- Volume 59, Issue 9, 2009

A novel actinomycete strain, YIM 61503T, isolated from the stem of Maytenus austroyunnanensis, was characterized by using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain YIM 61503T belonged to the genus Jiangella and exhibited 16S rRNA gene sequence similarities of 98.8 and 98.6 % to Jiangella alkaliphila D8-87T and Jiangella gansuensis YIM 002T. The chemotaxonomic properties of strain YIM 61503T were consistent with those of the genus Jiangella: the cell-wall peptidoglycan type was based on ll-diaminopimelic acid and MK-9(H4) was the predominant menaquinone. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0, iso-C14 : 0, C17 : 1 ω8c and anteiso-C17 : 0. The DNA G+C content was 71.9 mol%. Strain YIM 61503T was phenotypically distinct from recognized Jiangella species and was shown to belong to a separate genomic species based on DNA–DNA hybridization results. Thus, strain YIM 61503T is considered to represent a novel species of the genus Jiangella, for which the name Jiangella alba sp. nov. is proposed. The type strain is YIM 61503T (=DSM 45237T =CCTCC AA 208023T).

A halophilic actinomycete strain, designated YIM 91168T, was isolated from a salt lake in Xinjiang province, north-west China. The isolate grew at 20–40 °C, pH 5–8 and 6–22 % (w/v) NaCl; there was no growth in the absence of NaCl. The whole-cell hydrolysate contained meso-diaminopimelic acid, galactose and arabinose. The major fatty acids were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0. MK-9(H4) was the predominant menaquinone and the genomic DNA G+C content was 70.1 mol%. These chemotaxonomic data, together with its morphological properties, were consistent with the assignment of strain YIM 91168T to the genus Saccharopolyspora. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 91168T had highest sequence similarity (95.4 %) with Saccharopolyspora gregorii NCIB 12823T, and showed lower 16S rRNA gene sequence similarity (93.0–95.1 %) with the other species of the genus Saccharopolyspora. On the basis of evidence from this polyphasic study, the novel species Saccharopolyspora qijiaojingensis sp. nov. is proposed. The type strain is YIM 91168T (=DSM 45088T =KCTC 19235T).

A Gram-positive-staining, aerobic, catalase- and oxidase-positive, irregular short rod-shaped actinobacterium, designated strain YIM C003T, was isolated from a salt mine in Yunnan, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM C003T was most closely related to strains of the genera Knoellia (94.2–96.0 % similarity), Oryzihumus (95.6 %), Terrabacter (94.9–95.4 %), Janibacter (94.9–95.4 %), Kribbia (95.0 %), Lapillicoccus (95.0 %) and Phycicoccus (94.2–95.0 %) of the family Intrasporangiaceae and that it formed an independent monophyletic lineage with three strains of Oryzihumus leptocrescens. The DNA G+C content of strain YIM C003T was 72.0 mol%. The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. The predominant menaquinone was MK-8(H4). Mycolic acids were not detected. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unknown phospholipids. The major cellular fatty acids were C18 : 1 ω9c and C16 : 0. These chemotaxonomic properties, together with data from phylogenetic analysis, enabled the novel isolate to be differentiated from all other members of the family. A novel species in a new genus, Fodinibacter luteus gen. nov., sp. nov., is proposed, with strain YIM C003T (=DSM 21208T =CCTCC AA 208036T) as the type strain of Fodinibacter luteus.

A Gram-positive, milk–white coloured, aerobic strain, YIM 48868T, was isolated from the rhizosphere soil of Maytenus hookeri Loes in Xishuangbanna, China. 16S rRNA gene sequence similarity studies showed that strain YIM 48868T was a member of the genus Actinopolymorpha, showing 96.8 % sequence similarity to Actinopolymorpha singaporensis IM 7744T and 97.0 % similarity to Actinopolymorpha rutila YIM 45725T. Chemotaxonomic data (peptidoglycan type I, ll-diaminopimelic acid; sugar pattern C, glucose, rhamnose and ribose; polar lipids PI, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannosides and phosphatidylinositol) were characteristic of the genus Actinopolymorpha. A phylogenetic tree based on 16S rRNA gene sequences showed that strain YIM 48868T formed a distinct phylogenetic lineage within the genus Actinopolymorpha. Strain YIM 48868T could be differentiated from recognized species by means of phenotypic properties and the predominant menaquinones [MK-9(H6), MK-9(H8), MK-10(H6), MK-10(H8)]. The DNA G+C content was 66.6 mol%. The DNA–DNA relatedness values between strain YIM 48868T and the type strains of A. singaporensis and A. rutila were 48.7 % and 53.1 %, respectively. These data, in combination with phenotypic and chemotaxonomic data, demonstrate that strain YIM 48868T represents a novel species in the genus Actinopolymorpha, for which the name Actinopolymorpha alba sp. nov. is proposed. The type strain is YIM 48868T (=CCTCC AA 208030T=DSM 45243T).

An orange-coloured actinomycete, designated strain RP-B16T, was isolated from a rhizosphere soil. Cells of strain RP-B16T were strictly aerobic, Gram-positive-staining, oxidase-negative, catalase-positive, motile cocci. A phylogenetic tree, based on 16S rRNA gene sequences, showed that members of the genus Kineococcus were divided into two independent clusters and that strain RP-B16T formed a coherent clade with the type strains of Kineococcus aurantiacus (99.5 % sequence similarity) and Kineococcus radiotolerans (99.1 %). Levels of 16S rRNA gene sequence similarity between strain RP-B16T and Kineococcus marinus KST3-3T and ‘Kineococcus tegulae’ T2A-S27 were lower than 97.0 %. Chemotaxonomic characteristics were typical of the genus Kineococcus in having meso-diaminopimelic acid as the diagnostic diamino acid, MK-9(H2) as the predominant menaquinone, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unknown phospholipids, anteiso-C15 : 0 as the predominant fatty acid and a DNA G+C content of 73.8 mol%. Strain RP-B16T showed levels of DNA–DNA relatedness of 34.6–37.3 % to Kineococcus aurantiacus DSM 7487T and 31.2–32.7 % to Kineococcus radiotolerans DSM 14245T. On the basis of phenotypic features and DNA–DNA hybridization data, strain RP-B16T is considered to represent a novel species of the genus Kineococcus, for which the name Kineococcus rhizosphaerae sp. nov. is proposed. The type strain is RP-B16T (=KCTC 19366T =DSM 19711T).

A novel Gram-positive, aerobic, spore-forming actinobacterium, designated strain YIM 013T, was isolated from a mangrove sediment sample and subjected to a polyphasic taxonomic study. The peptidoglycan type was A1γ and the major whole-cell sugars contained glucose and xylose. The phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and some unknown phospholipids. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C15 : 0 and iso-C16 : 0. The genomic DNA G+C content was 69.3 mol%. blast search results based on an almost-complete 16S rRNA gene sequence showed that strain YIM 013T had the highest similarity with Verrucosispora gifhornensis DSM 44337T (98 %) and phylogenetic analysis revealed that strain YIM 013T should be assigned to the genus Verrucosispora. The mean level of DNA–DNA relatedness between strain YIM 013T and V. gifhornensis DSM 44337T was 38.2 %. Based on its phenotypic and genotypic characteristics, strain YIM 013T (=CCTCC AA207012T =KCTC 19195T) is proposed to be the type strain of a novel species, Verrucosispora lutea sp. nov.

The Mycobacterium avium complex (MAC) consists of four recognized species, Mycobacterium avium, Mycobacterium colombiense, Mycobacterium intracellulare and Mycobacterium chimaera, and a variety of other strains that may be members of undescribed taxa. We report on two isolates of a scotochromogenic, slowly growing, non-tuberculous Mycobacterium species within the M. avium complex from a lymph node and an infected wound after a dogbite of separate patients in The Netherlands. The extrapulmonary infections in immunocompetent patients suggested a high level of virulence. These isolates were characterized by a unique nucleotide sequence in the 16S rRNA gene, 99 % similar to Mycobacterium colombiense, and the MAC-Q 16S–23S internal transcribed spacer (ITS) sequence. Sequence analyses of the hsp65 gene revealed 97 % similarity to M. avium. The rpoB gene sequence was 98 % similar to M. colombiense. Phenotypically, the scotochromogenicity, positive semi-quantitative catalase and heat-stable catalase tests, negative tellurite reductase and urease tests and susceptibility to hydroxylamine and oleic acid set these isolates apart from related species. High-performance liquid chromatography analysis of cell-wall mycolic acid content revealed a unique pattern, related to that of M. avium and M. colombiense. Together, these findings supported a separate species status within the Mycobacterium avium complex. We propose elevation of scotochromogenic M. avium complex strains sharing this 16S gene and MAC-Q ITS sequence to separate species status, for which the name Mycobacterium vulneris sp. nov. is proposed. The type strain is NLA000700772T (=DSM 45247T=CIP 109859T).

Gram-positive, non-spore-forming rods (strain 6401990T), isolated from a human cutaneous discharge were subjected to a polyphasic taxonomy study. The only respiratory quinone was MK-7 and the major fatty acids were anteiso-C15 : 0 (34.3 %), anteiso-C17 : 0 (18.7 %) and iso-C16 : 0 (18.6 %). Mycolic acids were not present. Polar lipids present were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and unidentified glycolipids. The isomer of diaminopimelic acid identified was meso-diaminopimelic acid, and the analysis of whole-cell sugars showed the presence of high amounts of galactose, ribose and some glucose. The G+C content of strain 6401990T was 68.6 %. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed 95.1 % similarity with Dermabacter hominis. On the basis of phenotypic data and phylogenetic inference, it is proposed that this strain represents a novel species in a new genus of the family Dermabacteraceae, for which the name Helcobacillus massiliensis gen. nov., sp. nov. is proposed. The type strain is 6401990T (CSUR P17T=CIP 109418T=CCUG 53859T).

A novel red-pigmented halophilic archaeon, strain A29T, was isolated from shrimp jeotgal, a traditional salt-fermented food from Korea. This strain grows in the ranges 10–30 % (w/v) NaCl, 17–50 °C and pH 6.5–8.5, with optimal growth occurring at 15–20 % NaCl, 37–45 °C and pH 7.0–7.5. The isolate is Gram-negative and non-motile. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain A29T is associated with the genus Haloterrigena and closely related to the species Haloterrigena thermotolerans (99.0 % similarity). However, DNA–DNA hybridization experiments revealed that the level of hybridization between strain A29T and related strains of Haloterrigena is less than 70 %. The polar lipid fraction consists of phosphatidylglyerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me) and mannose-2,6-disulfate(1-2)-glucose glycerol diether (S2-DGD). The G+C content of genomic DNA of the type strain is 62.3 mol%. On the basis of this polyphasic taxonomic study, strain A29T should be placed in the genus Haloterrigena as a novel species, for which the name Haloterrigena jeotgali sp. nov. is proposed. The type strain of the new species is A29T (=KCTC 4020T=DSM 18794T=JCM 14585T=CECT 7218T).

An aerobic, pale-orange-pigmented, Gram-stain-negative bacterium, designated strain EM39T, was isolated from seawater from the eastern coast of Jeju Island, Korea, and its taxonomic status was established using a polyphasic approach. Comparative 16S rRNA gene sequence studies revealed that strain EM39T formed a distinct lineage within the family Flavobacteriaceae and could be distinguished from strains of members of the related genera Gaetbulibacter, Mariniflexile and Tamlana by 16S rRNA gene sequence analysis (similarity values between strain EM39T and related strains were all less than 93.8 %). Cells of strain EM39T were non-gliding, catalase- and oxidase-positive rods that were devoid of flexirubin pigments. Growth was observed at 15–35 °C (optimum, 25–30 °C) and pH 6.5–9.0 (optimum, pH 7.0–8.5). The genomic DNA G+C content was 34.6 mol% and the major respiratory quinone was MK-6. The predominant cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. On the basis of phenotypic and genotypic data, strain EM39T represents a novel species in a new genus in the family Flavobacteriaceae, for which the name Jejuia pallidilutea gen. nov., sp. nov. is proposed. The type strain is EM39T (=KCTC 22298T=DSM 21165T).

Flavobacteria are emerging as an important group of organisms associated with the degradation of complex organic matter in aquatic environments. A novel Gram-reaction-negative, heterotrophic, rod-shaped, aerobic, yellow-pigmented and gliding bacterium, strain SCB36T, was isolated from a protein-enriched seawater sample, collected at Scripps Pier, Southern California Bight (Eastern Pacific). Analysis of the 16S rRNA gene sequence showed that the bacterium was related to members of the genus Winogradskyella within the family Flavobacteriaceae, phylum Bacteroidetes. 16S rRNA gene sequence similarity to the other Winogradskyella species was 94.5–97.1 %. DNA–DNA relatedness between strain SCB36T and Winogradskyella thalassocola KMM 3907T, its closest relative in terms of 16S rRNA gene sequence similarity, was 20 %. On the basis of the phylogenetic and phenotypic data, strain SCB36T represents a novel species of the genus Winogradskyella, for which the name Winogradskyella rapida sp. nov. is proposed. The type strain is SCB36T (=CECT 7392T =CCUG 56098T).

A strictly anaerobic bacterial strain, 7401987T, was isolated from a human brain abscess sample. Cells were Gram-negative, non-spore-forming, coccoid to rod-shaped and motile by flagella in a lophotrichous arrangement. The isolate was asaccharolytic and the major cellular fatty acids were anteiso-C15 : 0 (28.2 %), C16 : 0 (18.0 %), iso-C15 : 0 (12.3 %) and iso-C17 : 0 3-OH (11.7 %). 16S rRNA gene sequence comparisons showed that the isolate was distantly related to members of the genera Bacteroides (<83.6 % similarity), Parabacteroides (<79.9 % similarity), Tannerella (<79.8 % similarity), Dysgonomonas (<79.6 % similarity), Porphyromonas (<79.3 % similarity) and Prevotella (<78.9 % similarity). The low 16S rRNA gene sequence similarity values and physiological and biochemical characteristics differentiated strain 7401987T from all known species and indicate that our isolate represents a novel species in a new genus within the phylum Bacteroidetes. The name Phocaeicola abscessus gen. nov., sp. nov. is proposed; the type strain of Phocaeicola abscessus is 7401987T (=CCUG 55929T =CSUR P22T =DSM 21584T).

The genus Sejongia was described in 2005, with the two species Sejongia antarctica and Sejongia jeonii, mainly on the basis of 16S rRNA gene sequence analysis. At that time, these organisms formed a quite separate branch in a 16S rRNA gene sequence-based tree, but, in subsequent studies, it became obvious that the species S. antarctica and S. jeonii and a third species, Sejongia marina, were most closely related (>95.0 % similarity) to some Chryseobacterium species (e.g. Chryseobacterium hominis, C. formosense and C. haifense). In addition, there is no evidence for clear phenotypic (i.e. chemotaxonomic) differences between these organisms that justifies their assignment to different genera. For these reasons, a proposal is made to transfer these species to the genus Chryseobacterium as Chryseobacterium antarcticum comb. nov. (type strain AT1013T =JCM 12381T =IMSNU 14040T =KCTC 12225T), Chryseobacterium jeonii comb. nov. (type strain AT1047T =JCM 12382T =IMSNU 14049T =KCTC 12226T) and Chryseobacterium marinum comb. nov. (type strain IMCC3228T =KCCM 42689T =NBRC 103143T) on the basis of 16S rRNA gene sequence data and published phenotypic data.

A facultatively anaerobic, moderately halophilic, Gram-negative, filamentous bacterium, designated JC2469T, was isolated from tidal flat sediment in Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the phylum Bacteroidetes and its closest taxonomic relative was Cytophaga fermentans NCIMB 2218T (89.6 % sequence similarity). Cells appeared as filaments during exponential growth, but became fragmented to rods at stationary phase. Spherical cells were also observed in aged cultures. Strain JC2469T contained iso-C15 : 0 (56.2 %) and MK-7 as the predominant fatty acid and respiratory quinone, respectively. On the basis of evidence from this polyphasic study, the isolate showed substantial differences from other genera. The phylogenetic and physiological data of the present study strongly suggest that the isolate represents a novel genus and species, for which the name Marinifilum fragile gen. nov., sp. nov. is proposed. The type strain of Marinifilum fragile is JC2469T (=IMSNU 14138T =KCTC 22488T =JCM 15579T).

A Lactobacillus strain, IMCC1736T, was isolated recently from a Korean freshwater pond following an extensive study of the microbial community in this ecosystem. Its 16S rRNA gene was sequenced and phylogenetic analysis placed this strain within the Lactobacillus salivarius group, closely related to Lactobacillus satsumensis NRIC 0604T, with 97.9 % sequence similarity. In the present work, the taxonomic status of strain IMCC1736T has been re-evaluated. It was characterized phylogenetically, genotypically and phenotypically and, based on DNA–DNA hybridization values, this strain represents a novel Lactobacillus species. Strain IMCC1736T can be differentiated genotypically from its closest relatives by randomly amplified polymorphic DNA analysis and ribotyping patterns; phenotypically, it can be distinguished by its inability to grow in 5 % NaCl and at pH 3.3 and by certain carbohydrate fermentations. Strain IMCC1736T is Gram-positive, catalase-negative and microaerophilic. Cells are motile rods and show homofermentative metabolism. The name Lactobacillus aquaticus sp. nov. is proposed, with strain IMCC1736T (=CECT 7355T =DSM 21051T) as the type strain.

A novel, moderately halophilic, endospore-forming bacterial strain, designated Hal 1T, was isolated from a permafrost core collected from the Canadian high Arctic. The temperature for growth of strain Hal 1T was 0–30 °C with no growth observed at either −5 or 37 °C (optimum growth at about 25 °C). Strain Hal 1T was able to grow at NaCl concentrations of 0–20 % (w/v) and did not have an absolute NaCl requirement for growth; optimal growth was at 5 % (w/v) NaCl. The level of 16S rRNA gene sequence similarity between strain Hal 1T and the type strains of Virgibacillus carmonensis and Virgibacillus necropolis was 98.2 %; values with respect to the type strains of other recognized Virgibacillus species were below 96.0 %. The DNA G+C content of strain Hal 1T was 38.2 mol%. Levels of DNA–DNA relatedness between strain Hal 1T and the type strains of V. carmonensis and V. necropolis were 14.0 and 21.0 %, respectively. The major fatty acid of strain Hal 1T was anteiso-C15 : 0, consistent with species of the genus Virgibacillus. The cell-wall peptidoglycan of strain Hal 1T was type A1α and the major respiratory quinone was MK-7. On the basis of genotypic and physiological results, strain Hal 1T (=DSM 19574T=JCM 14839T) is proposed as the type strain of a novel species of the genus Virgibacillus, namely Virgibacillus arcticus sp. nov.

Two novel spore-forming lactic acid bacteria, strains SL213T and SL1213, were isolated from vineyard soils in Korea. Cells of both isolates were rod-shaped bacilli and contained subterminal, ellipsoidal spores. Strains were facultatively anaerobic, catalase-positive, oxidase-negative and motile with single flagella. meso-Diaminopimelic acid, glucose and galactose were detected in whole-cell hydrolysates. Major fatty acids found in the strains were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0. The G+C contents of the DNA were 46.1 and 46.3 mol%. 16S rRNA gene sequences from the two strains were almost identical (99.9 %) and placed them in the genus Bacillus, according to phylogenetic analysis. The type strains most closely related to SL213T were Bacillus coagulans ATCC 7050T and Bacillus badius ATCC 14574T, with 16S rRNA gene sequence similarities of 96.9 and 95.9 %, respectively. Levels of DNA–DNA relatedness between strain SL213T and strain SL1213, B. coagulans ATCC 7050T and B. badius ATCC 14574T were 92.5, 49.0 and 27.5 %, respectively. On the basis of 16S rRNA gene sequences and chemotaxonomic and phenotypic evidence given in this study, we report that SL213T represents a novel species, for which the name Bacillus acidiproducens sp. nov. is proposed. The type strain is SL213T (=KCTC 13078T =JCM 14638T).