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Ying Huang - One of the best experts on this subject based on the ideXlab platform.
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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
International Journal of Systematic and Evolutionary Microbiology, 2010Co-Authors: Xiaoying Rong, Ying HuangAbstract: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.
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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
International Journal of Systematic and Evolutionary Microbiology, 2010Co-Authors: Xiaoying Rong, Ying HuangAbstract: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.
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Classification of Streptomyces griseus (Krainsky 1914) Waksman and Henrici 1948 and related species and the transfer of ‘Microstreptospora cinerea’ to the genus Streptomyces as Streptomyces yanii sp. nov.
International Journal of Systematic and Evolutionary Microbiology, 2005Co-Authors: Zhiheng Liu, Yanlin Shi, Yamei Zhang, Zhi-hong Zhou, Ying Huang, Carlos Rodríguez, Michael GoodfellowAbstract:A soil actinomycete, strain 80-133T, with the non-validly published name ‘Microstreptospora cinerea’, was the subject of a polyphasic study designed to clarify its taxonomic status. Comparative 16S rRNA gene sequence studies indicated that the organism belonged to the genus Streptomyces, a result in line with previous chemotaxonomic and morphological data. The strain belonged to the Streptomyces griseus clade, but could be distinguished from representatives of species assigned to this taxon by using DNA–DNA relatedness and phenotypic data. In light of these findings, it is proposed that the organism should be recognized as a novel species of the genus Streptomyces. The name proposed for this taxon is Streptomyces yanii sp. nov., with isolate 80-133T (=AS 4.1146T=JCM 3331T) as the type strain. It was also shown that representative strains of Streptomyces argenteolus, Streptomyces caviscabies, S. griseus and Streptomyces Setonii belong to the same genomic species and have key phenotypic properties in common. It is proposed that S. caviscabies and S. Setonii should be considered as later heterotypic synonyms of S. griseus and that S. argenteolus AS 4.1693T should also be assigned to this taxon.
Seung Bum Kim - One of the best experts on this subject based on the ideXlab platform.
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Reassessment of the status of Streptomyces Setonii and reclassification of Streptomyces fimicarius as a later synonym of
International Journal of Systematic and Evolutionary Microbiology, 2012Co-Authors: Kyoung-ok Kim, Kwang-soo Shin, Mi Na Kim, Kee-sun Shin, David P. Labeda, Ji-hye Han, Seung Bum KimAbstract:The 16S rRNA and gyrB genes of 22 Streptomyces strains belonging to the Streptomyces griseus cluster were sequenced, and their taxonomic positions were re-evaluated. For correct analysis, all of the publicly available sequences of the species were collected and compared with those obtained in this study. Species for which no consensus sequence could be identified were excluded from the phylogenetic analysis. The levels of 16S rRNA gene sequence similarity within the cluster ranged from 98.6 to 100 % with a mean value of 99.6±0.3 %, and those of the gyrB gene ranged from 93.6 to 99.9 % with a mean value of 96.3±1.5 %. The observed average nucleotide substitution rate of the gyrB gene was ten times higher than that of the 16S rRNA gene, showing a far higher degree of variation. Strains sharing 99.3 % or more gyrB sequence similarity (corresponding to an evolutionary distance of 0.0073) always formed monophyletic groups in both trees. Through the combined analysis of the two genes, clear cases of synonymy could be identified and, according to the priority rule, the assertion of the status of Streptomyces Setonii as a distinct species and the reclassification of Streptomyces fimicarius as a later synonym of S. Setonii and Streptomyces albovinaceus as a later synonym of Streptomyces globisporus are proposed. Emended descriptions of S. Setonii and S. globisporus are provided.
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Reassessment of the status of Streptomyces Setonii and reclassification of Streptomyces fimicarius as a later synonym of Streptomyces Setonii and Streptomyces albovinaceus as a later synonym of Streptomyces globisporus based on combined 16S rRNA/gyrB
International Journal of Systematic and Evolutionary Microbiology, 2012Co-Authors: Kyoung-ok Kim, Kwang-soo Shin, Mi Na Kim, Kee-sun Shin, David P. Labeda, Ji-hye Han, Seung Bum KimAbstract:The 16S rRNA and gyrB genes of 22 Streptomyces strains belonging to the Streptomyces griseus cluster were sequenced, and their taxonomic positions were re-evaluated. For correct analysis, all of the publicly available sequences of the species were collected and compared with those obtained in this study. Species for which no consensus sequence could be identified were excluded from the phylogenetic analysis. The levels of 16S rRNA gene sequence similarity within the cluster ranged from 98.6 to 100 % with a mean value of 99.6±0.3 %, and those of the gyrB gene ranged from 93.6 to 99.9 % with a mean value of 96.3±1.5 %. The observed average nucleotide substitution rate of the gyrB gene was ten times higher than that of the 16S rRNA gene, showing a far higher degree of variation. Strains sharing 99.3 % or more gyrB sequence similarity (corresponding to an evolutionary distance of 0.0073) always formed monophyletic groups in both trees. Through the combined analysis of the two genes, clear cases of synonymy could be identified and, according to the priority rule, the assertion of the status of Streptomyces Setonii as a distinct species and the reclassification of Streptomyces fimicarius as a later synonym of S. Setonii and Streptomyces albovinaceus as a later synonym of Streptomyces globisporus are proposed. Emended descriptions of S. Setonii and S. globisporus are provided.
Kyoung-ok Kim - One of the best experts on this subject based on the ideXlab platform.
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Reassessment of the status of Streptomyces Setonii and reclassification of Streptomyces fimicarius as a later synonym of
International Journal of Systematic and Evolutionary Microbiology, 2012Co-Authors: Kyoung-ok Kim, Kwang-soo Shin, Mi Na Kim, Kee-sun Shin, David P. Labeda, Ji-hye Han, Seung Bum KimAbstract:The 16S rRNA and gyrB genes of 22 Streptomyces strains belonging to the Streptomyces griseus cluster were sequenced, and their taxonomic positions were re-evaluated. For correct analysis, all of the publicly available sequences of the species were collected and compared with those obtained in this study. Species for which no consensus sequence could be identified were excluded from the phylogenetic analysis. The levels of 16S rRNA gene sequence similarity within the cluster ranged from 98.6 to 100 % with a mean value of 99.6±0.3 %, and those of the gyrB gene ranged from 93.6 to 99.9 % with a mean value of 96.3±1.5 %. The observed average nucleotide substitution rate of the gyrB gene was ten times higher than that of the 16S rRNA gene, showing a far higher degree of variation. Strains sharing 99.3 % or more gyrB sequence similarity (corresponding to an evolutionary distance of 0.0073) always formed monophyletic groups in both trees. Through the combined analysis of the two genes, clear cases of synonymy could be identified and, according to the priority rule, the assertion of the status of Streptomyces Setonii as a distinct species and the reclassification of Streptomyces fimicarius as a later synonym of S. Setonii and Streptomyces albovinaceus as a later synonym of Streptomyces globisporus are proposed. Emended descriptions of S. Setonii and S. globisporus are provided.
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Reassessment of the status of Streptomyces Setonii and reclassification of Streptomyces fimicarius as a later synonym of Streptomyces Setonii and Streptomyces albovinaceus as a later synonym of Streptomyces globisporus based on combined 16S rRNA/gyrB
International Journal of Systematic and Evolutionary Microbiology, 2012Co-Authors: Kyoung-ok Kim, Kwang-soo Shin, Mi Na Kim, Kee-sun Shin, David P. Labeda, Ji-hye Han, Seung Bum KimAbstract:The 16S rRNA and gyrB genes of 22 Streptomyces strains belonging to the Streptomyces griseus cluster were sequenced, and their taxonomic positions were re-evaluated. For correct analysis, all of the publicly available sequences of the species were collected and compared with those obtained in this study. Species for which no consensus sequence could be identified were excluded from the phylogenetic analysis. The levels of 16S rRNA gene sequence similarity within the cluster ranged from 98.6 to 100 % with a mean value of 99.6±0.3 %, and those of the gyrB gene ranged from 93.6 to 99.9 % with a mean value of 96.3±1.5 %. The observed average nucleotide substitution rate of the gyrB gene was ten times higher than that of the 16S rRNA gene, showing a far higher degree of variation. Strains sharing 99.3 % or more gyrB sequence similarity (corresponding to an evolutionary distance of 0.0073) always formed monophyletic groups in both trees. Through the combined analysis of the two genes, clear cases of synonymy could be identified and, according to the priority rule, the assertion of the status of Streptomyces Setonii as a distinct species and the reclassification of Streptomyces fimicarius as a later synonym of S. Setonii and Streptomyces albovinaceus as a later synonym of Streptomyces globisporus are proposed. Emended descriptions of S. Setonii and S. globisporus are provided.
Jose M. Domínguez - One of the best experts on this subject based on the ideXlab platform.
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Decarboxylation of Ferulic Acid to 4-Vinyl Guaiacol by Streptomyces Setonii
Applied Biochemistry and Biotechnology, 2012Co-Authors: Belén Max, Julia Carballo, Sandra Cortés, Jose M. DomínguezAbstract:4-Vinyl guaiacol (3-methoxy 4-hydroxystyrene) can be obtained by decarboxylation of ferulic acid by the strain Streptomyces Setonii ATCC 39116. The formation of this metabolite was favoured by microaerobic conditions and the culture medium employed, increasing progressively the product concentration from 543.3 up to 885.1 mg/l when aeration level was diminished, reaching a highest volumetric productivity of 70.4 mg/l h and a product yield of 1.11 mol/mol. The identity of the metabolite was confirmed by gas chromatography–mass spectrometry. A metabolic study of ferulic acid and the main degradation products (ferulic acid, 4-vinyl guaiacol, protocatechuic acid, vanillyl alcohol, vanillic acid and vanillin) suggested that ferulic acid was the only substrate capable to be transformed into 4-vinyl guaiacol by this strain of S. Setonii .
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Extraction of ferulic acid from agro-industrial wastes and evaluation of bioconversion of ferulic acid to vanillin by Streptomyces Setonii
2012Co-Authors: José Manuel Salgado, Belén Max, Raquel Leirós Rodríguez, Noelia Pérez, Jose M. DomínguezAbstract:Several agro-industrial wastes (as chestnut and pistachio shells, grass, leaf fruit, vine leaf, and, red and white grape stems) were evaluated to ferulic acid extraction. The chemical analysis of these raw materials shows a high content of xylan in pistachio shells (33%), following the biorefinery concept, this fraction can be used in xylitol manufacture. The lignocellulosic materials were submitted to an alkaline extraction to obtain phenolic compounds, reaching a concentration of 312 mg ferulic acid/L in grass wastes. Other phenolic compounds were also extracted (gallic acid, p-coumaric acid, syringic acid etc.) depending of used raw material. Besides, the ferulic fermentation into vanillin was assayed. The higher concentration of vainillin (2692 mg/L) was achieved at 27 h (QP = 99.704 mg/L·h and YP/S = 0.50 mg/mg) using Streptomyces Setonii.
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Purification of ferulic acid solubilized from agroindustrial wastes and further conversion into 4-vinyl guaiacol by Streptomyces Setonii using solid state fermentation.
Industrial Crops and Products, 2012Co-Authors: José Manuel Salgado, Belén Max, Raquel Rodríguez-solana, Jose M. DomínguezAbstract:Abstract This work deals with the screening of seven lignocellulosic residues: chestnut and pistachio shells, grass, leaf fruit, vine leaf, and, red and white grape stems as feedstocks for the release of ferulic acid by sequential pre-treatment with dilute sulfuric acid and alkaline hydrolysis with NaOH. Grass showed the highest concentration of both ferulic acid (312.0 mg/L) and p-coumaric acid (542.7 mg/L). Ferulic acid was further purified from the brown liquor by ethanol extraction, or adsorption with activated charcoal or polyvinylpolypyrrolidone (PVPP). Finally, streams coming from these treatments were fermented by Streptomyces Setonii after nutrients supplementation in solid state fermentation. Ferulic acid treated with PVPP presented the best results, achieving 92.1 mg/L 4-vinyl guaiacol (3-methoxy 4-hydroxystyrene) after 30 h of fermentation (QP = 3.071 mg/L h; YP/S = 0.44 g/g), thus confirming the efficacy of the materials as renewable feedstocks, and the treatments for producing natural food additives with high add value.
Xiaoying Rong - One of the best experts on this subject based on the ideXlab platform.
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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
International Journal of Systematic and Evolutionary Microbiology, 2010Co-Authors: Xiaoying Rong, Ying HuangAbstract: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.
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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
International Journal of Systematic and Evolutionary Microbiology, 2010Co-Authors: Xiaoying Rong, Ying HuangAbstract: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.