Showing papers by "Michael Goodfellow published in 2012"
TL;DR: The present phylogenetic study examines almost all described species within the family Streptomycetaceae based on 16S rRNA gene sequences and illustrates the species diversity within this family, which is observed to contain 130 statistically supported clades, as well as many unsupported and single member clusters.
Abstract: Species of the genus Streptomyces, which constitute the vast majority of taxa within the family Streptomycetaceae, are a predominant component of the microbial population in soils throughout the world and have been the subject of extensive isolation and screening efforts over the years because they are a major source of commercially and medically important secondary metabolites. Taxonomic characterization of Streptomyces strains has been a challenge due to the large number of described species, greater than any other microbial genus, resulting from academic and industrial activities. The methods used for characterization have evolved through several phases over the years from those based largely on morphological observations, to subsequent classifications based on numerical taxonomic analyses of standardized sets of phenotypic characters and, most recently, to the use of molecular phylogenetic analyses of gene sequences. The present phylogenetic study examines almost all described species (615 taxa) within the family Streptomycetaceae based on 16S rRNA gene sequences and illustrates the species diversity within this family, which is observed to contain 130 statistically supported clades, as well as many unsupported and single member clusters. Many of the observed clades are consistent with earlier morphological and numerical taxonomic studies, but it is apparent that insufficient variation is present in the 16S rRNA gene sequence within the species of this family to permit bootstrap-supported resolution of relationships between many of the individual clusters.
222 citations
01 Jan 2012
118 citations
TL;DR: Urgent action is needed to revitalise the practise of prokaryotic systematics in order to maintain this discipline as an attractive career choice for twenty first century life scientists.
Abstract: Prokaryotic systematics is a fundamentally important discipline that provides a framework for the activities of all microbiologists. Here we propose that the field has become mired in a sea of perceived rules and regulations, many of which stipulate what is considered ‘sufficient’ for the phenotypic characterisation of novel prokaryotic taxa. Importantly, we argue also that the principles and practise of prokaryotic systematics have not yet fully embraced the revolution in biological understanding that has occurred through the availability of huge numbers of whole genome sequences. We therefore propose that a significant reappraisal of the procedures used to describe novel prokaryotic taxa is needed, including the likely introduction of new publication formats. Urgent action is needed to revitalise the practise of prokaryotic systematics in order to maintain this discipline as an attractive career choice for twenty first century life scientists.
81 citations
TL;DR: The results of physiological and biochemical tests and low DNA–DNA relatedness demonstrated strain 234402T could be readily distinguished from the closely related Verrucosispora species.
Abstract: An actinomycete strain 234402T was isolated from a mangrove soil sample collected in Wenchang, China. Phylogenetic analysis of the 16S rRNA gene sequence of strain 234402T indicated that the highest similarity was to Verrucosispora sediminis MS426T (99.25%). The cell wall contained meso-diaminopimelic acid. The major menaquinones were MK-9(H4) and MK-9(H6), with MK-9(H8) as minor components. The characteristic whole-cell sugars were xylose, mannose and glucose. The phospholipid profile was found to comprise phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol mannoside and an unknown phospholipid. The DNA G+C content was 69.2 mol%. The results of physiological and biochemical tests and low DNA–DNA relatedness demonstrated strain 234402T could be readily distinguished from the closely related Verrucosispora species. On the basis of these phenotypic and genotypic data, strain 234402T represents a novel species of the genus Verrucosispora, for which the name Verrucosispora wenchangensis sp. nov. is proposed. The type strain is 234402T (=CCTCC AA 2011018T=DSM 45674T).
73 citations
01 Jan 2012
TL;DR: Click here to download PDF Bergeys Manual of Systematic Bacteriology Volume 5 The Actinobacteria.
Abstract: ments (1, 2, 5, 6). Jiangella alkaliphila sp. nov., an actinobacterium isolated Kreig NR, Staley JT (ed), Bergey's manual of systematic bacteriology, vol 1. Download PDF Bergeys Manual of Systematic Bacteriology Volume 5 The Actinobacteria. Ida. 1 Taxonomy, 2 Ecology, 3 Background, 4 Morphology and Cell Structure, 5 Growth The Actinobacteria, Part A. Bergey's Manual Of Systematic Bacteriology. Second ed. Vol.5. New York: Springer, 2012. 571-575. (5) NCBI. National Center.
69 citations
TL;DR: It is apparent from the combined genotypic and phenotypic data that strain AB-18-032T should be classified in the genus Verrucosispora as a new species.
Abstract: Verrucosispora isolate AB-18-032T, the abyssomicin- and proximicin-producing actinomycete, has chemotaxonomic and morphological properties consistent with its classification in the genus Verrucosispora. The organism formed a distinct phyletic line in the Verrucosispora 16S rRNA gene tree sharing similarities of 99.7%, 98.7% and 98.9% with Verrucosispora gifhornensis DSM 44337T, Verrucosispora lutea YIM 013T and Verrucosispora sediminis MS 426T, respectively. It was readily distinguished from the two latter species using a range of phenotypic features and from V. gifhornensis DSM 44337T, its nearest phylogenetic neighbor, by a DNA G+C content of 65.5 mol% obtained by thermal denaturation and fluorometry and DNA:DNA relatedness values of 64.0% and 65.0% using renaturation and fluorometric methods, respectively. It is apparent from the combined genotypic and phenotypic data that strain AB-18-032T should be classified in the genus Verrucosispora as a new species. The name Verrucosispora maris sp. nov. is proposed for this taxon with isolate AB-18-032T (= DSM 45365T = NRRL B-24793T) as the type strain.
57 citations
TL;DR: It is proposed that isolate C63T (CGMCC 4.6997T, = KACC 15425T) be classified as the type strain of Streptomyces deserti sp.
Abstract: The taxonomic position of a Streptomyces strain isolated from a hyper-arid desert soil was established using a polyphasic approach. The organism had chemical and morphological properties typical of the genus Streptomyces and formed a phyletic line at the periphery of the Streptomyces coeruleorubidus subcluster in the 16S rRNA gene tree. DNA:DNA relatedness values between the isolate and its nearest phylogenetic neighbours, Streptomyces lomondensis NRRL 3252T and Streptomyces lusitanus NRRL B-12501T were 42.5 (±0.48)% and 25.0 (±1.78)%, respectively. The isolate was readily distinguished from these organisms using a combination of morphological and phenotypic properties. On the basis of these results, it is proposed that isolate C63T (CGMCC 4.6997T, = KACC 15425T) be classified as the type strain of Streptomyces deserti sp. nov.
29 citations
TL;DR: The draft genome sequence of the human pathogen Streptomyces somaliensis is reported, a pathogen within a genus of largely saprophytic organisms that causes severe and debilitating deep tissue and bone infections.
Abstract: We report the draft genome sequence of the human pathogen Streptomyces somaliensis (DSM 40738), a pathogen within a genus of largely saprophytic organisms. S. somaliensis causes severe and debilitating deep tissue and bone infections. The genome sequence is deposited in DDBJ/EMBL/GenBank with the accession number AJJM01000000.
29 citations
TL;DR: The taxonomic position of a Streptomyces strain isolated from an extreme hyper-arid soil sample collected from the Atacama Desert was determined using a polyphasic approach and it is proposed that isolate C60(T) be classified in the genus Streptomeces as StrePTomyces atacamensis sp.
Abstract: The taxonomic position of a Streptomyces strain isolated from an extreme hyper-arid soil sample collected from the Atacama Desert was determined using a polyphasic approach. The strain, isolate C60(T), had chemical and morphological features typical of members of the genus Streptomyces and formed a distinct phyletic line in the Streptomyces 16S rRNA gene tree, together with the type strain of Streptomyces radiopugnans. The two strains were distinguished readily using a combination of phenotypic properties and by a DNA-DNA relatedness value of 23.17 (± 0.95)%. On the basis of these genotypic and phenotypic data, it is proposed that isolate C60(T) (=CGMCC 4.7018(T)=KACC 15492(T)) be classified in the genus Streptomyces as Streptomyces atacamensis sp. nov.
28 citations
TL;DR: Strain BK168(T) should be classified as the type strain of a novel species of the genus Streptomyces, for which the name StrePTomyces cocklensis sp.
Abstract: The taxonomic position of a streptomycete isolated from soil collected from Cockle Park Experimental Farm, Northumberland, UK, was determined by using a polyphasic approach. The organism had chemical and morphological features consistent with its classification in the genus Streptomyces. 16S rRNA gene sequence analysis supported classification of the strain in the genus Streptomyces and showed that it formed a distinct phyletic line loosely associated with members of the Streptomyces yeochonensis clade. It was related most closely to Streptomyces paucisporeus 1413 T (98.6%16S rRNA gene sequence similarity), but could be distinguished from the latter based on the low level of DNA–DNA relatedness (40%). It was readily distinguished from the type strains of all species assigned to the S. yeochonensis clade based on a combination of phenotypic properties. Strain BK168 T (5KACC 20908 T 5NCIMB 14704 T ) should therefore be classified as the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces cocklensis sp. nov. is proposed. The organism produces the antibiotic dioxamycin.
Book Chapter•
28 Jun 2012
TL;DR: 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 and it is proposed that the two isolates be classified in the genus Amycolatopsis as Amycol atopsis thermophila sp.
Abstract: 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 ).
TL;DR: The two isolates isolated from an arid Australian soil sample had chemical and morphological properties consistent with their classification in the genus Amycolatopsis and were distinguished from one another and from their respective nearest phylogenetic neighbours using a range of phenotypic properties.
Abstract: 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.
TL;DR: It is proposed that isolate BK179T (=KACC 20912T=NRRL B-24850T) be classified as the type strain of Streptomyces staurosporininus sp.
Abstract: The taxonomic position of a staurosporine-producing actinomycete isolated from a hay meadow soil was determined using a polyphasic approach. The organism had chemical and morphological characteristics consistent with its classification in the genus
Streptomyces
and formed a distinct branch between the
Streptomyces lydicus
and
Streptomyces noursei
clades in the 16S rRNA
Streptomyces
gene tree. DNA–DNA relatedness values between the isolate and its nearest phylogenetic neighbours, namely
Streptomyces lydicus
NBRC 13058T and
Streptomyces chattanoogensis
NBRC 12754T, were 53 % and 40 %, respectively. The isolate was also readily distinguished from the type strains of these species using a combination of morphological and other phenotypic properties. On the basis of these results, it is proposed that isolate BK179T ( = KACC 20912T = NRRL B-24850T) be classified as the type strain of
Streptomyces
staurosporininus sp. nov.
TL;DR: The taxonomic positions of three thermophilic actinomycetes isolated from arid soil samples were established by using a polyphasic approach and DNA-DNA relatedness studies between the isolates and their phylogenetic neighbours showed that they belonged to distinct genomic species.
Abstract: 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 GY307T = NCIMB 14709T = NRRL B-24844T), Amycolatopsis ruanii sp. nov. (type strain NMG112T = NCIMB 14711T = NRRL B-24848T) and Amycolatopsis thermalba sp. nov. (type strain SF45T = NCIMB 14705T = NRRL B-24845T).
TL;DR: The taxonomic positions of two actinomycetes isolated from a hay meadow soil sample were determined using a polyphasic approach and it is proposed that the isolates be assigned to the genus StrePTomyces as Streptomyces brevispora sp.
Abstract: The taxonomic positions of two actinomycetes isolated from a hay meadow soil sample were determined using a polyphasic approach. The isolates had chemical and morphological properties typical of streptomycetes and formed a distinct 16S rRNA gene subclade together with the type strain Streptomyces drozdowiczii NRRL B-24297T. DNA–DNA relatedness studies showed that the three strains belonged to different genomic species. The organisms were also distinguished using a combination of phenotypic properties. On the basis of these data it is proposed that the isolates be assigned to the genus Streptomyces as Streptomyces brevispora sp. nov. and Streptomyces laculatispora sp. nov., with BK160T ( = KACC 21093T = NCIMB 14702T) and BK166T ( = KACC 20907T = NCIMB 14703T) as the respective type strains.
TL;DR: DNA–DNA relatedness and phenotypic data demonstrated that strain N9999T was clearly distinguished from all closely related Streptosporangium species, demonstrating conclusively that the isolate should be classified as a new species of Strepto Porangium.
Abstract: A novel actinobacterium, strain N9999T, was isolated from soil and its taxonomic position determined using a polyphasic approach. The organism formed abundant aerial hyphae that differentiated into spherical spore vesicles. The cell wall contained meso-diaminopimelic acid; the whole-cell sugars were galactose, glucose, mannose, madurose and ribose; the predominant menaquinones MK-9 (H2) and MK-9 (H4); the major phospholipids phosphatidylethanolamine, diphosphatidylglycerol, a phosphaglycolipid and phosphatidylinositol mannosides; while the cellular fatty acids were rich in iso-C14:0, C15:0, cis-9-C17:1, iso-C16:0 and 10-methyl C17:0 components. Phylogenetic analyses based on an almost complete 16S rRNA gene sequence indicated that strain N9999T was closely related to a group that consisted of Streptosporangiumpseudovulgare DSM 43181T and Streptosporangium nondiastaticum DSM 43848T. However, DNA–DNA relatedness and phenotypic data demonstrated that strain N9999T was clearly distinguished from all closely related Streptosporangium species. The combined genotypic and phenotypic data demonstrate conclusively that the isolate should be classified as a new species of Streptosporangium.
TL;DR: This Special Edition of Antonie van Leeuwenhoek contains a series of invited Perspective papers based on contributions made at the Inaugural Meeting of Bergey’s International Society for Microbial Systematics, held in Beijing, China (19th–23rd May 2011).
Abstract: This Special Edition of Antonie van Leeuwenhoek contains a series of invited Perspective papers based on contributions made at the Inaugural Meeting of Bergey’s International Society for Microbial Systematics, held in Beijing, China (19th–23rd May 2011). The ‘BISMiS’ conference was an outstanding success, drawing together over 370 delegates for a meeting where the excellence of the science was well matched by the splendid hospitality and efficient organisation by the local organising committee. We thank Guoping Zhao, Li Huang, Zixin Deng, Lixin Zhang and their colleagues, notably Liz Ashcroft, for their support and hard work in ensuring the meeting was such a success. Likewise, the support of the Bergey’s Manual Trust was much appreciated. One of the major themes to emerge from the conference was that microbial systematics remains a fundamentally important discipline albeit one at an important stage of development. We are grateful to Peter Kampfer for an erudite overview on the current ‘state of the art’ and for spelling out the achievements of the past few decades. These achievements have been many, with significant growth in the numbers of published descriptions of microbial taxa. Nevertheless, significant challenges remain and these are addressed in the other contributions to this Special Issue. Not least among these is how to respond to our improved understanding of the vast diversity of the microbial world, a challenge elegantly described by Jim Staley in an influential article in the BISMiS bulletin as ‘‘the fourth goal of microbial taxonomy’’ (Staley 2010). Secondly, there is the challenge of embracing the technological drive and impact of the enormous and increasing mountains of sequence data that are being generated though microbial genome sequencing and metagenomic analyses. Addressing these unavoidable (but not insurmountable) challenges will be a defining feature of systematics in the next decade and should energise the next generation of microbial systematists. It was encouraging that so many young scientists contributed to the success of the Inaugural BISMiS meeting. The challenge of embracing data derived from the application of new technologies has always been at the heart of systematics. In the last century, one such challenge was the application and integration of computational biology into the taxonomic framework through the development of numerical taxonomy. It is with great sadness that we learnt recently of the death I. C. Sutcliffe (&) School of Life Sciences, Northumbria University, Newcastle Upon Tyne NE1 8ST, UK e-mail: iain.sutcliffe@northumbria.ac.uk
TL;DR: The taxonomic positions of three streptomycetes isolated from a soil sample from a hay meadow were determined using a polyphasic approach and it is proposed that the novel strains be assigned to the genus Streptomyces as StrePTomyces herbaceus sp.
Abstract: The taxonomic positions of three streptomycetes isolated from a soil sample from a hay meadow were determined using a polyphasic approach The isolates had chemical and morphological properties typical of the genus
Streptomyces
and, in phylogenetic analyses based on 16S rRNA gene sequences, formed a distinct subclade that was most closely related to the
Streptomyces prasinus
subclade DNA–DNA relatedness studies showed that the novel strains belonged to three different genomic species The novel strains could be distinguished from one another and from the type strains of the species classified in the
S prasinus
subclade using a combination of genotypic and phenotypic properties On the basis of these data, it is proposed that the novel strains be assigned to the genus
Streptomyces
as Streptomyces herbaceus sp nov, Streptomyces incanus sp nov and Streptomyces pratens sp nov, with BK119T ( = KACC 21001T = CGMCC 45797T), BK128T ( = KACC 21002T = CGMCC 45799T) and BK138T ( = KACC 20904T = CGMCC 45800T) as the respective type strains