scholarly journals Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA–DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species

2010 ◽  
Vol 60 (3) ◽  
pp. 696-703 ◽  
Author(s):  
Xiaoying Rong ◽  
Ying Huang
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Streptomyces Griseus ◽  
Multilocus Sequence Analysis ◽  
Rrna Gene ◽  
Good Resolution ◽  
Species Definition ◽  
Genomic Species

Streptomyces griseus and related species form the biggest but least well-defined clade in the whole Streptomyces 16S rRNA gene tree. Multilocus sequence analysis (MLSA) has shown promising potential for refining Streptomyces systematics. In this investigation, strains of 18 additional S. griseus clade species were analysed and data from a previous pilot study were integrated in a larger MLSA phylogeny. The results demonstrated that MLSA of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) is better than the previous six-gene scheme, as it provides equally good resolution and stability and is more cost-effective; MLSA using three or four of the genes also shows good resolution and robustness for differentiating most of the strains and is therefore of value for everyday use. MLSA is more suitable for discriminating strains that show >99 % 16S rRNA gene sequence similarity. DNA–DNA hybridization (DDH) between strains with representative MLSA distances revealed a strong correlation between the data of MLSA and DDH. The 70 % DDH value for current species definition corresponds to a five-gene MLSA distance of 0.007, which could be considered as the species cut-off for the S. griseus clade. It is concluded that the MLSA procedure can be a practical, reliable and robust alternative to DDH for the identification and classification of streptomycetes at the species and intraspecies levels. Based on the data from MLSA and DDH, as well as cultural and morphological characteristics, 18 species and three subspecies of the S. griseus clade are considered to be later heterotypic synonyms of 11 genomic species: Streptomyces griseinus and Streptomyces mediolani as synonyms of Streptomyces albovinaceus; Streptomyces praecox as a synonym of Streptomyces anulatus; Streptomyces olivoviridis as a synonym of Streptomyces atroolivaceus; Streptomyces griseobrunneus as a synonym of Streptomyces bacillaris; Streptomyces cavourensis subsp. washingtonensis as a synonym of Streptomyces cyaneofuscatus; Streptomyces acrimycini, Streptomyces baarnensis, Streptomyces caviscabies and Streptomyces flavofuscus as synonyms of Streptomyces fimicarius; Streptomyces flavogriseus as a synonym of Streptomyces flavovirens; Streptomyces erumpens, ‘Streptomyces ornatus’ and Streptomyces setonii as synonyms of Streptomyces griseus; Streptomyces graminofaciens as a synonym of Streptomyces halstedii; Streptomyces alboviridis, Streptomyces griseus subsp. alpha, Streptomyces griseus subsp. cretosus and Streptomyces luridiscabiei as synonyms of Streptomyces microflavus; and Streptomyces californicus and Streptomyces floridae as synonyms of Streptomyces puniceus.

scholarly journals Kaistia terrae sp. nov., isolated from a wetland in Korea

2010 ◽  
Vol 60 (4) ◽  
pp. 949-952 ◽  
Author(s):  
Soo-Jin Kim ◽  
Hang-Yeon Weon ◽  
Yi-Seul Kim ◽  
Rangasamy Anandham ◽  
Seung-Hee Yoo ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

An ivory-coloured bacterium, designated strain 5YN7-3T, was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3T belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8T (97.8 %), Kaistia granuli Ko04T (97.6 %) and Kaistia adipata Chj404T (97.4 %). Strain 5YN7-3T showed DNA–DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04T, K. soli 5YN9-8T and K. adipata Chj404T, respectively. The major fatty acids were C18 : 1 ω7c (51.2 %), C19 : 0 cyclo ω8c (25.0 %), C18 : 0 (12.9 %) and C16 : 0 (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA–DNA hybridization data clearly define strain 5YN7-3T as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3T (=KACC 12910T =DSM 21341T).

Description of Hymenobacter daejeonensis sp. nov., isolated from grass soil, based on multilocus sequence analysis of the 16S rRNA gene, gyrB and tuf genes

2018 ◽  
Vol 111 (12) ◽  
pp. 2283-2292 ◽  
Author(s):  
Long Jin ◽  
Xuewen Wu ◽  
So-Ra Ko ◽  
Feng-Jie Jin ◽  
Taihua Li ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Multilocus Sequence Analysis ◽  
Rrna Gene ◽  
The 16S Rrna Gene

scholarly journals Paenibacillus taiwanensis sp. nov., isolated from soil in Taiwan

2007 ◽  
Vol 57 (6) ◽  
pp. 1351-1354 ◽  
Author(s):  
Fwu-Ling Lee ◽  
Hsiao-Ping Kuo ◽  
Chun-Ju Tai ◽  
Akira Yokota ◽  
Chi-Chu Lo
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

Among a large collection of Taiwanese soil isolates, a novel Gram-variable, rod-shaped, motile and endospore-forming bacterial strain, designated G-soil-2-3T, was isolated from farmland soil in Wu-Feng, Taiwan. The isolate was subjected to a polyphasic study including 16S rRNA gene sequence analysis, DNA–DNA hybridization experiments, fatty acid analysis and comparative phenotypic characterization. 16S rRNA gene sequence analysis indicated that the organism belongs within the genus Paenibacillus. It contained menaquinone MK-7 as the predominant isoprenoid quinone and anteiso-C15 : 0 (40.5 %), iso-C15 : 0 (13.1 %), iso-C16 : 0 (10.8 %) and anteiso-C17 : 0 (7.3 %) as the major fatty acids. Phylogenetically, the closest relatives of strain G-soil-2-3T were the type strains of Paenibacillus assamensis, Paenibacillus alvei and Paenibacillus apiarius, with 16S rRNA gene sequence similarity of 95.7, 95 and 95.2 %, respectively. DNA–DNA hybridization experiments showed levels of relatedness of 2.8–9.0 % of strain G-soil-2-3T with these strains. The G+C content of the DNA was 44.6 mol%. Strain G-soil-2-3T was clearly distinguishable from P. assamensis, P. alvei and P. apiarius and thus represents a novel species of the genus Paenibacillus, for which the name Paenibacillus taiwanensis sp. nov. is proposed. The type strain is G-soil-2-3T (=BCRC 17411T=IAM 15414T=LMG 23799T=DSM 18679T).

scholarly journals Reclassification of Paralactobacillus selangorensis Leisner et al. 2000 as Lactobacillus selangorensis comb. nov.

2011 ◽  
Vol 61 (12) ◽  
pp. 2979-2983 ◽  
Author(s):  
Monique Haakensen ◽  
Vanessa Pittet ◽  
Barry Ziola
Keyword(s):  
Cell Division ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Taxonomic Status ◽  
Multilocus Sequence Analysis ◽  
Rrna Gene ◽  
Phenotypic Information ◽  
The 16S Rrna Gene

The taxonomic status of Paralactobacillus selangorensis is described and, based on evidence presented, transfer of the species to the genus Lactobacillus with the name Lactobacillus selangorensis comb. nov. is proposed. This reclassification is supported by multilocus sequence analysis of the 16S rRNA gene and portions of the cpn60, pheS and rpoA genes. Mode of cell division and existing phenotypic information also show that P. selangorensis cannot be differentiated from the genus Lactobacillus. The type strain of Lactobacillus selangorensis comb. nov. is ATCC BAA-66T ( = LMG 17710T  = CIP 106482T).

scholarly journals Use of the novel phylogenetic marker dnaJ and DNA–DNA hybridization to clarify interrelationships within the genus Aeromonas

2007 ◽  
Vol 57 (6) ◽  
pp. 1232-1237 ◽  
Author(s):  
Pham Hong Nhung ◽  
Hiroyuki Hata ◽  
Kiyofumi Ohkusu ◽  
Makiko Noda ◽  
Mohammad Monir Shah ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Dna Relatedness ◽  
Aeromonas Veronii ◽  
Dna Reassociation ◽  
Sequence Similarities

The interrelationships of 27 Aeromonas strains were investigated using dnaJ sequences and DNA–DNA hybridization. dnaJ sequence similarities showed a stronger relationship with DNA–DNA relatedness values than did 16S rRNA gene sequence similarities. Additionally, dnaJ sequence analysis, with interspecies divergence over 5.2 % in most cases, gave better resolution than 16S rRNA gene sequences for the differentiation of strains at the species level. Relationships among Aeromonas species were therefore elucidated on the basis of dnaJ sequences and DNA–DNA reassociation. Strains of Aeromonas encheleia and Aeromonas sp. HG11 were unquestionably grouped in the same genetic species, since they shared 98.7 % dnaJ sequence similarity and 82–85 % genomic relatedness. The phylogenetically close relationships obtained from dnaJ sequence analysis (1.7–3.3 % genetic distance) were corroborated by high DNA–DNA relatedness (73–97 %) to support the previous suggestion that Aeromonas culicicola and Aeromonas allosaccharophila are later heterotypic synonyms of Aeromonas veronii. Our findings will contribute to the clarification of controversial relationships in the genus Aeromonas and also demonstrate that analysis of dnaJ sequences can be a powerful tool for interspecies study of the genus.

scholarly journals Multilocus sequence analysis of phytopathogenic species of the genus Streptomyces

2011 ◽  
Vol 61 (10) ◽  
pp. 2525-2531 ◽  
Author(s):  
David P. Labeda
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Multilocus Sequence Analysis ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Genus Streptomyces ◽  
Type Strains

The identification and classification of species within the genus Streptomyces is difficult because there are presently 576 species with validly published names and this number increases every year. The value of multilocus sequence analysis applied to the systematics of Streptomyces species has been well demonstrated in several recently published papers. In this study the sequence fragments of four housekeeping genes, atpD, recA, rpoB and trpB, were determined for the type strains of 10 known phytopathogenic species of the genus Streptomyces, including Streptomyces scabiei, Streptomyces acidiscabies, Streptomyces europaeiscabiei, Streptomyces luridiscabiei, Streptomyces niveiscabiei, Streptomyces puniciscabiei, Streptomyces reticuliscabiei, Streptomyces stelliscabiei, Streptomyces turgidiscabies and Streptomyces ipomoeae, as well as six uncharacterized phytopathogenic Streptomyces isolates. The type strains of 52 other species, including 19 species observed to be phylogenetically closely related to these, based on 16S rRNA gene sequence analysis, were also included in the study. Phylogenetic analysis of single gene alignments and a concatenated four-gene alignment demonstrated that the phytopathogenic species are taxonomically distinct from each other in spite of high 16S rRNA gene sequence similarities and provided a tool for the identification of unknown putative phytopathogenic Streptomyces strains at the species level.

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 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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