 68.3 mol%. On the basis of the chemotaxonomic markers and phylogenetic distinctiveness presented here, it is evident that the isolate represents a novel taxon within the suborder Micrococcineae. The name Koreibacter algae gen. nov., sp. nov. is proposed, with the type strain DSW-2T (=KCTC 13436T =DSM 22126T).

Gram-positive, non-spore-forming rods were isolated from a human osteo-articular sample (strain 7400942T). Based on cellular morphology and the results of biochemical analysis, this strain was tentatively identified as a novel species of the genus Actinomyces. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the bacterium was closely related to the type strain of Actinomyces denticolens (96.9 % 16S rRNA gene sequence similarity). A comparison of biochemical traits showed that strain 7400942T was distinct from A. denticolens in a number of characteristics, i.e. in contrast with A. denticolens, strain 7400942T was negative for nitrate reduction and for β-galactosidase, α-glucosidase and alanine arylamidase activities, it was positive for acid production from N-acetylglucosamine, melezitose and glycogen, and it was negative for acid production from turanose. Matrix-assisted laser-desorption/ionization time-of-flight MS protein analysis confirmed that strain 7400942T represents a novel species, as scores obtained for its spectra were significant (>2.2) only with strain 7400942T. On the basis of phenotypic data and phylogenetic inference, it is proposed that this strain should be designated Actinomyces timonensis sp. nov.; the type strain is strain 7400942T (=CSUR P35T=CCUG 55928T).

The C3H/HeJBir mouse model of intestinal inflammation was used for isolation of a Gram-positive, rod-shaped, non-spore-forming bacterium (B7T) from caecal suspensions. On the basis of partial 16S rRNA gene sequence analysis, strain B7T was a member of the class Actinobacteria, family Coriobacteriaceae, and was related closely to Enterorhabdus mucosicola Mt1B8T (97.6 %). The major fatty acid of strain B7T was C16 : 0 (19.1 %) and the respiratory quinones were mono- and dimethylated. Cells were aerotolerant, but grew only under anoxic conditions. Strain B7T did not convert the isoflavone daidzein and was resistant to cefotaxime. The results of DNA–DNA hybridization experiments and additional physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain B7T from the type strain of E. mucosicola. Therefore, strain B7T represents a novel species, for which the name Enterorhabdus caecimuris sp. nov. is proposed. The type strain is B7T (=DSM 21839T =CCUG 56815T).

A novel actinobacterium strain, CAP 290T, was isolated from a surface-sterilized root of an Australian native pine tree, Callitris preissii. Comparative 16S rRNA gene sequence analysis showed that the strain belongs to the family Nocardiaceae. Strain CAP 290T was most closely related to Nocardia nova JCM 6044T (97.4 % 16S rRNA gene sequence similarity) and Nocardia terpenica IFM 0706T (96.7 %); similarity to other type strains of the genus Nocardia ranged from 95 to 97 %. Chemotaxonomic data [meso-diaminopimelic acid, major menaquinone MK-8(H4ωcycl.), major fatty acid C16 : 0 and mycolate in the cell wall] confirmed the affiliation of strain CAP 290T to the genus Nocardia. The results of the phylogenetic analysis, together with the physiological and biochemical tests, allowed the differentiation of strain CAP 290T from strains of other Nocardia species. Therefore, strain CAP 290T represents a novel species, the first endophytic actinobacterium to be identified as belonging to the genus Nocardia, for which the name Nocardia callitridis sp. nov. is proposed. The type strain is strain CAP 290T (=DSM 45353T =ACM 5287T).

Two actinomycete strains, CM2-8T and CM2-12, were isolated from temperate peat swamp forest soil in Chiang Mai Province, Thailand. Their taxonomic positions were determined using a polyphasic approach. Chemotaxonomic characteristics of these strains coincided with those of the family Micromonosporaceae, i.e. cell wall chemotype II, N-glycolyl type of muramic acid, and type II phospholipids. Phylogenetic analysis based on 16S rRNA gene sequence data also indicated that these strains fell within the family Micromonosporaceae and formed a distinct taxon in the Micromonosporaceae phylogenetic tree. On the basis of phylogenetic analysis, characteristic patterns of 16S rRNA gene signature nucleotides and chemotaxonomic data, it is proposed that the novel isolates belong to a new genus, Actinaurispora gen. nov. The type species of the genus is proposed as Actinaurispora siamensis sp. nov., with strain CM2-8T (=JCM 15677T=BCC 34762T) as the type strain.

A Gram-positive, rod-shaped, catalase-positive, oxidase-negative, white-coloured bacterium, designated strain JS18-1T, was isolated from a soil sample collected from Halla mountain, Jeju island, Korea. 16S rRNA gene sequence analysis revealed that the strain was most closely related to members of the genus Tsukamurella with levels of sequence similarity of 95.4–96.5 %. Strain JS18-1T shared highest 16S rRNA gene sequence similarity with Tsukamurella strandjordii DSM 44573T (96.5 %), Tsukamurella carboxydivorans Y2T (96.4 %) and Tsukamurella tyrosinosolvens DSM 44234T (96.4 %). The G+C content of the total DNA of strain JS18-1T was 70 mol%. The cell-wall peptidoglycan type was A1γ and mycolic acids were also detected. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major quinone was menaquinone-9 (MK-9) and major cell-wall sugars were arabinose, ribose and glucose. The major fatty acids (>10 % of the total fatty acids) were C16 : 0, C18 : 1 ω9c, C18 : 0 10-methyl and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). Phylogenetic analysis based on 16S rRNA gene sequences and chemotaxonomic, biochemical and physiological characteristics indicate that strain JS18-1T represents a novel species of the genus Tsukamurella, for which the name Tsukamurella soli sp. nov. is proposed. The type strain is JS18-1T (=KACC 20764T=DSM 45046T).

The taxonomic position of a Gram-positive, non-spore-forming strain, designated CAU 59T, from activated sludge was investigated. Colony morphology, biochemical tests and chemotaxonomic investigations revealed that strain CAU 59T possessed the characteristics of the genus Pseudoclavibacter. Comparative 16S rRNA gene sequence analysis showed sequence divergence values between strain CAU 59T and other described Pseudoclavibacter species of more than 3.6 %, and the strain formed a hitherto-unknown subline within the genus Pseudoclavibacter. DNA–DNA hybridization studies showed that strain CAU 59T displayed 20.9 % relatedness to its closest phylogenetic neighbour, Pseudoclavibacter helvolus DSM 20419T. The DNA G+C content was 66.2 mol%. The phenotypic, chemotaxonomic and genotypic data indicated that strain CAU 59T represents a novel species of the genus Pseudoclavibacter, for which the name Pseudoclavibacter chungangensis sp. nov. is proposed. The type strain is CAU 59T (=KCTC 22691T =CCUG 58142T).

A coryneform bacterium (strain 1094T) was isolated from a wound swab taken from an 89-year-old female patient. Chemotaxonomic investigations suggested that this bacterium was related to the genera Actinomyces, Arcanobacterium and Actinobaculum. Phylogenetic analysis of 16S rRNA gene sequences showed that strain 1094T was most closely related to Actinomyces europaeus CCUG 32789 AT (94.3 % similarity). Phenotypically, the isolate could be separated from its closest phylogenetic neighbours on the basis of being positive for catalase, CAMP reaction, acid phosphatase, N-acetyl-β-glucosaminidase and raffinose fermentation. Based on the data presented, it is proposed that strain 1094T should be classified in a novel species, Actinomyces hominis sp. nov. The type strain is 1094T (=CCUG 57540T =DSM 22168T).

Microbacterium strain AI-S262T was isolated from the rhizoplane of neem seedlings in the Botanical garden of Tamilnadu Agricultural University, Coimbatore, India, and subjected to phenotypic, chemotaxonomic and genetic characterization. Cells of this strain were Gram-stain-positive, motile, non-spore-forming, short rods and formed light-yellow-pigmented colonies on nutrient agar. Strain AI-S262T contained MK-12 and MK-13 as the main respiratory quinones, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 as the predominant fatty acids, peptidoglycan-type B2β with glycolyl residues, and had a DNA G+C content of 69.5 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed 98.0–98.6 % pair-wise similarity with respect to close relatives in the genus Microbacterium. DNA–DNA hybridization experiments revealed a low level of DNA–DNA relatedness (less than 39%) between strain AI-S262T and its closest relatives. Data from DNA–DNA hybridization and phenotypic analyses supported the conclusion that strain AI-S262T represents a novel species in the genus Microbacterium, for which the name Microbacterium azadirachtae sp. nov. is proposed. The type strain is AI-S262T (=JCM 15681T =LMG 24772T =KCTC 19668T).

A strictly aerobic, Gram-staining-negative, oxidase- and catalase-positive, non-motile, rod-shaped bacterium, designated strain 5416T-29T, was isolated from air and was characterized by using a polyphasic approach. Colonies were reddish pink and circular with entire margins. Flexirubin-type pigments were absent. The strain formed a distinct phylogenetic lineage within the family Cytophagaceae of the phylum Bacteroidetes. Strain 5416T-29T did not show more than 88 % 16S rRNA gene sequence similarity to the type strain of any recognized species. The major cellular fatty acids were C16 : 1 ω5c, iso-C17 : 0 3-OH and iso-C15 : 0. The polar lipids were phosphatidylethanolamine, one unknown amino lipid and several unknown polar lipids. Menaquinone-7 (MK-7) was the major respiratory quinone. The G+C content of the DNA of strain 5416T-29T was 45.5 mol%. Results of phenotypic and phylogenetic analyses clearly indicate that strain 5416T-29T represents a novel species of a new genus in the family Cytophagaceae, for which the name Rhodocytophaga aerolata gen. nov., sp. nov. is proposed. The type strain of Rhodocytophaga aerolata is 5416T-29T (=KACC 12507T =DSM 22190T).

A pale-yellowish-pigmented strain, 022-2-26T, was isolated from a starfish, Stellaster equestris. Cells of strain 022-2-26T were Gram-negative short rods that were chemo-organotrophic, alkalitolerant and mesophilic. The predominant menaquinone was MK-6. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1, C15 : 0, iso-C15 : 0 2-OH and iso-C17 : 0 3-OH (together representing 87 % of the total fatty acids). The DNA G+C content was 30.1 mol%. A 16S rRNA gene sequence of the isolate was determined and phylogenetic analyses revealed that strain 022-2-26T formed a robust clade (neighbour-joining algorithm with a bootstrap value of 95 % and parsimony and maximum-likelihood algorithms) with type strains of species in the genus Winogradskyella. The closest phylogenetic neighbour of strain 022-2-26T was Winogradskyella poriferorum UST030701-295T (96 % 16S rRNA gene sequence similarity; 59 differences between sequences). On the basis of the phenotypic and chemotaxonomic characteristics and the phylogenetic evidence, it is proposed that strain 022-2-26T represents a novel species, Winogradskyella exilis sp. nov. The type strain is 022-2-26T (=KMM 6013T =CIP 109976T).

A yellow-coloured bacterium, T41T, was isolated from a soil sample of a subtropical rainforest in Nepal. Cells were Gram-reaction-positive, aerobic, non-motile, short rods. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain formed a cluster with Terrimonas ferruginea, Terrimonas lutea, Niabella soli, Flavisolibacter ginsengiterrae, Flavisolibacter ginsengisoli, Niastella yeongjuensis and Niastella koreensis in the phylum Bacteroidetes. The strain showed the highest sequence similarity to the type strain of Terrimonas lutea (93.2 %). The major isoprenoid quinone was MK-7 and the predominant cellular fatty acids (>10 %) were iso-15 : 0 (33.8 %), iso-15 : 1 G (13.3 %) and iso-17 : 0 3-OH (12.9 %). The DNA G+C content was 48.1 mol%. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strain T41T represents a novel species in a new genus in the phylum Bacteroidetes, for which the name Flavihumibacter petaseus gen. nov., sp. nov. is proposed. The type strain of Flavihumibacter petaseus is strain T41T (=CGMCC 1.7723T =NBRC 106054T).

Four strains (NUM 1903T, NUM 1904, NUM 1912 and NUM 1925) that were obligately anaerobic, pigmented, Gram-negative-staining rods were isolated from the oral cavity of donkeys. These strains were analysed using the Rapid ID 32A, API 20A and API ZYM systems, by DNA–DNA hybridization with other related species and by 16S rRNA gene sequencing. 16S rRNA gene sequence analysis showed that each of the new isolates was a member of the genus Prevotella and related to Prevotella multiformis PPPA21T, showing about 93 % sequence similarity. Based on phylogenetic and phenotypic evidence, it is proposed that the four strains are representatives of a novel species, for which the name Prevotella dentasini sp. nov. is proposed. The type strain is NUM 1903T (=JCM 15908T=DSM 22229T).

A Gram-negative, aerobic bacterium, designated strain BZ26T, was isolated from hydrocarbon-contaminated soil. The strain was psychrophilic, showing good growth over a temperature range of 1–20 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ26T was related to members of the genus Dyadobacter and had highest 16S rRNA gene sequence similarity to Dyadobacter alkalitolerans 12116T (98.1 %), Dyadobacter koreensis KCTC 12537T (97.5 %) and Dyadobacter ginsengisoli Gsoil 043T (97.2 %). Strain BZ26T had MK-7 as the major menaquinone and summed feature 3 (C16 : 1 ω7c/iso-C15 : 0 2-OH), C16 : 1 ω5c and iso-C15 : 0 as major fatty acids. The genomic DNA G+C content of strain BZ26T was 48.9 mol%. On the basis of phenotypic characteristics and genotypic analysis, strain BZ26T is considered to represent a novel species of the genus Dyadobacter, for which the name Dyadobacter psychrophilus sp. nov. is proposed. The type strain is BZ26T (=DSM 22270T =CGMCC 1.8951T).

An aerobic, yellow–orange-pigmented, Gram-staining-negative bacterium, designated strain EM44T, was isolated from seawater on the eastern coast of Jeju Island, Korea. Growth was observed at 15–35 °C (optimum 25–30 °C), pH 6.5–9.0 (optimum pH 7.0–8.5) and between 1 and 5 % NaCl (w/v) (optimum 2–4 %). Cells of strain EM44T were non-motile, straight rods and showed catalase and oxidase activities. The G+C content of the genomic DNA was 47.9 mol% and the major respiratory quinone was MK-6. The major fatty acids were iso-C15 : 0 G, iso-C15 : 0, iso-C17 : 0 3-OH and iso-C16 : 0 3-OH. Strain EM44T contained phosphatidylethanolamine as a major polar phospholipid. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain EM44T fell within the family Flavobacteriaceae in the phylum Bacteroidetes and was most closely related to members of the genera Eudoraea, Zeaxanthinibacter and Robiginitalea with 92–94.5 % gene sequence similarities. On the basis of chemotaxonomic data and molecular properties, it is clear that strain EM44T represents a novel genus within the family Flavobacteriaceae, for which the name Muriicola jejuensis gen. nov., sp. nov. is proposed. The type strain of the type species is EM44T (=KCTC 22299T=DSM 21206T).