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Michael Goodfellow - One of the best experts on this subject based on the ideXlab platform.
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Revisiting the Taxonomic Status of the Biomedically and Industrially Important Genus Amycolatopsis, Using a Phylogenomic Approach.
Frontiers in microbiology, 2018Co-Authors: Vartul Sangal, Michael Goodfellow, Geok Yuan Annie Tan, Jochen Blom, Hans-peter Klenk, Iain C. SutcliffeAbstract:Strains belonging to the genus Amycolatopsis are well known for the production of a number of important antimicrobials and other bioactive molecules. In this study, we have sequenced the genomes of five Amycolatopsis strains including Amycolatopsis circi DSM 45561T, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis thermalba NRRL B-24845T. The genome sequences were analyzed with 52 other publically available Amycolatopsis genomes, representing 34 species, and 12 representatives from related genera including Saccharomonospora, Saccharopolyspora, Saccharothrix, Pseudonocardia and Thermobispora. Based on the core genome phylogeny, Amycolatopsis strains were subdivided into four major clades and several singletons. The genus Amycolatopsis is homogeneous with only three strains noted to group with other genera. Amycolatopsis halophila YIM93223T is quite distinct from other Amycolatopsis strains, both phylogenetically and taxonomically, and belongs to a distinct genus. In addition, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis marina CGMCC4 3568T grouped in a clade with Saccharomonospora strains and showed similar taxogenomic differences to this genus as well as other Amycolatopsis strains. The study found a number of strains, particularly those identified as Amycolatopsis orientalis, whose incorrect identification could be resolved by taxogenomic analyses. Similarly, some unclassified strains could be assigned with species designations. The genome sequences of some strains that were independently sequenced by different laboratories were almost identical (99-100% average nucleotide and amino acid identities) consistent with them being the same strain, and confirming the reproducibility and robustness of genomic data. These analyses further demonstrate that whole genome sequencing can reliably resolve intra- and, inter-generic structures and should be incorporated into prokaryotic systematics.
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Amycolatopsis vastitatis sp. nov., an isolate from a high altitude subsurface soil on Cerro Chajnantor, northern Chile
Antonie van Leeuwenhoek, 2018Co-Authors: Hamidah Idris, Wasu Pathom-aree, Imen Nouioui, Jean Franco Castro, Alan T. Bull, Barbara A. Andrews, Juan A. Asenjo, Michael GoodfellowAbstract:The taxonomic position of a novel Amycolatopsis strain isolated from a high altitude Atacama Desert subsurface soil was established using a polyphasic approach. The strain, isolate H5^T, was shown to have chemical properties typical of members of the genus Amycolatopsis such as meso -diaminopimelic acid as the diamino acid in the cell wall peptidoglycan, arabinose and galactose as diagnostic sugars and MK-9(H_4) as the predominant isoprenologue. It also has cultural and morphological properties consistent with its classification in the genus, notably the formation of branching substrate hyphae which fragment into rod-like elements. 16S rRNA gene sequence analyses showed that the strain is closely related to the type strain of Amycolatopsis mediterranei but could be distinguished from this and other related Amycolatopsis strains using a broad range of phenotypic properties. It was separated readily from the type strain of Amycolatopsis balhymycina , its near phylogenetic neighbour, based on multi-locus sequence data, by low average nucleotide identity (92.9%) and in silico DNA/DNA relatedness values (51.3%) calculated from draft genome assemblies. Consequently, the strain is considered to represent a novel species of Amycolatopsis for which the name Amycolatopsis vastitatis sp. nov. is proposed. The type strain is H5^T (= NCIMB 14970^T = NRRL B-65279^T).
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comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species
BMC Genomics, 2018Co-Authors: Martina Adamek, Michael Goodfellow, Alan T. Bull, Mohammad Alanjary, Anika Winkler, Daniel Wibberg, Jörn Kalinowski, Helena Salesortells, Nadine ZiemertAbstract:Genome mining tools have enabled us to predict biosynthetic gene clusters that might encode compounds with valuable functions for industrial and medical applications. With the continuously increasing number of genomes sequenced, we are confronted with an overwhelming number of predicted clusters. In order to guide the effective prioritization of biosynthetic gene clusters towards finding the most promising compounds, knowledge about diversity, phylogenetic relationships and distribution patterns of biosynthetic gene clusters is necessary. Here, we provide a comprehensive analysis of the model actinobacterial genus Amycolatopsis and its potential for the production of secondary metabolites. A phylogenetic characterization, together with a pan-genome analysis showed that within this highly diverse genus, four major lineages could be distinguished which differed in their potential to produce secondary metabolites. Furthermore, we were able to distinguish gene cluster families whose distribution correlated with phylogeny, indicating that vertical gene transfer plays a major role in the evolution of secondary metabolite gene clusters. Still, the vast majority of the diverse biosynthetic gene clusters were derived from clusters unique to the genus, and also unique in comparison to a database of known compounds. Our study on the locations of biosynthetic gene clusters in the genomes of Amycolatopsis’ strains showed that clusters acquired by horizontal gene transfer tend to be incorporated into non-conserved regions of the genome thereby allowing us to distinguish core and hypervariable regions in Amycolatopsis genomes. Using a comparative genomics approach, it was possible to determine the potential of the genus Amycolatopsis to produce a huge diversity of secondary metabolites. Furthermore, the analysis demonstrates that horizontal and vertical gene transfer play an important role in the acquisition and maintenance of valuable secondary metabolites. Our results cast light on the interconnections between secondary metabolite gene clusters and provide a way to prioritize biosynthetic pathways in the search and discovery of novel compounds.
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Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species
BMC Genomics, 2018Co-Authors: Martina Adamek, Michael Goodfellow, Alan T. Bull, Mohammad Alanjary, Helena Sales-ortells, Anika Winkler, Daniel Wibberg, Jörn Kalinowski, Nadine ZiemertAbstract:Background Genome mining tools have enabled us to predict biosynthetic gene clusters that might encode compounds with valuable functions for industrial and medical applications. With the continuously increasing number of genomes sequenced, we are confronted with an overwhelming number of predicted clusters. In order to guide the effective prioritization of biosynthetic gene clusters towards finding the most promising compounds, knowledge about diversity, phylogenetic relationships and distribution patterns of biosynthetic gene clusters is necessary. Results Here, we provide a comprehensive analysis of the model actinobacterial genus Amycolatopsis and its potential for the production of secondary metabolites. A phylogenetic characterization, together with a pan-genome analysis showed that within this highly diverse genus, four major lineages could be distinguished which differed in their potential to produce secondary metabolites. Furthermore, we were able to distinguish gene cluster families whose distribution correlated with phylogeny, indicating that vertical gene transfer plays a major role in the evolution of secondary metabolite gene clusters. Still, the vast majority of the diverse biosynthetic gene clusters were derived from clusters unique to the genus, and also unique in comparison to a database of known compounds. Our study on the locations of biosynthetic gene clusters in the genomes of Amycolatopsis ’ strains showed that clusters acquired by horizontal gene transfer tend to be incorporated into non-conserved regions of the genome thereby allowing us to distinguish core and hypervariable regions in Amycolatopsis genomes. Conclusions Using a comparative genomics approach, it was possible to determine the potential of the genus Amycolatopsis to produce a huge diversity of secondary metabolites. Furthermore, the analysis demonstrates that horizontal and vertical gene transfer play an important role in the acquisition and maintenance of valuable secondary metabolites. Our results cast light on the interconnections between secondary metabolite gene clusters and provide a way to prioritize biosynthetic pathways in the search and discovery of novel compounds.
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Data_Sheet_1_Revisiting the Taxonomic Status of the Biomedically and Industrially Important Genus Amycolatopsis, Using a Phylogenomic Approach.PDF
2018Co-Authors: Vartul Sangal, Michael Goodfellow, Geok Yuan Annie Tan, Jochen Blom, Hans-peter Klenk, Iain C. SutcliffeAbstract:Strains belonging to the genus Amycolatopsis are well known for the production of a number of important antimicrobials and other bioactive molecules. In this study, we have sequenced the genomes of five Amycolatopsis strains including Amycolatopsis circi DSM 45561T, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis thermalba NRRL B-24845T. The genome sequences were analyzed with 52 other publically available Amycolatopsis genomes, representing 34 species, and 12 representatives from related genera including Saccharomonospora, Saccharopolyspora, Saccharothrix, Pseudonocardia and Thermobispora. Based on the core genome phylogeny, Amycolatopsis strains were subdivided into four major clades and several singletons. The genus Amycolatopsis is homogeneous with only three strains noted to group with other genera. Amycolatopsis halophila YIM93223T is quite distinct from other Amycolatopsis strains, both phylogenetically and taxonomically, and belongs to a distinct genus. In addition, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis marina CGMCC4 3568T grouped in a clade with Saccharomonospora strains and showed similar taxogenomic differences to this genus as well as other Amycolatopsis strains. The study found a number of strains, particularly those identified as Amycolatopsis orientalis, whose incorrect identification could be resolved by taxogenomic analyses. Similarly, some unclassified strains could be assigned with species designations. The genome sequences of some strains that were independently sequenced by different laboratories were almost identical (99–100% average nucleotide and amino acid identities) consistent with them being the same strain, and confirming the reproducibility and robustness of genomic data. These analyses further demonstrate that whole genome sequencing can reliably resolve intra- and, inter-generic structures and should be incorporated into prokaryotic systematics.
Geok Yuan Annie Tan - One of the best experts on this subject based on the ideXlab platform.
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Revisiting the Taxonomic Status of the Biomedically and Industrially Important Genus Amycolatopsis, Using a Phylogenomic Approach.
Frontiers in microbiology, 2018Co-Authors: Vartul Sangal, Michael Goodfellow, Geok Yuan Annie Tan, Jochen Blom, Hans-peter Klenk, Iain C. SutcliffeAbstract:Strains belonging to the genus Amycolatopsis are well known for the production of a number of important antimicrobials and other bioactive molecules. In this study, we have sequenced the genomes of five Amycolatopsis strains including Amycolatopsis circi DSM 45561T, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis thermalba NRRL B-24845T. The genome sequences were analyzed with 52 other publically available Amycolatopsis genomes, representing 34 species, and 12 representatives from related genera including Saccharomonospora, Saccharopolyspora, Saccharothrix, Pseudonocardia and Thermobispora. Based on the core genome phylogeny, Amycolatopsis strains were subdivided into four major clades and several singletons. The genus Amycolatopsis is homogeneous with only three strains noted to group with other genera. Amycolatopsis halophila YIM93223T is quite distinct from other Amycolatopsis strains, both phylogenetically and taxonomically, and belongs to a distinct genus. In addition, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis marina CGMCC4 3568T grouped in a clade with Saccharomonospora strains and showed similar taxogenomic differences to this genus as well as other Amycolatopsis strains. The study found a number of strains, particularly those identified as Amycolatopsis orientalis, whose incorrect identification could be resolved by taxogenomic analyses. Similarly, some unclassified strains could be assigned with species designations. The genome sequences of some strains that were independently sequenced by different laboratories were almost identical (99-100% average nucleotide and amino acid identities) consistent with them being the same strain, and confirming the reproducibility and robustness of genomic data. These analyses further demonstrate that whole genome sequencing can reliably resolve intra- and, inter-generic structures and should be incorporated into prokaryotic systematics.
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Data_Sheet_1_Revisiting the Taxonomic Status of the Biomedically and Industrially Important Genus Amycolatopsis, Using a Phylogenomic Approach.PDF
2018Co-Authors: Vartul Sangal, Michael Goodfellow, Geok Yuan Annie Tan, Jochen Blom, Hans-peter Klenk, Iain C. SutcliffeAbstract:Strains belonging to the genus Amycolatopsis are well known for the production of a number of important antimicrobials and other bioactive molecules. In this study, we have sequenced the genomes of five Amycolatopsis strains including Amycolatopsis circi DSM 45561T, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis thermalba NRRL B-24845T. The genome sequences were analyzed with 52 other publically available Amycolatopsis genomes, representing 34 species, and 12 representatives from related genera including Saccharomonospora, Saccharopolyspora, Saccharothrix, Pseudonocardia and Thermobispora. Based on the core genome phylogeny, Amycolatopsis strains were subdivided into four major clades and several singletons. The genus Amycolatopsis is homogeneous with only three strains noted to group with other genera. Amycolatopsis halophila YIM93223T is quite distinct from other Amycolatopsis strains, both phylogenetically and taxonomically, and belongs to a distinct genus. In addition, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis marina CGMCC4 3568T grouped in a clade with Saccharomonospora strains and showed similar taxogenomic differences to this genus as well as other Amycolatopsis strains. The study found a number of strains, particularly those identified as Amycolatopsis orientalis, whose incorrect identification could be resolved by taxogenomic analyses. Similarly, some unclassified strains could be assigned with species designations. The genome sequences of some strains that were independently sequenced by different laboratories were almost identical (99–100% average nucleotide and amino acid identities) consistent with them being the same strain, and confirming the reproducibility and robustness of genomic data. These analyses further demonstrate that whole genome sequencing can reliably resolve intra- and, inter-generic structures and should be incorporated into prokaryotic systematics.
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Table_3_Revisiting the Taxonomic Status of the Biomedically and Industrially Important Genus Amycolatopsis, Using a Phylogenomic Approach.XLSX
2018Co-Authors: Vartul Sangal, Michael Goodfellow, Geok Yuan Annie Tan, Jochen Blom, Hans-peter Klenk, Iain C. SutcliffeAbstract:Strains belonging to the genus Amycolatopsis are well known for the production of a number of important antimicrobials and other bioactive molecules. In this study, we have sequenced the genomes of five Amycolatopsis strains including Amycolatopsis circi DSM 45561T, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis thermalba NRRL B-24845T. The genome sequences were analyzed with 52 other publically available Amycolatopsis genomes, representing 34 species, and 12 representatives from related genera including Saccharomonospora, Saccharopolyspora, Saccharothrix, Pseudonocardia and Thermobispora. Based on the core genome phylogeny, Amycolatopsis strains were subdivided into four major clades and several singletons. The genus Amycolatopsis is homogeneous with only three strains noted to group with other genera. Amycolatopsis halophila YIM93223T is quite distinct from other Amycolatopsis strains, both phylogenetically and taxonomically, and belongs to a distinct genus. In addition, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis marina CGMCC4 3568T grouped in a clade with Saccharomonospora strains and showed similar taxogenomic differences to this genus as well as other Amycolatopsis strains. The study found a number of strains, particularly those identified as Amycolatopsis orientalis, whose incorrect identification could be resolved by taxogenomic analyses. Similarly, some unclassified strains could be assigned with species designations. The genome sequences of some strains that were independently sequenced by different laboratories were almost identical (99–100% average nucleotide and amino acid identities) consistent with them being the same strain, and confirming the reproducibility and robustness of genomic data. These analyses further demonstrate that whole genome sequencing can reliably resolve intra- and, inter-generic structures and should be incorporated into prokaryotic systematics.
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Amycolatopsis granulosa sp. nov., Amycolatopsis ruanii sp. nov. and Amycolatopsis thermalba sp. nov., thermophilic actinomycetes isolated from arid soils.
International journal of systematic and evolutionary microbiology, 2011Co-Authors: Tiago Domingues Zucchi, Geok Yuan Annie Tan, Avinash Naga Venkata Bonda, Sarah Frank, Jenileima Devi Kshetrimayum, Michael GoodfellowAbstract:The taxonomic positions of three thermophilic actinomycetes isolated from arid soil samples were established by using a polyphasic approach. The organisms had chemical and morphological features that were consistent with their classification in the genus Amycolatopsis. 16S rRNA gene sequence data supported the classification of the isolates in the genus Amycolatopsis and showed that they formed distinct branches in the Amycolatopsis methanolica subclade. DNA-DNA relatedness studies between the isolates and their phylogenetic neighbours showed that they belonged to distinct genomic species. The three isolates were readily distinguished from one another and from the type strains of species classified in the A. methanolica subclade based on a combination of phenotypic properties and by genomic fingerprinting. Consequently, it is proposed that the three isolates be classified in the genus Amycolatopsis as representatives of Amycolatopsis granulosa sp. nov. (type strain GY307(T) = NCIMB 14709(T) = NRRL B-24844(T)), Amycolatopsis ruanii sp. nov. (type strain NMG112(T) = NCIMB 14711(T) = NRRL B-24848(T)) and Amycolatopsis thermalba sp. nov. (type strain SF45(T) = NCIMB 14705(T) = NRRL B-24845(T)).
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Amycolatopsis thermophila sp. nov. and Amycolatopsis viridis sp. nov., thermophilic actinomycetes isolated from arid soil.
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Tiago Domingues Zucchi, Geok Yuan Annie Tan, Michael GoodfellowAbstract:The taxonomic positions of two thermophilic actinomycetes isolated from an arid Australian soil sample were established based on an investigation using a polyphasic taxonomic approach. The organisms had chemical and morphological properties typical of members of the genus Amycolatopsis and formed distinct phyletic lines in the Amycolatopsis methanolica 16S rRNA subclade. The two organisms were distinguished from one another and from the type strains of related species of the genus Amycolatopsis using a range of phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the two isolates be classified in the genus Amycolatopsis as Amycolatopsis thermophila sp. nov. (type strain GY088 T 5NCIMB 14699 T 5NRRL B-24836 T ) and Amycolatopsis viridis sp. nov. (type strain GY115 T 5NCIMB 14700 T 5NRRL B-24837 T ).
Paul R. Meyers - One of the best experts on this subject based on the ideXlab platform.
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Amycolatopsis roodepoortensis sp. nov. and Amycolatopsis speibonae sp. nov.: antibiotic-producing actinobacteria isolated from South African soils
The Journal of Antibiotics, 2014Co-Authors: Gareth J. Everest, Marilize Roes-hill, Jeffrey Rohland, Salomi Enslin, Paul R. MeyersAbstract:Two novel members of the genus Amycolatopsis were isolated from soil samples collected in South Africa. Strains JS72^T and M29^T clustered in the same clade in the 16S-rRNA, gyrB -16S-rRNA and gyrB - recN gene trees. Both strains showed anti-mycobacterial activity. The oxyB P450 monooxygenase B gene required for the production of glycopeptide antibiotics was detected in both strains, while strain JS72^T was also shown to contain the 3-amino-5-hydroxy-benzoic acid synthase gene, which is required for the production of the ansamycin class of antibiotics. Genetic distance values (based on the gyrB and recN genes) were calculated between strains JS72^T and M29^T and their closest phylogenetic relatives. The values for strain JS72^T were all above the threshold values of 0.02 and 0.04, respectively, that have been proposed to distinguish Amycolatopsis -type strains. The gyrB -based values for strain M29^T were above the threshold for all but one strain; the recN -based values were all above the threshold. These data, along with DNA–DNA hybridization data, showed that strains JS72^T and M29^T belong to distinct genomic species. The physiological, phylogenetic and genetic distance data support the description of strains JS72^T and M29^T as the type strains of novel species, for which the names Amycolatopsis speibonae sp. nov. (=DSM 46660^T=NRRL B-24958^T) and Amycolatopsis roodepoortensis sp. nov. (=DSM 46661^T=NRRL B-24959^T) are proposed, respectively.
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Amycolatopsis roodepoortensis sp. nov. and Amycolatopsis speibonae sp. nov.: antibiotic-producing actinobacteria isolated from South African soils
The Journal of antibiotics, 2014Co-Authors: Gareth J. Everest, Marilize Roes-hill, Jeffrey Rohland, Salomi Enslin, Paul R. MeyersAbstract:Amycolatopsis roodepoortensis sp. nov. and Amycolatopsis speibonae sp. nov.: antibiotic-producing actinobacteria isolated from South African soils
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Amycolatopsis umgeniensis sp. nov., isolated from soil from the banks of the Umgeni River in South Africa
Antonie van Leeuwenhoek, 2013Co-Authors: Gareth J. Everest, Candice M. Goodwin, Marilize Roes-hill, Clifford Omorogie, Shuk-kwan Cheung, Andrew E. Cook, Paul R. MeyersAbstract:A novel member of the genus Amycolatopsis was isolated from soil collected from the banks of the Umgeni River, KwaZulu Natal province, South Africa. The strain, designated UM16^T, grouped with the type strains of Amycolatopsis alba , Amycolatopsis coloradensis and Amycolatopsis thailandensis by 16S rRNA gene based phylogeny. Genetic distance values, based on the gyrB and recN genes, between strain UM16^T and its closest relatives were all above the threshold values of 0.02 and 0.04, respectively, that have been proposed to distinguish Amycolatopsis type strains. DNA–DNA hybridisation experiments confirmed that strain UM16^T represents a unique genomic species, sharing 18.4 ± 5.1, 16.2 ± 1.8 and 45.8 ± 8.9 % DNA relatedness to the type strains of A . alba , A . coloradensis and A . thailandensis , respectively. The physiological, phylogenetic and DNA-relatedness data support the description of strain UM16^T as the type strain of a novel species, for which the name Amycolatopsis umgeniensis sp. nov. is proposed (= DSM 45272^T = NRRL B-24724^T).
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Evaluation of the use of recN sequence analysis in the phylogeny of the genus Amycolatopsis
Antonie van Leeuwenhoek, 2011Co-Authors: Gareth J. Everest, Bronwyn M. Kirby, Andrew E. Cook, Paul R. MeyersAbstract:Partial recN gene sequences (>1 kb) were obtained from 35 type strains of the genus Amycolatopsis . Phylogenetic trees were constructed to determine the effectiveness of using this gene to predict taxonomic relationships within the genus. The use of recN sequence analysis as an alternative to DNA–DNA hybridization (DDH) for distinguishing closely related species was also assessed. The recN based phylogeny mostly confirmed the conventional 16S rRNA and gyrB gene-based phylogenies and thus provides further support for these phylogenetic groupings. As is the case for the gyrB gene, pairwise recN sequence similarities cannot be used to predict the DNA relatedness between type strains but the recN genetic distance can be used as a means to assess quickly whether an isolate is likely to represent a new species in the genus Amycolatopsis . A recN genetic distance of >0.04 between two Amycolatopsis strains is proposed to provide a good indication that they belong to different species (and that polyphasic taxonomic characterization of the unknown strain is worth undertaking).
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Evaluation of the antibiotic biosynthetic potential of the genus Amycolatopsis and description of Amycolatopsis circi sp. nov., Amycolatopsis equina sp. nov. and Amycolatopsis hippodromi sp. nov.
Journal of applied microbiology, 2011Co-Authors: Gareth J. Everest, Paul R. MeyersAbstract:AIMS: To describe three new Amycolatopsis strains and assess the antibiotic biosynthetic potential of the genus. METHODS AND RESULTS: Three strains, designated S1·3(T) , S3·6(T) and SE(8)3(T) , belonging to the genus Amycolatopsis were isolated and found to cluster together by 16S rRNA and gyrB gene-based phylogenetic analysis. Genetic distance values, based on the gyrB gene, were calculated between the strains and their closest relatives and were all above the threshold value of 0·02 that has been proposed to distinguish Amycolatopsis type strains. DNA-DNA hybridization experiments against related type strains confirmed that strain S3·6(T) represents a unique genomic species. Strain S3·6(T) was also found to be distinct from strains S1·3(T) and SE(8)3(T) , the latter two of which were also shown to be distinct from each other. Antibiotic biosynthetic genes were identified from multiple Amycolatopsis strains, and their presence was found to be phylogenetically associated. CONCLUSIONS: The data presented in this study indicate that strains S1·3(T) , SE(8)3(T) and S3·6(T) belong to three novel species, for which the names Amycolatopsis circi sp. nov. (= DSM 45561(T) = NRRL B-24841(T) ), Amycolatopsis equina sp. nov. (= DSM 45563(T) = NRRL B-24842(T) ) and Amycolatopsis hippodromi sp. nov. (= DSM 45562(T) = NRRL B-24843(T) ) are proposed. SIGNIFICANCE AND IMPACT OF THE STUDY: Three new species of Amycolatopsis are described, and the knowledge of the antibiotic biosynthetic potential of the genus has been extended.
Tiago Domingues Zucchi - One of the best experts on this subject based on the ideXlab platform.
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classification of thermophilic actinobacteria isolated from arid desert soils including the description of Amycolatopsis deserti sp nov
Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2016Co-Authors: Tiago Domingues Zucchi, Wallace Rafael De Souza, Kanungnid Busarakam, Alan T. Bull, Ros Brown, Leonardo Jose Silva, Michael GoodfellowAbstract:The taxonomic position of 26 filamentous actinobacteria isolated from a hyper-arid Atacama Desert soil and 2 from an arid Australian composite soil was established using a polyphasic approach. All of the isolates gave the diagnostic amplification product using 16S rRNA oligonucleotide primers specific for the genus Amycolatopsis. Representative isolates had chemotaxonomic and morphological properties typical of members of the genus Amycolatopsis. 16S rRNA gene analyses showed that all of the isolates belong to the Amycolatopsis methanolica 16S rRNA gene clade. The Atacama Desert isolates were assigned to one or other of two recognised species, namely Amycolatopsis ruanii and Amycolatopsis thermalba, based on 16S rRNA gene sequence, DNA:DNA relatedness and phenotypic data; emended descriptions are given for these species. In contrast, the two strains from the arid Australian composite soil, isolates GY024T and GY142, formed a distinct branch at the periphery of the A. methanolica 16S rRNA phyletic line, a taxon that was supported by all of the tree-making algorithms and by a 100 % bootstrap value. These strains shared a high degree of DNA:DNA relatedness and have many phenotypic properties in common, some of which distinguished them from all of the constituent species classified in the A. methanolica 16S rRNA clade. Isolates GY024T and GY142 merit recognition as a new species within the A. methanolica group of thermophilic strains. The name proposed for the new species is Amycolatopsis deserti sp. nov.; the type strain is GY024T (=NCIMB 14972T = NRRL B-65266T).
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Amycolatopsis rhabdoformis sp. nov., an actinomycete isolated from a tropical forest soil.
International Journal of Systematic and Evolutionary Microbiology, 2015Co-Authors: Wallace Rafael De Souza, Michael Goodfellow, Rafael Eduardo Da Silva, Kanungnid Busarakam, Fernanda Sales Figueiro, Douglas Ferreira, Edson Rodrigues-filho, Luiz Alberto Beraldo De Moraes, Tiago Domingues ZucchiAbstract:Strain SB026T was isolated from Brazilian rainforest soil and its taxonomic position established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological features consistent with its classification in the genus Amycolatopsis and formed a branch in the Amycolatopsis 16S rRNA gene tree together with Amycolatopsis bullii NRRL B-24847T, Amycolatopsis plumensis NRRL B-24324T, Amycolatopsis tolypomycina DSM 44544T and Amycolatopsis vancoresmycina NRRL B-24208T. It was related most closely to A. bullii NRRL B-24847T (99.0 % 16S rRNA gene sequence similarity), but was distinguished from this strain by a low level of DNA–DNA relatedness (~46 %) and discriminatory phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the isolate should be classified in the genus Amycolatopsis as representing a novel species, Amycolatopsis rhabdoformis sp. nov. The type strain is SB026T ( = CBMAI 1694T = CMAA 1285T = NCIMB 14900T).
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Amycolatopsis bartoniae sp. nov. and Amycolatopsis bullii sp. nov., mesophilic actinomycetes isolated from arid Australian soils
Antonie van Leeuwenhoek, 2012Co-Authors: Tiago Domingues Zucchi, Avinash Naga Venkata Bonda, Sarah Frank, Jenileima Devi Kshetrimayum, Byung-yong Kim, Michael GoodfellowAbstract:The status of two mesophilic filamentous actinomycetes isolated from an arid Australian soil sample was determined using a polyphasic taxonomic approach. The isolates had chemical and morphological properties consistent with their classification in the genus Amycolatopsis, assignments that were supported by analysis of 16S rRNA gene sequence data. Isolate SF26T formed a distinct phyletic line and hence was sharply separated from its nearest phylogenetic neighbour, Amycolatopsis sacchari DSM 44468T. In contrast, isolate SF27T formed a subclade in the Amycolatopsis tree with Amycolatopsis vancoresmycina DSM 44592T but was separated readily from the latter by DNA:DNA pairing data. The two isolates were distinguished from one another and from their respective nearest phylogenetic neighbours using a range of phenotypic properties. These data indicate that the two isolates should be recognized as new species in the genus Amycolatopsis. The names proposed for these new taxa are Amycolatopsis bartoniae sp. nov. and Amycolatopsis bullii sp. nov. with isolates SF26T (=NCIMB 14706T = NRRL B-2846T) and SF27T (=NCIMB 14707T = NRRL B-24847T) as the respective type strains.
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Amycolatopsis granulosa sp. nov., Amycolatopsis ruanii sp. nov. and Amycolatopsis thermalba sp. nov., thermophilic actinomycetes isolated from arid soils.
International journal of systematic and evolutionary microbiology, 2011Co-Authors: Tiago Domingues Zucchi, Geok Yuan Annie Tan, Avinash Naga Venkata Bonda, Sarah Frank, Jenileima Devi Kshetrimayum, Michael GoodfellowAbstract:The taxonomic positions of three thermophilic actinomycetes isolated from arid soil samples were established by using a polyphasic approach. The organisms had chemical and morphological features that were consistent with their classification in the genus Amycolatopsis. 16S rRNA gene sequence data supported the classification of the isolates in the genus Amycolatopsis and showed that they formed distinct branches in the Amycolatopsis methanolica subclade. DNA-DNA relatedness studies between the isolates and their phylogenetic neighbours showed that they belonged to distinct genomic species. The three isolates were readily distinguished from one another and from the type strains of species classified in the A. methanolica subclade based on a combination of phenotypic properties and by genomic fingerprinting. Consequently, it is proposed that the three isolates be classified in the genus Amycolatopsis as representatives of Amycolatopsis granulosa sp. nov. (type strain GY307(T) = NCIMB 14709(T) = NRRL B-24844(T)), Amycolatopsis ruanii sp. nov. (type strain NMG112(T) = NCIMB 14711(T) = NRRL B-24848(T)) and Amycolatopsis thermalba sp. nov. (type strain SF45(T) = NCIMB 14705(T) = NRRL B-24845(T)).
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Amycolatopsis thermophila sp. nov. and Amycolatopsis viridis sp. nov., thermophilic actinomycetes isolated from arid soil.
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Tiago Domingues Zucchi, Geok Yuan Annie Tan, Michael GoodfellowAbstract:The taxonomic positions of two thermophilic actinomycetes isolated from an arid Australian soil sample were established based on an investigation using a polyphasic taxonomic approach. The organisms had chemical and morphological properties typical of members of the genus Amycolatopsis and formed distinct phyletic lines in the Amycolatopsis methanolica 16S rRNA subclade. The two organisms were distinguished from one another and from the type strains of related species of the genus Amycolatopsis using a range of phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the two isolates be classified in the genus Amycolatopsis as Amycolatopsis thermophila sp. nov. (type strain GY088 T 5NCIMB 14699 T 5NRRL B-24836 T ) and Amycolatopsis viridis sp. nov. (type strain GY115 T 5NCIMB 14700 T 5NRRL B-24837 T ).
Gareth J. Everest - One of the best experts on this subject based on the ideXlab platform.
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Amycolatopsis roodepoortensis sp. nov. and Amycolatopsis speibonae sp. nov.: antibiotic-producing actinobacteria isolated from South African soils
The Journal of Antibiotics, 2014Co-Authors: Gareth J. Everest, Marilize Roes-hill, Jeffrey Rohland, Salomi Enslin, Paul R. MeyersAbstract:Two novel members of the genus Amycolatopsis were isolated from soil samples collected in South Africa. Strains JS72^T and M29^T clustered in the same clade in the 16S-rRNA, gyrB -16S-rRNA and gyrB - recN gene trees. Both strains showed anti-mycobacterial activity. The oxyB P450 monooxygenase B gene required for the production of glycopeptide antibiotics was detected in both strains, while strain JS72^T was also shown to contain the 3-amino-5-hydroxy-benzoic acid synthase gene, which is required for the production of the ansamycin class of antibiotics. Genetic distance values (based on the gyrB and recN genes) were calculated between strains JS72^T and M29^T and their closest phylogenetic relatives. The values for strain JS72^T were all above the threshold values of 0.02 and 0.04, respectively, that have been proposed to distinguish Amycolatopsis -type strains. The gyrB -based values for strain M29^T were above the threshold for all but one strain; the recN -based values were all above the threshold. These data, along with DNA–DNA hybridization data, showed that strains JS72^T and M29^T belong to distinct genomic species. The physiological, phylogenetic and genetic distance data support the description of strains JS72^T and M29^T as the type strains of novel species, for which the names Amycolatopsis speibonae sp. nov. (=DSM 46660^T=NRRL B-24958^T) and Amycolatopsis roodepoortensis sp. nov. (=DSM 46661^T=NRRL B-24959^T) are proposed, respectively.
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Amycolatopsis roodepoortensis sp. nov. and Amycolatopsis speibonae sp. nov.: antibiotic-producing actinobacteria isolated from South African soils
The Journal of antibiotics, 2014Co-Authors: Gareth J. Everest, Marilize Roes-hill, Jeffrey Rohland, Salomi Enslin, Paul R. MeyersAbstract:Amycolatopsis roodepoortensis sp. nov. and Amycolatopsis speibonae sp. nov.: antibiotic-producing actinobacteria isolated from South African soils
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Amycolatopsis umgeniensis sp. nov., isolated from soil from the banks of the Umgeni River in South Africa
Antonie van Leeuwenhoek, 2013Co-Authors: Gareth J. Everest, Candice M. Goodwin, Marilize Roes-hill, Clifford Omorogie, Shuk-kwan Cheung, Andrew E. Cook, Paul R. MeyersAbstract:A novel member of the genus Amycolatopsis was isolated from soil collected from the banks of the Umgeni River, KwaZulu Natal province, South Africa. The strain, designated UM16^T, grouped with the type strains of Amycolatopsis alba , Amycolatopsis coloradensis and Amycolatopsis thailandensis by 16S rRNA gene based phylogeny. Genetic distance values, based on the gyrB and recN genes, between strain UM16^T and its closest relatives were all above the threshold values of 0.02 and 0.04, respectively, that have been proposed to distinguish Amycolatopsis type strains. DNA–DNA hybridisation experiments confirmed that strain UM16^T represents a unique genomic species, sharing 18.4 ± 5.1, 16.2 ± 1.8 and 45.8 ± 8.9 % DNA relatedness to the type strains of A . alba , A . coloradensis and A . thailandensis , respectively. The physiological, phylogenetic and DNA-relatedness data support the description of strain UM16^T as the type strain of a novel species, for which the name Amycolatopsis umgeniensis sp. nov. is proposed (= DSM 45272^T = NRRL B-24724^T).
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Evaluation of the use of recN sequence analysis in the phylogeny of the genus Amycolatopsis
Antonie van Leeuwenhoek, 2011Co-Authors: Gareth J. Everest, Bronwyn M. Kirby, Andrew E. Cook, Paul R. MeyersAbstract:Partial recN gene sequences (>1 kb) were obtained from 35 type strains of the genus Amycolatopsis . Phylogenetic trees were constructed to determine the effectiveness of using this gene to predict taxonomic relationships within the genus. The use of recN sequence analysis as an alternative to DNA–DNA hybridization (DDH) for distinguishing closely related species was also assessed. The recN based phylogeny mostly confirmed the conventional 16S rRNA and gyrB gene-based phylogenies and thus provides further support for these phylogenetic groupings. As is the case for the gyrB gene, pairwise recN sequence similarities cannot be used to predict the DNA relatedness between type strains but the recN genetic distance can be used as a means to assess quickly whether an isolate is likely to represent a new species in the genus Amycolatopsis . A recN genetic distance of >0.04 between two Amycolatopsis strains is proposed to provide a good indication that they belong to different species (and that polyphasic taxonomic characterization of the unknown strain is worth undertaking).
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Evaluation of the antibiotic biosynthetic potential of the genus Amycolatopsis and description of Amycolatopsis circi sp. nov., Amycolatopsis equina sp. nov. and Amycolatopsis hippodromi sp. nov.
Journal of applied microbiology, 2011Co-Authors: Gareth J. Everest, Paul R. MeyersAbstract:AIMS: To describe three new Amycolatopsis strains and assess the antibiotic biosynthetic potential of the genus. METHODS AND RESULTS: Three strains, designated S1·3(T) , S3·6(T) and SE(8)3(T) , belonging to the genus Amycolatopsis were isolated and found to cluster together by 16S rRNA and gyrB gene-based phylogenetic analysis. Genetic distance values, based on the gyrB gene, were calculated between the strains and their closest relatives and were all above the threshold value of 0·02 that has been proposed to distinguish Amycolatopsis type strains. DNA-DNA hybridization experiments against related type strains confirmed that strain S3·6(T) represents a unique genomic species. Strain S3·6(T) was also found to be distinct from strains S1·3(T) and SE(8)3(T) , the latter two of which were also shown to be distinct from each other. Antibiotic biosynthetic genes were identified from multiple Amycolatopsis strains, and their presence was found to be phylogenetically associated. CONCLUSIONS: The data presented in this study indicate that strains S1·3(T) , SE(8)3(T) and S3·6(T) belong to three novel species, for which the names Amycolatopsis circi sp. nov. (= DSM 45561(T) = NRRL B-24841(T) ), Amycolatopsis equina sp. nov. (= DSM 45563(T) = NRRL B-24842(T) ) and Amycolatopsis hippodromi sp. nov. (= DSM 45562(T) = NRRL B-24843(T) ) are proposed. SIGNIFICANCE AND IMPACT OF THE STUDY: Three new species of Amycolatopsis are described, and the knowledge of the antibiotic biosynthetic potential of the genus has been extended.
