scholarly journals Massilia dura sp. nov., Massilia albidiflava sp. nov., Massilia plicata sp. nov. and Massilia lutea sp. nov., isolated from soils in China

2006 ◽  
Vol 56 (2) ◽  
pp. 459-463 ◽  
Author(s):  
Yu-Qin Zhang ◽  
Wen-Jun Li ◽  
Ke-Yun Zhang ◽  
Xin-Peng Tian ◽  
Yi Jiang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Gene Sequence Analysis

Four Gram-negative, motile, rod-shaped bacterial strains were isolated from soil samples collected from south-east China. A taxonomic study including phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics was performed. DNA G+C contents of the four strains were 63–66 mol%. Their predominant ubiquinone was Q-8. The fatty acid profiles contained C16 : 1 ω7c (36·9–54·7 %) and C16 : 0 (22·8–25·5 %) as the major components. Based on their phenotypic characteristics, phylogenetic position as determined by 16S rRNA gene sequence analysis and DNA–DNA hybridization results, the four isolates are considered to represent four novel species of the genus Massilia, for which the names Massilia dura sp. nov. (type strain 16T=CCTCC AB 204070T=KCTC 12342T), Massilia albidiflava sp. nov. (type strain 45T=CCTCC AB 204071T=KCTC 12343T), Massilia plicata sp. nov. (type strain 76T=CCTCC AB 204072T=KCTC 12344T) and Massilia lutea sp. nov. (type strain 101T=CCTCC AB 204073T=KCTC 12345T) are proposed.

scholarly journals Ancylobacter polymorphus sp. nov. and Ancylobacter vacuolatus sp. nov.

2006 ◽  
Vol 56 (6) ◽  
pp. 1185-1188 ◽  
Author(s):  
Yu Hua Xin ◽  
Yu Guang Zhou ◽  
Wen Xin Chen
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Gene Sequence Analysis

The taxonomic positions of ‘Renobacter vacuolatum’ DSM 1277 and ‘Ancylobacter polymorphus’ DSM 2457 were investigated in this study. 16S rRNA gene sequence analysis indicated that both strains belonged to the genus Ancylobacter. DNA–DNA hybridization showed that they differed from Ancylobacter aquaticus DSM 101T and Ancylobacter rudongensis AS 1.1761T. According to molecular and phenotypic characteristics, strain DSM 1277T (=AS 1.2807T) is proposed as the type strain of Ancylobacter vacuolatus sp. nov. At the same time, valid publication of the name Ancylobacter polymorphus sp. nov. is proposed, with the type strain DSM 2457T (=AS 1.2800T=NCIMB 10516T).

scholarly journals Plantactinospora sonchi sp. nov., an actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.)

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4895-4901 ◽  
Author(s):  
Zhaoxu Ma ◽  
Chongxi Liu ◽  
Jianlong Fan ◽  
Hairong He ◽  
Chuang Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Sonchus Oleraceus

A novel actinobacterium, designated strain NEAU-QY2T, was isolated from the leaves of Sonchus oleraceus L. specimen, collected from Wuchang, Heilongjiang Province, China. A polyphasic study was carried out to establish the taxonomic position of this strain. The organism formed single spores with rough surfaces on substrate mycelia. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-QY2T belonged to the genus Plantactinospora and formed a monophyletic clade with its closest related strains Plantactinospora endophytica YIM 68255T (99.2 % 16S rRNA gene sequence similarity), Plantactinospora veratri NEAU-FHS4T (98.8 %) and Plantactinospora mayteni YIM 61359T (98.7 %), an association that was supported by a bootstrap value of 90 % in the neighbour-joining tree and also recovered with the maximum-likelihood algorithm. However, DNA–DNA hybridization values between strain NEAU-QY2T and the three closely related strains were below 70 %. With reference to phenotypic characteristics, phylogenetic data and DNA–DNA hybridization results, strain NEAU-QY2T was distinguished from closely related strains and is classified as representing a novel species of the genus Plantactinospora, for which the name Plantactinospora sonchi sp. nov. is proposed. The type strain is NEAU-QY2T ( = CGMCC 4.7216T = JCM 30345T).

scholarly journals Characterization of alkaliphilic Bacillus strains used in industry: proposal of five novel species

2005 ◽  
Vol 55 (6) ◽  
pp. 2309-2315 ◽  
Author(s):  
Yuichi Nogi ◽  
Hideto Takami ◽  
Koki Horikoshi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Novel Species ◽  
16S Rrna Gene Sequencing ◽  
Industrial Applications ◽  
Rrna Gene ◽  
Bacterial Strains

Twenty alkaliphilic bacterial strains from industrial applications or enzyme studies were subjected to a polyphasic taxonomic investigation, including 16S rRNA gene sequencing, determination of genomic DNA G+C content, DNA–DNA hybridization, fatty acid analysis and standard bacteriological characterization. By comparing the groupings obtained based on the genomic DNA G+C content and the construction of a phylogenetic tree based on the 16S rRNA gene sequence, 12 clusters of similar strains were recognized. DNA–DNA hybridization revealed that these clusters represented five novel genospecies. Further analysis supported the proposal of five novel species in the genus Bacillus: Bacillus wakoensis sp. nov. (type strain N-1T=JCM 9140T=DSM 2521T), Bacillus hemicellulosilyticus sp. nov. (type strain C-11T=JCM 9152T=DSM 16731T), Bacillus cellulosilyticus sp. nov. (type strain N-4T=JCM 9156T=DSM 2522T), Bacillus akibai sp. nov. (type strain 1139T=JCM 9157T=ATCC 43226T) and Bacillus mannanilyticus sp. nov. (type strain AM-001T=JCM 10596T=DSM 16130T).

scholarly journals Limnohabitans planktonicus sp. nov. and Limnohabitans parvus sp. nov., planktonic betaproteobacteria isolated from a freshwater reservoir, and emended description of the genus Limnohabitans

2010 ◽  
Vol 60 (12) ◽  
pp. 2710-2714 ◽  
Author(s):  
Vojtěch Kasalický ◽  
Jan Jezbera ◽  
Karel Šimek ◽  
Martin W. Hahn
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Phylogenetic Cluster ◽  
The 16S Rrna Gene

Two bacterial strains, II-B4T and II-D5T, isolated from the meso-eutrophic freshwater Římov reservoir (Czech Republic), were characterized phenotypically, phylogenetically and chemotaxonomically. Both strains were chemo-organotrophic, facultatively anaerobic, non-motile rods, with identical DNA G+C contents of 59.9 mol%. Their major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and their major fatty acids were C16 : 1 ω7c/C16 : 1 ω6c, C16 : 0, C18 : 1 ω7c/C18 : 1 ω6c and C12 : 0. Both strains contained Q-8 as the only respiratory quinone component. The 16S rRNA gene sequences of the two strains possessed 99.1 % similarity; however, the level of DNA–DNA reassociation was only 26.7 %. The strains can also be discriminated from each other by several chemotaxonomic and biochemical traits. Phylogenetic analysis of the 16S rRNA gene sequences revealed the affiliation of both strains with the genus Limnohabitans within the family Comamonadaceae. The two investigated strains represent the first isolated members of a narrow phylogenetic cluster (the so-called R-BT065 cluster) formed by a large number of environmental sequences and abundant populations detected in the pelagic zones of various freshwater habitats. We propose to place the two strains in separate novel species within the genus Limnohabitans, Limnohabitans planktonicus sp. nov., with the type strain II-D5T (=DSM 21594T =CIP 109844T), and Limnohabitans parvus sp. nov., with the type strain II-B4T (=DSM 21592T =CIP 109845T). The description of the genus Limnohabitans is emended accordingly.

scholarly journals Prauserella shujinwangii sp. nov., from a desert environment

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3833-3837 ◽  
Author(s):  
Mei Liu ◽  
Li Zhang ◽  
Biao Ren ◽  
Na Yang ◽  
Xiaoyun Yu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Taxonomic Analysis ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Xinjiang Uyghur Autonomous Region

A Gram-positive, spore-forming, rod-shaped actinomycete, designated XJ46T, was isolated from Xinjiang Uyghur Autonomous Region, China and subjected to a polyphasic taxonomic analysis. Morphological and chemotaxonomic characteristics of XJ46T were identified as being similar to those of members of the genus Prauserella . The phylogenetic tree based on 16S rRNA gene sequences showed that XJ46T shared the highest similarity (95.9 %) with Prauserella marina MS498T. Based on its phenotypic characteristics, chemotaxonomic analysis and 16S rRNA gene sequence analysis, strain XJ46T is proposed to represent a novel species of the genus Prauserella , named Prauserella shujinwangii sp. nov. The type strain is XJ46T ( = CGMCC 4.7125T = JCM 19736T).

scholarly journals Pediococcus cellicola sp. nov., a novel lactic acid coccus isolated from a distilled-spirit-fermenting cellar

2005 ◽  
Vol 55 (5) ◽  
pp. 2167-2170 ◽  
Author(s):  
Bin Zhang ◽  
Huichun Tong ◽  
Xiuzhu Dong
Keyword(s):  
Lactic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
The Mean ◽  
Gene Similarity

Two novel Pediococcus strains, Z-1 and Z-8T, were isolated from a distilled-spirit-fermenting cellar in Hebei Province, China. The cells were Gram-positive, non-spore-forming, non-motile cocci, occurring in pairs or tetrads. The strains were facultatively anaerobic and produced 50 % (−)-d-/50 % (+)-l-lactic acid exclusively from glucose fermentation, but did not produce catalase. Both strains fermented rhamnose, ribose, xylose, lactose, maltose, trehalose and sucrose, and tolerated 10 % ethanol. The mean G+C content of the two strains was 38±1 mol% (37 mol% for the type strain, Z-8T). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Z-8T clustered within the Pediococcus damnosus–Pediococcus inopinatus–Pediococcus parvulus group, with 98·3–98·5 % 16S rRNA gene similarity. DNA–DNA relatedness between strain Z-8T and P. damnosus LMG 11484T, P. inopinatus LMG 11409T and P. parvulus LMG 11486T was 19±4, 35±5 and 31±5 %, respectively. Therefore, based on the distinctive phenotypic characteristics, and genotypic and phylogenetic analyses, a novel Pediococcus species, Pediococcus cellicola sp. nov., is proposed. The type strain is Z-8T (=AS 1.3787T=LMG 22956T).

scholarly journals Dactylosporangium luridum sp. nov., Dactylosporangium luteum sp. nov. and Dactylosporangium salmoneum sp. nov., nom. rev., isolated from soil

2010 ◽  
Vol 60 (8) ◽  
pp. 1813-1823 ◽  
Author(s):  
Byung-Yong Kim ◽  
James E. M. Stach ◽  
Hang-Yeon Weon ◽  
Soon-Wo Kwon ◽  
Michael Goodfellow
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Morphological Properties ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Gene Sequence Analysis ◽  
Type Strains

Forty strains isolated from soil taken from a hay meadow were assigned to the genus Dactylosporangium on the basis of colonial properties. 16S rRNA gene sequence analysis showed that the isolates formed a group that was most closely related to the type strain of Dactylosporangium aurantiacum, but well separated from other Dactylosporangium type strains and from ‘Dactylosporangium salmoneum’ NRRL B-16294. Twelve of 13 representative isolates had identical 16S rRNA gene sequences and formed a subclade that was distinct from corresponding phyletic lines composed of the remaining isolate, strain BK63T, the ‘D. salmoneum’ strain and the type strains of recognized Dactylosporangium species. DNA–DNA relatedness data indicated that representatives of the multi-membered 16S rRNA gene subclade, isolate BK63T and the ‘D. salmoneum’ subclade formed distinct genomic species; all of these organisms had chemotaxonomic and morphological properties consistent with their classification in the genus Dactylosporangium. They were also distinguished from one another and from the type strains of recognized Dactylosporangium species based on a range of phenotypic properties. Combined genotypic and phenotypic data showed that isolate BK63T, isolates BK51T, BK53 and BK69, and strain NRRL B-16294T should be classified in the genus Dactylosporangium as representing novel species. The names proposed for these species are Dactylosporangium luridum sp. nov. (type strain BK63T  = DSM 45324T  = KACC 20933T  = NRRL B-24775T), Dactylosporangium luteum sp. nov. (type strain BK51T  = DSM 45323T  = KACC 20899T  = NRRL B-24774T) and Dactylosporangium salmoneum sp. nov., nom. rev. (type strain NRRL B-16294T  = ATCC 31222T  = DSM 43910T  = JCM 3272T  = NBRC 14103T).

scholarly journals Pseudomonas reinekei sp. nov., Pseudomonas moorei sp. nov. and Pseudomonas mohnii sp. nov., novel species capable of degrading chlorosalicylates or isopimaric acid

2007 ◽  
Vol 57 (5) ◽  
pp. 923-931 ◽  
Author(s):  
Beatriz Cámara ◽  
Carsten Strömpl ◽  
Susanne Verbarg ◽  
Cathrin Spröer ◽  
Dietmar H. Pieper ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Phenotypic Characteristics ◽  
Isopimaric Acid ◽  
Gene Sequence Analysis

Three bacterial strains, designated MT1T, RW10T and IpA-2T, had been isolated previously for their ability to degrade chlorosalicylates or isopimaric acid. 16S rRNA gene sequence analysis demonstrated that these bacteria are related to species of the genus Pseudomonas. Analysis of the results of DNA–DNA hybridization with several close phylogenetic neighbours revealed a low level of hybridization (less than 57 %). On the basis of phenotypic characteristics, phylogenetic analysis, DNA–DNA relatedness data and chemotaxonomic analysis, it is concluded that these isolates represent separate novel species, for which the names Pseudomonas reinekei sp. nov. (type strain MT1T =DSM 18361T=CCUG 53116T), Pseudomonas moorei sp. nov. (type strain RW10T =DSM 12647T=CCUG 53114T) and Pseudomonas mohnii sp. nov. (type strain IpA-2T =DSM 18327T=CCUG 53115T) are proposed.

scholarly journals Emended description of the genus Pantoea, description of four species from human clinical samples, Pantoea septica sp. nov., Pantoea eucrina sp. nov., Pantoea brenneri sp. nov. and Pantoea conspicua sp. nov., and transfer of Pectobacterium cypripedii (Hori 1911) Brenner et al. 1973 emend. Hauben et al. 1998 to the genus as Pantoea cypripedii comb. nov.

2010 ◽  
Vol 60 (10) ◽  
pp. 2430-2440 ◽  
Author(s):  
Carrie L. Brady ◽  
Ilse Cleenwerck ◽  
Stephanus N. Venter ◽  
Katrien Engelbeen ◽  
Paul De Vos ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
16S Rrna Gene Sequencing ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Enterobacter Agglomerans ◽  
Bacterial Strains ◽  
Separate Species

Bacterial strains belonging to DNA hybridization groups (HG) II, IV and V, in the Erwinia herbicola–Enterobacter agglomerans complex, of Brenner et al. [Int J Syst Bacteriol 34 (1984), 45–55] were suggested previously to belong to the genus Pantoea, but have never been formally described and classified. Additionally, it has been shown in several studies that Pectobacterium cypripedii is more closely related to species of Pantoea than to those of Pectobacterium. In this study, the phylogenetic positions of Brenner's DNA HG II, IV and V and Pectobacterium cypripedii were re-examined by both 16S rRNA gene sequencing and multilocus sequence analyses (MLSA) based on the gyrB, rpoB, atpD and infB genes. The analyses revealed that DNA HG II, IV and V and Pectobacterium cypripedii form five separate branches within the genus Pantoea (strains from HG V were split into two branches). DNA–DNA hybridization data further confirmed that DNA HG II, IV and V constitute four separate species. Pectobacterium cypripedii was shown to be a close phylogenetic relative of Pantoea dispersa and DNA HG IV by both 16S rRNA gene sequence and MLSA analyses. Biochemical analyses performed on strains from DNA HG II, IV and V and Pectobacterium cypripedii confirmed their taxonomic position within the genus Pantoea and revealed phenotypic characteristics that allow the differentiation of these species from each other and from their closest phylogenetic neighbours. It is proposed to emend the description of the genus Pantoea and to describe Pantoea septica sp. nov. for DNA HG II (type strain LMG 5345T =BD 874T =CDC 3123-70T), Pantoea eucrina sp. nov. for DNA HG IV (type strain LMG 2781T =BD 872T =CDC 1741-71T =LMG 5346T), Pantoea brenneri sp. nov. for strains of DNA HG V excluding LMG 24534 (type strain LMG 5343T =BD 873T =CDC 3482-71T) and Pantoea conspicua sp. nov. for the remaining strain of DNA HG V (type strain LMG 24534T =BD 805T =CDC 3527-71T) and to transfer Pectobacterium cypripedii to the genus as Pantoea cypripedii comb. nov. (type strain LMG 2657T =ATCC 29267T =DSM 3873T =LMG 2655T).

scholarly journals Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA–DNA hybridization in the Bacillus subtilis group

2007 ◽  
Vol 57 (8) ◽  
pp. 1846-1850 ◽  
Author(s):  
Li-Ting Wang ◽  
Fwu-Ling Lee ◽  
Chun-Ju Tai ◽  
Hiroaki Kasai
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

The Bacillus subtilis group comprises eight closely related species that are indistinguishable from one another by 16S rRNA gene sequence analysis. Therefore, the gyrB gene, which encodes the subunit B protein of DNA gyrase, was selected as an alternative phylogenetic marker. To determine whether gyrB gene sequence analysis could be used for phylogenetic analysis and species identification of members of the B. subtilis group, the congruence of gyrB grouping with both 16S rRNA gene sequencing and DNA–DNA hybridization data was evaluated. Ranges of gyrB nucleotide and translated amino acid sequence similarities among the eight type strains were 75.4–95.0 % and 88.5–99.2 %, respectively, whereas 16S rRNA gene sequence similarities were 98.1–99.8 %. Results showed that gyrB gene sequences provide higher resolution than 16S rRNA gene sequences. The classification achieved by gyrB sequence analysis was in agreement with results obtained with DNA–DNA hybridization. It is concluded that the gyrB gene may be an efficient alternative target for identification and taxonomic analysis of members of the B. subtilis group.

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