scholarly journals Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. nov., K. gansuensis sp. nov., K. nipponensis sp. nov., K. paranensis sp. nov. and K. terrestris sp. nov.

2004 ◽  
Vol 54 (6) ◽  
pp. 2121-2129 ◽  
Author(s):  
Ingrid Groth ◽  
Carlos Rodríguez ◽  
Barbara Schütze ◽  
Petra Schmitz ◽  
Eckhard Leistner ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Gene Sequence ◽  
Sequence Data ◽  
16S Rrna Gene Sequence ◽  
Morphological Properties ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data

A polyphasic study was carried out to establish the taxonomic positions of six strains isolated from diverse soil samples and provisionally assigned to the genus Kitasatospora. The isolates were found to have chemical and morphological properties consistent with their classification as Kitasatospora strains. Direct 16S rRNA gene sequence data confirmed the taxonomic position of the strains following the generation of phylogenetic trees by using three tree-making algorithms. Five of the isolates were considered to merit species status using complementary genotypic and phenotypic data. These organisms were designated Kitasatospora arboriphila sp. nov. (HKI 0189T=2291-120T=DSM 44785T=NCIMB 13973T), Kitasatospora gansuensis sp. nov. (HKI 0314T=2050-015T=DSM 44786T=NCIMB 13974T), Kitasatospora nipponensis sp. nov. (HKI 0315T=2148-013T=DSM 44787T=NCIMB 13975T), Kitasatospora paranensis sp. nov. (HKI 0190T=2292-041T=DSM 44788T=NCIMB 13976T) and Kitasatospora terrestris sp. nov. (HKI 0186T=2293-012T=DSM 44789T=NCIMB 13977T). The remaining organism, isolate HKI 0316 (=2122-022=DSM 44790=NCIMB 13978), was considered to be a strain of Kitasatospora kifunensis on the basis of 16S rRNA gene sequence, DNA–DNA relatedness and phenotypic data.

scholarly journals Reclassification of Lactobacillus ferintoshensis as a later heterotypic synonym of Lactobacillus parabuchneri

2005 ◽  
Vol 55 (5) ◽  
pp. 2195-2198 ◽  
Author(s):  
Marc Vancanneyt ◽  
Katrien Engelbeen ◽  
Marjan De Wachter ◽  
Katrien Vandemeulebroecke ◽  
Ilse Cleenwerck ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data ◽  
Lactobacillus Kefiri

Lactobacillus ferintoshensis has recently been described as a novel species, distinct from its close phylogenetic neighbours Lactobacillus buchneri, Lactobacillus kefiri and Lactobacillus hilgardii. Two highly related species with validly published names, Lactobacillus parakefiri and Lactobacillus parabuchneri, were not considered in the study due to the lack of 16S rRNA gene sequence data at that time. Since the publication of the study, the sequences have become available and have revealed that L. ferintoshensis and L. parabuchneri share 99·7 % 16S rRNA gene sequence similarity. Further genomic and phenotypic data, derived from fluorescent amplified fragment length polymorphism, DNA–DNA hybridization and API 50 CHL analyses, have demonstrated that the species are synonymous.

scholarly journals Paraperlucidibaca baekdonensis gen. nov., sp. nov., isolated from seawater

2011 ◽  
Vol 61 (6) ◽  
pp. 1382-1385 ◽  
Author(s):  
Ki-Hoon Oh ◽  
Soo-Young Lee ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data ◽  
Gene Sequence Analysis

A Gram-negative, non-spore-forming, rod-shaped bacterial strain, RL-2T, was isolated from seawater of the East Sea in Korea and was subjected to a polyphasic taxonomic study. Strain RL-2T grew optimally at pH 7.5–8.0, at 20 °C and in the absence of NaCl. Phylogenetic trees based on 16S rRNA gene sequence analysis showed that strain RL-2T forms a cluster with Perlucidibaca piscinae IMCC1704T and various uncultured and unidentified gammaproteobacteria. Strain RL-2T exhibited 16S rRNA gene sequence similarity values of 96.1 % to Perlucidibaca piscinae IMCC1704T and 93.7–99.7 % to the uncultured bacterial clones belonging to the cluster and an unidentified gammaproteobacterium. The fatty acid profile of strain RL-2T was similar to that of Perlucidibaca piscinae IMCC1704T, but the predominant ubiquinone type (Q-11) of strain RL-2T was different from that (Q-8) of Perlucidibaca piscinae IMCC1704T. The DNA G+C content of strain RL-2T was 61.3 mol%. On the basis of phylogenetic, chemotaxonomic and phenotypic data, strain RL-2T is considered to represent a novel species of a new genus in the family Moraxellaceae, for which the name Paraperlucidibaca baekdonensis gen. nov., sp. nov. is proposed. The type strain of Paraperlucidibaca baekdonensis is RL-2T ( = KCTC 23145T  = CCUG 59307T).

scholarly journals Fibrisoma limi gen. nov., sp. nov., a filamentous bacterium isolated from tidal flats

2011 ◽  
Vol 61 (6) ◽  
pp. 1418-1424 ◽  
Author(s):  
Manuela Filippini ◽  
Andres Kaech ◽  
Urs Ziegler ◽  
Homayoun C. Bagheri
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The North ◽  
Gram Staining

An orange-pigmented, Gram-staining-negative, non-motile, filament-forming, rod-shaped bacterium (BUZ 3T) was isolated from a coastal mud sample from the North Sea (Fedderwardersiel, Germany) and characterized taxonomically using a polyphasic approach. According to 16S rRNA gene sequence data, it belonged to the family Cytophagaceae, exhibiting low 16S rRNA gene sequence similarity (<90 %) with members of the genera Spirosoma, Rudanella and Fibrella. The DNA G+C content was 52.0 mol%. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 1ω5c and iso-C17 : 0 3-OH. The major polar lipids consisted of phosphatidylethanolamine and several aminolipids. On the basis of phenotypic, chemotaxonomic and phylogenetic data, it is proposed that strain BUZ 3T represents a novel genus and species, for which the name Fibrisoma limi gen. nov., sp. nov. is proposed. The type strain is BUZ 3T ( = DSM 22564T  = CCUG 58137T).

scholarly journals Nocardioides iriomotensis sp. nov., an actinobacterium isolated from forest soil

2011 ◽  
Vol 61 (9) ◽  
pp. 2205-2209 ◽  
Author(s):  
Hideki Yamamura ◽  
Shin-ya Ohkubo ◽  
Youji Nakagawa ◽  
Yuumi Ishida ◽  
Moriyuki Hamada ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Forest Soil ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data

An actinomycete strain, designated IR27-S3T, was isolated from a forest soil sample collected from Iriomote Island, Okinawa, Japan. Cells of the isolate were Gram-stain-positive, aerobic, non-sporulating, non-motile coccoids or short rods. The strain grew in the presence of 0–7 % (w/v) NaCl, at pH 6–8 and at 12–37 °C, with optimum growth at 30 °C. Chemotaxonomically, the strain contained ll-diaminopimelic acid as the diagnostic diamino acid and MK-8(H4) as the predominant menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown phospholipid. The major cellular fatty acids were iso-C16 : 0, C17 : 1 cis-9, C15 : 0 and iso-C15 : 0. The DNA G+C content was 73.7 mol%. On the basis of 16S rRNA gene sequence analysis, strain IR27-S3T was closely related to Nocardioides mesophilus MSL-22T (98.1 % 16S rRNA gene sequence similarity), Marmoricola bigeumensis MSL-05T (97.2 %) and Nocardioides jensenii DSM 20641T (96.5 %). On the basis of fatty acid analysis, phylogenetic analysis and phenotypic data, the isolate should be classified in a novel species of the genus Nocardioides, for which the name Nocardioides iriomotensis sp. nov. is proposed. The type strain is IR27-S3T ( = NBRC 105384T  = KACC 14926T).

scholarly journals Alkalimicrobium pacificum gen. nov., sp. nov., a marine bacterium in the family Rhodobacteraceae

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2453-2458 ◽  
Author(s):  
Gaiyun Zhang ◽  
Yanliu Yang ◽  
Shuang Wang ◽  
Zhilei Sun ◽  
Kailin Jiao
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Unidentified Phospholipid ◽  
The Family

A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated strain F15T, was isolated from a deep-sea sediment of the western Pacific Ocean. The temperature, pH and NaCl ranges for growth were 4–50 °C, pH 6–11 and 0–10 % (w/v), respectively. Strain F15T showed the highest 16S rRNA gene sequence similarity to Sagittula stellata E-37T (96.4 %), followed by Ponticoccus litoralis CL-GR66T (96.4 %), Antarctobacter heliothermus EL-219T (96.3 %) and Thalassococcus lentus YCS-24T (96.0 %). Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain F15T formed a lineage within the family Rhodobacteraceae of the class Alphaproteobacteria. The polar lipid profile of strain F15T comprised significant amounts of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified glycolipid and one unidentified phospholipid. The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 40.2 %), anteiso-C15 : 0 (30.4 %) and anteiso-C17 : 0 (9.7 %). The genomic DNA G+C content of strain F15T was 60.2 mol% and the major respiratory quinone was Q-10. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain F15T is considered to represent a novel species of a new genus within the family Rhodobacteraceae, for which the name Alkalimicrobium pacificum gen. nov., sp. nov. is proposed. The type strain is F15T ( = LMG 28107T = JCM 19851T = CGMCC 1.12763T = MCCC 1A09948T).

scholarly journals Streptomyces durmitorensis sp. nov., a producer of an FK506-like immunosuppressant

2007 ◽  
Vol 57 (9) ◽  
pp. 2119-2124 ◽  
Author(s):  
Miloje Savic ◽  
Ivana Bratic ◽  
Branka Vasiljevic
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Gene Sequence ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
23S Rrna ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Screening of soil samples from the Durmitor National Park, Serbia and Montenegro, for strains producing immunosuppressants with a similar mechanism of action to FK506 resulted in the isolation of the actinomycete strain MS405T. Isolate MS405T was found to have morphological and phenotypic properties that were consistent with its classification as a Streptomyces strain. The DNA G+C content of strain MS405T was 72 mol%. 16S rRNA gene sequence data confirmed the taxonomic position of the strain, following the generation of phylogenetic trees by using various treeing algorithms. On the basis of 16S rRNA gene sequence similarity, strain MS405T was shown to belong to the Streptomyces albidoflavus ‘supercluster’, being related to Streptomyces aureus DSM 41785T (99.59 % similarity) and Streptomyces kanamyceticus DSM 40500T (99.32 %). The 16S–23S rRNA internally transcribed spacer (ITS) region exhibited variations in length and sequence composition, showing limited usefulness in phylogenetic analyses. However, DNA relatedness values support the classification of this isolate within a novel species. A number of physiological and biochemical tests distinguished strain MS405T from its closest phylogenetic neighbours. Therefore, strain MS405T represents a novel species, for which the name Streptomyces durmitorensis sp. nov. is proposed, with the type strain MS405T (=DSM 41863T =CIP 108995T).

scholarly journals Nocardia pigrifrangens sp. nov., a novel actinomycete isolated from a contaminated agar plate

2004 ◽  
Vol 54 (5) ◽  
pp. 1683-1686 ◽  
Author(s):  
Liming Wang ◽  
Yamei Zhang ◽  
Ying Huang ◽  
Luis A. Maldonado ◽  
Zhiheng Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Gene Sequence ◽  
Agar Plate ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Actinomycete Strain

A polyphasic study was undertaken to establish the taxonomic position of an actinomycete strain isolated from a contaminated agar plate. The strain, designated 7031T, had morphological and chemotaxonomic properties typical of the genus Nocardia. An almost-complete 16S rRNA gene sequence determined for the strain was aligned with available sequences for nocardiae, and phylogenetic trees were inferred using three tree-generating algorithms. Strain 7031T clustered with the type strains of Nocardia carnea and Nocardia flavorosea, showing low 16S rRNA gene sequence similarities to these species (97·2 and 97·5 %, respectively). The strain was also distinguished from the closest species by a range of phenotypic properties. It is proposed that the strain be recognized as a novel species of Nocardia, Nocardia pigrifrangens sp. nov., the type strain of which is 7031T (=AS 4.1808T=JCM 11884T).

Amnibacterium soli sp. nov., an actinobacterium isolated from grass soil

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4750-4753 ◽  
Author(s):  
Long Jin ◽  
Hyung-Gwan Lee ◽  
Hee-Sik Kim ◽  
Chi-Yong Ahn ◽  
Hee-Mock Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

A Gram-stain-positive, aerobic, non-motile, non-spore-forming, short rod-shaped actinobacterium, designated strain PB243T, was isolated from grass soil sampled in Daejeon, Republic of Korea. Comparative 16S rRNA gene sequence studies showed the isolate was clearly affiliated with the class Actinobacteria , and most closely related to Amnibacterium kyonggiense KEMC 51201-037T, showing 98.8 % 16S rRNA gene sequence similarity. Cells of strain PB243T formed yellow colonies on R2A agar, contained MK-11 and MK-12 as the predominant menaquinones, l-2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid, and anteiso-C15 : 0 and iso-C16 : 0 among the major fatty acids. The acyl type of the muramic acid was acetyl. The G+C content of the genomic DNA of strain PB243T was 71.5 mol%. Thus, the combined genotypic and phenotypic data supported the conclusion that strain PB243T represents a novel species of the genus Amnibacterium , for which the name Amnibacterium soli sp. nov. is proposed. The type strain is PB243T ( = KCTC 33147T = JCM 19015T).

scholarly journals Kineococcus gypseus sp. nov., isolated from saline sediment

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3703-3708 ◽  
Author(s):  
Qinyuan Li ◽  
Guiding Li ◽  
Xiu Chen ◽  
Fangji Xu ◽  
Yong Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data

A novel Gram-stain-positive, aerobic, motile, non-spore-forming coccus-shaped actinomycete, designated strain YIM 121300T, was isolated from alkaline sediment in Yuanjiang, Yunnan province, south-west China. Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain YIM 121300T was affiliated to the genus Kineococcus, and was closely related to Kineococcus aurantiacus IFO 15268T (97.3 % similarity). 16S rRNA gene sequence similarity to other species of the genus Kineococcus was < 97 %. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The whole-cell sugars contained arabinose, galactose, glucose, mannose and ribose. The predominant menaquinone was MK-9(H2). Mycolic acids were not detected. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unknown phospholipid. The predominant fatty acids were anteiso-C15 : 0 and anteiso-C15 : 1 A. The G+C content of the genomic DNA was 75.1 mol%. DNA–DNA relatedness (55 ± 4 % to K. aurantiacus IFO 15268T) and differential phenotypic data demonstrated that strain YIM 121300T was distinguished from all related species of the genus Kineococcus. On the basis of data from the present polyphasic study, the organism should be assigned to a novel species of the genus Kineococcus, for which the name Kineococcus gypseus sp. nov. is proposed. The type strain is YIM 121300T ( = CCTCC AA 2013232T = DSM 27627T).

scholarly journals The genus Listonella MacDonell and Colwell 1986 is a later heterotypic synonym of the genus Vibrio Pacini 1854 (Approved Lists 1980) – a taxonomic opinion

2011 ◽  
Vol 61 (12) ◽  
pp. 3023-3027 ◽  
Author(s):  
Fabiano L. Thompson ◽  
Cristiane C. Thompson ◽  
Graciela M. Dias ◽  
Hiroaki Naka ◽  
Christopher Dubay ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Vibrio Anguillarum ◽  
16S Rrna Gene Sequence ◽  
Published Data ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data

We analysed the taxonomic position of the genus Listonella based on phylogenetic, genomic and phenotypic data. The species of the genus Listonella were nested within the genus Vibrio according to the 16S rRNA gene sequence-based phylogenetic tree. The closest neighbour of Vibrio (Listonella) anguillarum strains LMG 4437T and ATCC 68554 ( = strain 775) was Vibrio ordalii LMG 13544T, with more than 99.5 % 16S rRNA gene sequence similarity. Furthermore, Vibrio (Listonella) pelagius is highly related to Vibrio splendidus. According to average amino acid identity (AAI), multilocus sequence analysis (MLSA) and Karlin genome signature, the closest neighbour of L. anguillarum ATCC 68554 is V. ordalii LMG 13544T, with 95 % AAI, 98 % MLSA and 5 in Karlin. V. anguillarum ATCC 68554 and Vibrio cholerae N16961 had 77 % similarity in AAI, 85 % in MLSA and 14 in the Karlin signature. Phenotypic analyses of previously published data for V. (L.) anguillarum and V. (L.) pelagius revealed that the genus Listonella is extremely similar to the genus Vibrio. V. ordalii and L. anguillarum strains yielded up to 67 % DNA–DNA hybridization. There are only a few phenotypic features that might be used to discriminate these two species: L. anguillarum is positive for the Voges–Proskauer reaction, citrate utilization, starch hydrolysis, lipase activity and acid production from glycerol, sorbitol and trehalose, whereas V. ordalii is negative for these traits. We suggest that the genus Listonella is a later heterotypic synonym of the genus Vibrio and propose to use the names Vibrio anguillarum and Vibrio pelagius in place of Listonella anguillarum and Listonella pelagia, respectively.

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