Showing papers by "Michael Goodfellow published in 2010"
TL;DR: The bioprospecting strategy is based upon the premise that new secondary metabolites can be found by screening relatively small numbers of dereplicated, novel actinomycetes isolated from marine sediments and is exemplified by the discovery of a range of novel bioactive compounds.
Abstract: New structurally diverse natural products are discovered when novel screening procedures are introduced or when high quality biological materials from new sources are examined in existing screens, hence it is important to foster these two aspects of novelty in drug discovery programmes. Amongst prokaryotes, actinomycetes, notably streptomycetes, remain a rich source of new natural products though it has become increasingly difficult to find such metabolites from common actinomycetes as screening ‘old friends’ leads to the costly rediscovery of known compounds. The bioprospecting strategy which is the subject of this review is based upon the premise that new secondary metabolites can be found by screening relatively small numbers of dereplicated, novel actinomycetes isolated from marine sediments. The success of the strategy is exemplified by the discovery of a range of novel bioactive compounds, notably atrop-abyssomicin C and proximicins A, B and C from Verrucosispora strains isolated from sediment samples taken from the Sea of Japan and the Raune Fjord, respectively, and the dermacozines derived from Dermacoccus strains isolated from the Challenger Deep of the Mariana Trench in the Pacific Ocean. The importance of current advances in prokaryotic systematics in work of this nature is stressed and a plea made that resources be sought to train, support and employ the next generation of actinobacterial systematists.
308 citations
TL;DR: A novel structural class of phenazine derivatives, the dermacozines, which exhibited moderate cytotoxic activity against leukaemia cell line K562 with IC(50) values of 9 and 7 microM, respectively, while the highest radical scavenger activity was observed for der Macozine C (3) with an IC( 50) value of 8.4 microM.
Abstract: Dermacoccus abyssi sp. nov., strains MT1.1 and MT1.2 are actinomycetes isolated from Mariana Trench sediment at a depth of 10898 m. Fermentation using ISP2 and 410 media, respectively, lead to production of seven new oxidized and reduced phenazine-type pigments, dermacozines A–G (1–7), together with the known phenazine-1-carboxylic acid (8) and phenazine-1,6-dicarboxylic acid (9). Extensive use was made of 1D and 2D-NMR data, and high resolution MS to determine the structures of the compounds. To confirm the structure of the most complex pentacyclic analogue (5) we made use of electronic structure calculations to compare experimental and theoretical UV-Vis spectra, which confirmed a novel structural class of phenazine derivatives, the dermacozines. The absolute stereochemistry of dermacozine D (4) was determined as S by a combination of CD spectroscopy and electronic structure calculations. Dermacozines F (6) and G (7) exhibited moderate cytotoxic activity against leukaemia cell line K562 with IC50 values of 9 and 7 μM, respectively, while the highest radical scavenger activity was observed for dermacozine C (3) with an IC50 value of 8.4 μM.
119 citations
TL;DR: The taxonomic positions of two gamma- and UV-ray-resistant strains isolated from radiation-polluted soil in north-west China were determined in a polyphasic study, and two species, Deinococcus wulumuqiensis sp.
Abstract: The taxonomic positions of two gamma- and UV-ray-resistant strains isolated from radiation-polluted soil in north-west China were determined in a polyphasic study. The organisms, designated R12(T) and R13(T), were Gram-stain-positive, non-spore-forming cocci, which contained MK-8 as the major respiratory quinone and C(16 : 1)omega7c and C(16 : 0) as major fatty acids. The cell walls of strains R12(T) and R13(T) contained ornithine. Phylogenetic analysis based on 16S rRNA gene sequences and DNA-DNA hybridizations showed that strains R12(T) and R13(T) are members of novel species belonging to the genus Deinococcus, with Deinococcus radiodurans DSM 20539(T) as the closest relative. The isolates R12(T) and R13(T) shared 97 and 97.1 % 16S rRNA gene similarity, respectively, and 29.5 and 33.3 % DNA-DNA relatedness, respectively, with D. radiodurans DSM 20539(T). The DNA G+C contents of isolates R12(T) and R13(T) were 66.7 and 63.8 %, respectively. On the basis of phenotypic tests and other results, two species, Deinococcus wulumuqiensis sp. nov. (type strain R12(T) =CGMCC 1.8884(T) =NBRC 105665(T)) and Deinococcus xibeiensis sp. nov. (type strain R13(T) =CGMCC 1.8885(T) =NBRC 105666(T)), are proposed.
41 citations
TL;DR: A polyphasic study was undertaken to determine the taxonomic status of six strains received as Streptomyces hygroscopicus, showing that all six strains form distinct centres of taxonomic variation within the genus StrePTomyces.
Abstract: A polyphasic study was undertaken to determine the taxonomic status of
six strains received as Streptomyces hygroscopicus. The strains had
chemotaxonomic and morphological properties typical of members of the genus Streptomyces and formed distinct phyletic lines in the Streptomyces 16S rRNA gene tree. These strains were distinguished from one another
and from phylogenetically close neighbours using a combination of phenotypic
properties. The combined genotypic and phenotypic data showed that all six
strains form distinct centres of taxonomic variation within the genus Streptomyces. The following novel species are proposed to accommodate
the strains: Streptomyces aldersoniae sp. nov. (type strain
DSM 41909T =NRRL 18513T), Streptomyces
angustmyceticus sp. nov., comb. nov. (type strain DSM 41683T=NRRL B-2347T), Streptomyces ascomycinicus sp. nov. (type strain DSM 40822T =NBRC 13981T), Streptomyces decoyicus sp. nov., comb. nov. (type
strain DSM 41427T =NRRL 2666T), Streptomyces
milbemycinicus sp. nov. (type strain DSM 41911T =NRRL
5739T) and Streptomyces wellingtoniae sp. nov. (type
strain DSM 40632T =NRRL B-1503T).
33 citations
TL;DR: Large numbers of alkaliphilic streptomycetes isolated from a beach and dune sand system were dereplicated manually based on aerial spore mass, colony reverse and diffusible pigment colours formed on oatmeal agar, and on their capacity to produce melanin pigments on peptone-yeast extract-iron agar.
Abstract: Large numbers of alkaliphilic streptomycetes isolated from a beach and dune sand system were dereplicated manually based on aerial spore mass, colony reverse and diffusible pigment colours formed on oatmeal agar, and on their capacity to produce melanin pigments on peptone-yeast extract-iron agar. The resultant data were converted to their respective red, blue and green shade intensities. The Euclidean distances between each of the colours were calculated by considering red, green and blue shade intensity values as X, Y and Z coordinates in three dimensional space. The clusters of isolates delineated in the dendrogram generated using the distances were found to match those obtained by manual colour-grouping of the isolates. A reasonable linear correlation was found between the colour-group and corresponding rep-PCR data. The implications of the computer-assisted colour-grouping method for bioprospecting and ecological studies are discussed.
29 citations
01 Jan 2010
TL;DR: The application of reliable selective isolation and characterization procedures to surveys of the cultivable actinobacteria in poorly studied and neglected habitats is yielding a steady flow of novel taxa.
Abstract: This chapter deals with the principles and practices currently used to selectively isolate and recognize previously uncultivated taxa. Actinobacteria mainly occur as saprophytes in diverse natural habitats, including soil, the initial focus of selective isolation studies. Various pretreatments can be used to select for different fractions of actinobacterial communities present in environmental samples. Nutrient amendment and baiting techniques are used to increase the populations of specific fractions of actinobacterial communities in environmental samples to facilitate their isolation on nutrient and selective media. Soil amendments with substrates such as chitin and keratin were first used by Jensen to boost the numbers of streptomycetes. This approach has fallen into neglect to some extent, but does provide an effective way of enhancing specific components of actinobacterial communities in soil. Until recently, relatively little effort was made to evaluate the effectiveness of procedures recommended for the isolation of specific fractions of actinobacterial communities present in natural habitats. The assignment of unknown actinobacteria to either formally described or novel taxa is essentially a two-stage process. The identity of representative isolates can also be achieved by using other molecular systematic procedures, notably by the use of taxon-specific 16S rRNA oligonucleotide primers. The application of reliable selective isolation and characterization procedures to surveys of the cultivable actinobacteria in poorly studied and neglected habitats is yielding a steady flow of novel taxa.
29 citations
TL;DR: In the course of the HPLC screening program, freshly isolated actinomycete strains from selected terrestrial and limnetic habitats are investigated with the aim of detecting novel drugs for pharmaceutical applications.
Abstract: In the course of our HPLC screening program, we investigated freshly isolated actinomycete strains from selected terrestrial and limnetic habitats with the aim of detecting novel drugs for pharmaceutical applications. The strains were grown in submerged culture in different media, and extracts prepared from mycelia and culture filtrates at various fermentation times.
27 citations
TL;DR: The taxonomic positions of three Lechevalieria-like strains isolated from hyperarid soils of the Atacama Desert, Chile, were established by using a polyphasic approach and a combination of the genotypic and phenotypic data showed that the three isolates represent three novel species of the genus Lefebvreia.
Abstract: The taxonomic positions of three Lechevalieria-like strains isolated from hyperarid soils of the Atacama Desert, Chile, were established by using a polyphasic approach. The organisms had chemical and morphological properties consistent with their classification in the genus Lechevalieria. They formed a distinct subclade in the Lechevalieria 16S rRNA gene clade and were most closely related to the type strain of Lechevalieria xinjiangensis. DNA-DNA relatedness data showed that each of the isolates and Lechevalieria xinjiangensis DSM 45081(T) belong to distinct genomic species. The new isolates and the type strains of recognized Lechevalieria species were readily distinguished based on a number of phenotypic properties. A combination of the genotypic and phenotypic data showed that the three isolates represent three novel species of the genus Lechevalieria. The names proposed for these taxa are Lechevalieria atacamensis sp. nov. (type strain C61(T) =CGMCC 4.5536(T) =NRRL B-24706(T)), Lechevalieria deserti sp. nov. (type strain C68(T) =CGMCC 4.5535(T) =NRRL B-24707(T)) and Lechevalieria roselyniae sp. nov. (type strain C81(T) =CGMCC 4.5537(T) =NRRL B-24708(T)).
25 citations
TL;DR: Combined genotypic and phenotypic data showed that isolate BK63T, isolates BK51T, BK53 and BK69, and strain NRRL B-16294T should be classified in the genus Dactylosporangium as representing novel species.
Abstract: Forty strains isolated from soil taken from a hay meadow were assigned to the genus Dactylosporangium on the basis of colonial properties. 16S rRNA gene sequence analysis showed that the isolates formed a group that was most closely related to the type strain of Dactylosporangium aurantiacum, but well separated from other Dactylosporangium type strains and from ‘Dactylosporangium salmoneum’ NRRL B-16294. Twelve of 13 representative isolates had identical 16S rRNA gene sequences and formed a subclade that was distinct from corresponding phyletic lines composed of the remaining isolate, strain BK63T, the ‘D. salmoneum’ strain and the type strainsof recognized Dactylosporangium species. DNA–DNA relatedness data indicated that representatives of the multi-membered 16S rRNA gene subclade, isolate BK63T and the ‘D. salmoneum’ subclade formed distinct genomic species; all of these organisms had chemotaxonomic and morphological properties consistent with their classification in the genus Dactylosporangium. They were also distinguished from one another and from the type strainsof recognized Dactylosporangium species based on a range of phenotypic properties. Combined genotypic and phenotypic data showed that isolate BK63T, isolates BK51T, BK53 and BK69, and strain NRRL B-16294T should be classified in the genus Dactylosporangium as representing novel species. The names proposed for these species are Dactylosporangium luridum sp. nov. (type strain BK63T = DSM 45324T = KACC 20933T = NRRL B-24775T), Dactylosporangium luteum sp. nov. (type strain BK51T = DSM 45323T = KACC 20899T = NRRL B-24774T) and Dactylosporangium salmoneum sp. nov., nom. rev. (type strain NRRL B-16294T = ATCC 31222T = DSM 43910T = JCM 3272T = NBRC 14103T).
23 citations
TL;DR: In the course of a phylogenetic study of the taxa with validly published names within the suborder Pseudonocardineae based on 16S rRNA gene sequences, it became apparent that this species was misplaced in the genus Amycolatopsis and the description of the genus Actinokineospora is emended to accommodate species that do not produce motile spores.
Abstract: The species Amycolatopsis fastidiosa (ex Celmer et al. 1977) Henssen et al. 1987 was proposed, based on morphological and chemotaxonomic observations, for a strain originally described as ‘Pseudonocardia fastidiosa’ Celmer et al. 1977 in a US patent. In the course of a phylogenetic study of the taxa with validly published names within the suborder Pseudonocardineae based on 16S rRNA gene sequences, it became apparent that this species was misplaced in the genus Amycolatopsis. After careful evaluation of the phylogeny, morphology, chemotaxonomy and physiology of the type strain, it was concluded that this strain represents a species of the genus Actinokineospora that is unable to produce motile spores. The description of the genus Actinokineospora is therefore emended to accommodate species that do not produce motile spores, and it is proposed that Amycolatopsis fastidiosa be transferred to the genus Actinokineospora as Actinokineospora fastidiosa comb. nov. The type strain is NRRL B-16697T =ATCC 31181T =DSM 43855T =JCM 3276T =NBRC 14105T =VKM Ac-1419T.
18 citations
TL;DR: The taxonomic status of an actinomycete isolated from soil collected from a hay meadow was determined using a polyphasic approach and strain N1350(T) is considered to represent a novel species of the genus Williamsia.
Abstract: The taxonomic status of an actinomycete isolated from soil collected from a hay meadow was determined using a polyphasic approach. The strain, designated N1350T, had morphological and chemotaxonomic properties consistent with its classification in the genus Williamsia and formed a distinct phyletic line within the clade comprising the type strains of species of the genus Williamsia in the 16S rRNA gene tree. Strain N1350T shared highest 16S rRNA gene sequence similarities with Williamsia marianensis MT8T (98.1 %) and Williamsia muralis MA140-96T (98.3 %). However, strain N1350T was readily distinguished from the type strains of Williamsia species using a combination of phenotypic properties. On the basis of these data, strain N1350T is considered to represent a novel species of the genus Williamsia. The name proposed for this taxon is Williamsia faeni sp. nov., with the type strain N1350T (=DSM 45372T =NCIMB 14575T =NRRL B-24794T).
TL;DR: The results are in line with current trends in nocardial systematics thereby indicating that restriction polymorphism ribosomal RNA analyses provide valuable data for the classification and identification of novel and pathogenic nocardiae at the species level.
Abstract: Fifty-three Nocardia strains were the subject of a restriction polymorphic ribosomal RNA analysis (ribotyping) designed to distinguish between representatives of clinically significant species and related strains. The organisms were assigned to 19 groups using a combination of EcoRV gene restriction endonuclease patterns and a digoxigenin-labelled Streptomyces violaceoruber TK21 rDNA probe. Each ribotype group contained 4 to 13 restriction fragments that ranged in size from 20.7 to 0.9 kb. The N. brasiliensis, N. crassostreae, N. farcinica, N. otitidiscaviarum, and N. seriolea strains showed distinct ribotype patterns. Unique banding patterns were also seen for the type strains of N. brevicatena, N. carnea, N. salmonicida, N. uniformis, and N. vaccinii, and for the single representatives of "N. fusca", "N. pseudosporangifera", and "N. violaceofusca". More than one banding pattern was detected for the N. asteroides, N. flavorosea, N. nova, N. pseudobrasiliensis, and N. transvalensis strains. The results are in line with current trends in nocardial systematics thereby indicating that restriction polymorphism ribosomal RNA analyses provide valuable data for the classification and identification of novel and pathogenic nocardiae at the species level.
Journal Article•
TL;DR: The extensive application of polythetic numerical method by increasing number of experts was proved to be successful in developing a more sounding streptomycete classification system which is applicable to delimit species within the genus.
Abstract: Systematics plays an important role in the utilization of streptomycete strains as an outstanding producer of thousands documented bioactive compounds. The chaotic state of streptomycete systematics resulted from the application of traditional monothetic approach had clearly hampered the progress of development of reliable identification system for potential streptomycete strains. However, the extensive application of polythetic numerical method by increasing number of experts was proved to be successful in developing a more sounding streptomycete classification system. As a consequence, such classification system can subsequently be used as a rigorous basis to generate a more reliable identification system in attempt to unravel the extent of streptomycete diversity in natural habitats both at the inter and intraspecies level. This review addresses the problem and the role of numerical systematics in the development of current status of streptomycete systematics which is applicable to delimit species within the genus. Key words: streptomycete systematics, monothetic, polythetic, streptomycete diversity
01 Oct 2010
TL;DR: Preliminary findings suggested that pulmonary nocardiosis might occur in patients who suffer from chronic lung disease in Sudan, and clinicians in Chest Units should consider this condition, especially when patients with respiratory infections fail to respond to antitubercula r therapy.
Abstract: Objective: The aims of the present study were to decide the occurrence of nocardia spp. among Sudanese patients suspected with tuberculosis and to investigate all proteins expressed by the genome of Nocardia africana (formerly isolated from patients with pulmonary infection misdiagnosed as MDR and their structures and functions compared to Mycobacterium tuberculosis. Materials and Methods: Three hundred and twenty-nine patients, presented with pulmonary infection were included in this study. Those patients were examined for the presence of acid- fast bacilli. Two tubes of Lownstein- Jensen (L.J) medium were inoculated with 20 μl of the neutralized sputum sample. All cultures were incubated at 37 °C for 8 weeks before being discarded. Phenotypic characterizations were performed. For nocardia proteom poly acrylamide gele lectrophoresis (PAGE)-based analyses of the four nocardia strains N. farcinica SD1828, N. africana SD 925, and N. asteroides N317 are discussed. In-gel tryptic digestion of these isolates was also performed, then the resulting peptides were introduced to MALDI-TOF peptide mass fingerprints were searched using MASCOT software. Results: Ten isolates showed rapid growth pattern within 2-3 days after inoculation, further conventional methods suggested that all these isolates were belonging to the family nocardiacea. Two Dimentional Poly Acrylamide Gel Electrophoresis (2D-PAGE) using pH strips 3-10 revealed that the soluble proteins were visible in a much smaller pI range. All strains exhibited similar protein distributions. A similarity analysis revealed that mycobacterium sequences are of high relevance for the investigated strains. Conclusions: Nocardia revealed considerable occurrence among patients with pulmonary infections (3.3%) giving clinical symptoms similar to those occur by M. tuberculosis infection, this may be due to similarities in functional proteins expressed by their genomes. This finding suggested that pulmonary nocardiosis might occur in patients who suffer from chronic lung disease in Sudan. It is important, therefore, that clinicians in Chest Units should consider this condition, especially when patients with respiratory infections fail to respond to antitubercula r therapy.