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PubMed2001

Random amplified ribosomal DNA restriction analysis for rapid identification of thermophilic Actinomycete-like bacteria involved in hypersensitivity pneumonitis.

Hypersensitivity pneumonitis (HP) is a pulmonary disease characterised by inflammation that can be caused by, amongst other substances, a subset of 4 thermophilic mycelial bacteria: Saccharopolyspora rectivirgula, Saccharomonospora viridis, Thermoactinomyces sacchari, and Thermoactinomyces vulgaris. Air sampling analyses in highly contaminated environments are often performed to evaluate exposure to these species which are difficult and fastidious to identify by conventional techniques. The aim of this study was to use amplified ribosomal DNA restriction analysis (ARDRA) to develop a method of identification for those thermophilic organisms that would be more rapid and simple. Strains of these 4 species were obtained from the American type culture collection (ATCC) and were characterized using biochemical tests and ARDRA patterns obtained on their partial-lenght amplified 16S rDNAs. To validate this approach, ARDRA with two restriction enzymes, TaqI and HhaI, was applied to 49 thermophilic actinomycete-like strains from environmental samples (sawmills). The results obtained show that combining some cultural characteristics and biochemical tests, such as xanthine or hypoxanthine decomposition, growth in the presence of NaCl, lysozyme or novobiocin, and spore resistance over 100 degrees C provide a rough identification and selection of the genera of interest. Consequently, target species could be confirmed by digestion of partial-lenght 16S rDNA with the use of Taql and HhaI restriction enzymes that gave specific restriction patterns. ARDRA analyses on the 49 environmental actinomycete-like organisms revealed the presence of 8 Saccharopolyspora rectivirgula, 2 Saccharomonospora viridis, and 15 Thermoactinomyces vulgaris strains, the other strains had restriction patterns different than those of the species of interest. Results of the present study will be applicable to other potential HP environments such as dairy barns, peat bogs and compost plants.

Actinomycetales↗
PubMed1991

Polyacrylamide gel electrophoresis analysis of ribosomal protein AT-L30 as a novel approach to actinomycete taxonomy: application to the genera Actinomadura and Microtetraspora.

Actinomycete ribosomal protein AT-L30 exhibits electrophoretic mobility that is specific for each genus. On the basis of this fact, we analyzed ribosomal AT-L30 proteins from 26 type strains of species belonging to the genera Actinomadura and Microtetraspora. The electrophoretic mobilities of AT-L30 preparations from these strains, as determined by two-dimensional polyacrylamide gel electrophoresis, revealed that they could be divided into two groups, one group with relative electrophoretic mobilities of 14.0 to 41.5 and another group with relative electrophoretic mobilities of -6.5 to 0. The first group corresponded to the genus Actinomadura, and the second group corresponded to the genus Microtetraspora. Partial amino acid sequencing of AT-L30 preparations from several strains proved that we were indeed dealing with the specified protein homologous to ribosomal protein L30 of Escherichia coli. Our results strongly supported the conclusions of previous work and thus proved the efficacy of ribosomal protein analysis as a novel approach for taxonomy of actinomycetes.

Actinomycetales↗
PubMed1992

Electrophoretic heterogeneity of ribosomal protein AT-L30 among actinomycete genera.

The ribosomal proteins from 17 type strains of species belonging to various actinomycete genera were compared by two-dimensional polyacrylamide gel electrophoresis. I detected a striking variability among certain ribosomal proteins (designated AT-L30 proteins) with respect to electrophoretic mobility in the first dimension. In contrast, such variability was not observed among ribosomal L30 proteins from other bacteria, such as Escherichia coli, Bacillus subtilis, Pseudomonas aeruginosa, and Staphylococcus aureus. Although actinomycete AT-L30 proteins from different taxa exhibited considerable heterogeneity in electrophoretic mobility, within each genus the proteins had a specific mobility characteristic. On the basis of this observation, the ribosomal AT-L30 proteins from 11 type strains of species belonging to the mycolic acid-containing genera Nocardia, Rhodococcus, Gordona, and Tsukamurella were analyzed. The relative electrophoretic mobilities of AT-L30 protein preparations from these strains, as determined by two-dimensional gel electrophoresis, revealed that the genera Nocardia, Rhodococcus, Gordona, and Tsukamurella can be sharply separated from each other. My results are consistent with the previously discussed view that each of these genera merits separate genus status.

Actinomycetales↗
PubMed1994

Is the solubilized product from the degradation of lignocellulose by actinomycetes a precursor of humic substances?

Three actinomycetes (Streptomyces sp. EC22, Streptomyces viridosporus T7A and Thermomonospora fusca BD25) were assessed for their ability to degrade ball-milled wheat straw. All gave maximum levels of solubilized lignocellulose products (APPL) at the beginning of the stationary phase of growth (72-96 h). Low-molecular-mass aromatic compounds extracted from the APPL were analysed by reverse-phase and gas chromatography. Although the number of chromatographic peaks detected made identification of the products difficult, p-coumaric acid (4-hydroxycinnamic acid), protocatechuic acid (3,4-dihydroxybenzoic acid), gallic acid (3,4,5-trihydroxybenzoic acid), gallic acid methyl ester (methyl-3,4,5-trihydroxybenzoate) and 4-methoxyphenol were recognized. The infrared spectra of the three strains were similar to the spectra of humic acids, with all APPL extracts showing carbonyl, amino, carboxyl, aliphatic and aromatic group vibrations. Also detected were peptide linkages of proteins. The results suggest a role for actinomycetes in the formation of humic substances in soils and composts.

Actinomycetales↗
PubMed2004

Taxonomic study of neutrotolerant acidophilic actinomycetes isolated from soil and description of Streptomyces yeochonensis sp. nov.

Acidophilic actinomycete strains that represent the two major neutrotolerant clusters defined by numerical taxonomy (Seong, 1992) were the subject of a polyphasic taxonomic study. The centrotypes of each cluster, designated as strain JL164 (=KCTC 9924) of cluster 21 and strain CN732T (=KCTC 9926T=IMSNU 50114T=NRRL B-24245T) of cluster 13, were assigned initially to the genus Streptomyces on the basis of morphological and chemotaxonomic characteristics; this assignation was confirmed by 16S rRNA gene sequence data. Strain CN732T formed a distinct phyletic line within the Streptomyces tree, whereas strain JL164 was related closely to the type strain of Streptomyces mirabilis. It is evident from the present and previous studies that neutrotolerant acidophilic actinomycetes comprise taxonomically diverse groups within the variation encompassed by the genus Streptomyces. It is also apparent that strain CN732T and other members of cluster 13 merit recognition as a novel species, for which the name Streptomyces yeochonensis sp. nov. is proposed.

Actinomycetales↗
PubMed2004

Rhodococcus gordoniae sp. nov., an actinomycete isolated from clinical material and phenol-contaminated soil.

The taxonomic relationships of two actinomycetes provisionally assigned to the genus Rhodococcus were determined using a polyphasic taxonomic approach. The generic assignment was confirmed by 16S rRNA gene similarity data, as the organisms, strains MTCC 1534 and W 4937(T), were shown to belong to the Rhodococcus rhodochrous subclade. These organisms had phenotypic properties typical of rhodococci; they were aerobic, Gram-positive, weakly acid-fast actinomycetes that showed an elementary branching-rod-coccus growth cycle and contained meso-diaminopimelic acid, arabinose and galactose in whole-organism hydrolysates, N-glycolated muramic acid residues, dehydrogenated menaquinones with eight isoprene units as the predominant isoprenologue and mycolic acids that co-migrated with those extracted from the type strain of R. rhodochrous. The strains had identical phenotypic profiles and belong to the same genomic species, albeit one distinguished from Rhodococcus pyridinivorans, with which they formed a distinct phyletic line. They were also distinguished from representatives of all of the species classified in the R. rhodochrous 16S rRNA gene tree using a set of phenotypic features. The genotypic and phenotypic data show that the strains merit recognition as a novel species of Rhodococcus. The name proposed is Rhodococcus gordoniae sp. nov., with the type strain W 4937(T) (=DSM 44689(T)=NCTC 13296(T)).

DNA, Bacterial↗
PubMed2005

Jiangella gansuensis gen. nov., sp. nov., a novel actinomycete from a desert soil in north-west China.

A novel actinomycete strain, designated YIM 002(T), was isolated from a desert soil sample in Gansu Province, north-west China. This actinomycete isolate formed well-differentiated aerial and substrate mycelia. In the early stages of growth, the substrate mycelia fragmented into short or elongated rods. Chemotaxonomically, it contained ll-2,6-diaminopimelic acid in the cell wall. The cell-wall sugars contained ribose and glucose. Phospholipids present were phosphatidylinositol mannosides, phosphatidylinositol and diphosphatidylglycerol. MK-9(H(4)) was the predominant menaquinone. The major fatty acids were anteiso C(15 : 0) (35.92 %), anteiso C(17 : 0) (15.84 %), iso C(15 : 0) (10.40 %), iso C(16 : 0) (7.07 %) and C(17 : 1)omega8c (9.37 %). The G+C content of the DNA was 70 mol%. Phylogenetic analysis and signature nucleotide data based on 16S rRNA gene sequences showed that strain YIM 002(T) is distinct from all recognized genera of the family Nocardioidaceae in the suborder Propionibacterineae. On the basis of the phenotypic and genotypic characteristics, it is proposed that isolate YIM 002(T) be classified as a novel species in a new genus, Jiangella gansuensis gen. nov., sp. nov. The type strain is YIM 002(T) (=DSM 44835(T)=CCTCC AA 204001(T)=KCTC 19044(T)).

Actinomycetales↗
PubMed2005

Terrabacter terrae sp. nov., a novel actinomycete isolated from soil in Spain.

A Gram-positive, aerobic, long-rod-shaped, non-spore-forming bacterium (strain PPLB(T)) was isolated from soil mixed with Iberian pig hair. This actinomycete showed keratinase activity in vitro when chicken feathers were added to the culture medium. Strain PPLB(T) was oxidase-negative and catalase-positive and produced lipase and esterase lipase. This actinomycete grew at 40 degrees C on nutrient agar and in the same medium containing 5 % (w/v) NaCl. Growth was observed with many different carbohydrates as the sole carbon source. On the basis of 16S rRNA gene sequence similarity, strain PPLB(T) was shown to belong to the genus Terrabacter of the family Intrasporangiaceae. Strain PPLB(T) showed 98.8 % 16S rRNA gene sequence similarity to Terrabacter tumescens. Chemotaxonomic data, such as the main ubiquinone (MK-8), the main polar lipids (phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol) and the main fatty acids (i-C(15 : 0), ai-C(15 : 0), i-C(16 : 0) and ai-C(17 : 0)) supported the affiliation of strain PPLB(T) to the genus Terrabacter. The G+C content of the DNA was 71 mol%. The results of DNA-DNA hybridization (36.6 % relatedness between Terrabacter tumescens and strain PPLB(T)) and physiological and biochemical tests suggested that strain PPLB(T) belongs to a novel species of the genus Terrabacter, for which the name Terrabacter terrae sp. nov. is proposed. The type strain is PPLB(T) (=CECT 3379T=LMG 22921T).

Actinomycetales↗
PubMed2005

Dietzia strain X: a newly described Actinomycete isolated from confluent and reticulated papillomatosis.

Confluent and reticulated papillomatosis (CRP) is a rare skin disorder. To date its aetiology remains uncertain. The possibility of an infectious aetiology has been supported by case reports of therapeutic response to antibiotic therapy. We have isolated and identified a previously unknown Dietzia strain, an Actinomycete, from skin scrapings of a 17-year-old boy with CRP. We propose that this organism may be the aetiological agent of CRP. Further investigations are necessary to determine the potential role of this Actinomycete in the pathogenesis of CRP.

Actinomycetales↗
PubMed2005

Specificity of the mutualistic association between actinomycete bacteria and two sympatric species of Acromyrmex leaf-cutting ants.

Acromyrmex leaf-cutting ants maintain two highly specialized, vertically transmitted mutualistic ectosymbionts: basidiomycete fungi that are cultivated for food in underground gardens and actinomycete Pseudonocardia bacteria that are reared on the cuticle to produce antibiotics that suppress the growth of Escovopsis parasites of the fungus garden. Mutualism stability has been hypothesized to benefit from genetic uniformity of symbionts, as multiple coexisting strains are expected to compete and, thus, reduce the benefit of the symbiosis. However, the Pseudonocardia symbionts are likely to be involved in Red-Queen-like antagonistic co-evolution with Escovopsis so that multiple strains per host might be favoured by selection provided the cost of competition between bacterial strains is low. We examined the genetic uniformity of the Pseudonocardia symbionts of two sympatric species of Acromyrmex ants by comparing partial sequences of the nuclear Elongation Factor-Tu gene. We find no genetic variation in Pseudonocardia symbionts among nest mate workers, neither in Acromyrmex octospinosus, where colonies are founded by a single queen, nor in Acromyrmex echinatior, where mixing of bacterial lineages might happen when unrelated queens cofound a colony. We further show that the two ant species maintain the same pool of Pseudonocardia symbionts, indicating that horizontal transmission occasionally occurs, and that this pool consists of two distinct clades of closely related Pseudonocardia strains. Our finding that individual colonies cultivate a single actinomycete strain is in agreement with predictions from evolutionary theory on host-symbiont conflict over symbiont mixing, but indicates that there may be constraints on the effectiveness of the bacterial symbionts on an evolutionary timescale.

Actinomycetales↗
PubMed2004

Identification of the Entner-Doudoroff pathway in an antibiotic-producing actinomycete species.

The metabolic network of the central carbon metabolism represents the backbone of cellular metabolism and provides the precursors and cofactors required for synthesis of secondary metabolites. It is therefore pivotal to map the operating metabolic network in the central carbon metabolism in order to design metabolic engineering strategies towards construction of more efficient producers of specific metabolites. In this context, methods that allow rapid and reliable mapping of the central carbon metabolism are valuable. In the present study, a (13)C labelling-based method was used to identify the primary metabolic pathways of the poorly characterized antibiotic-producing actinomycete Nonomuraea sp. ATCC 39727. Surprisingly, it was found that Nonomuraea sp. ATCC 39272 predominantly metabolizes glucose via the Entner-Doudoroff (ED) pathway. This represents the first time that the ED pathway has been recognized as the main catabolic pathway in an actinomycete. The Nonomuraea genes encoding the key enzymes of the ED pathway were subsequently identified, sequenced and functionally described.

Actinobacteria↗
PubMed1996

A general approach for cloning and characterizing dNDP-glucose dehydratase genes from actinomycetes.

Oligonucleotide primers were designed and successfully applied to amplify DNA fragments of dNDP-glucose dehydratase genes from actinomycete species producing natural compounds which contain deoxysugar moieties. The deduced amino acid sequence of the isolated fragments revealed similarity to known dNDP-glucose dehydratases. A phylogeny for the deduced proteins of the obtained fragments and for dNDP-glucose dehydratases described in the data bases was constructed. dNDP-glucose dehydratases from actinomycetes were more related to each other than to dehydratases from species of other orders. The phylogenetic analysis also revealed a close relation between dehydratases from strains producing natural compounds with similar deoxysugar moieties.

Actinomyces↗
PubMed2001

Phylogenetic diversity of thermophilic actinomycetes and Thermoactinomyces spp. isolated from mushroom composts in Korea based on 16S rRNA gene sequence analysis.

Forty one strains isolated from 21 samples of various mushroom composts in Korea were analyzed by 16S rRNA gene sequencing to investigate the phylogenetic diversity of thermophilic actinomycetes. The 25 strains of thermophilic actinomycete isolates were related to the five genera, Pseudonocardia, Saccharomonospora, Saccharopolyspora, Streptomyces, and Thermobifida, within the order Actinomycetales, and 16 strains were classified into the genus Thermoactinomyces within the family Bacillaceae. Most of 41 isolates were encompassed by two genera, Streptomyces and Thermoactinomyces, that were isolated mainly in composts prepared from waste cotton and hay, respectively. Among them, M104 and M109 were placed in distinct taxonomic positions although these strains formed phylogenetic lineages related to the genus Streptomyces and to the family Streptosporangiaceae, respectively. Therefore, a phenetic and genetic characterization of these strains will be needed to pinpoint their taxonomic position.

Agaricales↗
PubMed1983

Gene cloning in the actinomycetes.

The production of antibiotics by soil-borne micro-organisms, the actinomycetes, has considerable economic importance. The manipulation of antibiotic producers has become a prime target for the application of recombinant DNA technology. Certain technical requirements have had to be met for gene cloning to be successful in the actinomycetes. These requirements, including the development of cloning vectors and transformation procedures, have been satisfied, in part, for some members of the Streptomyces genus. Some problems including sequence rearrangement and stability of plasmid maintenance are now being recognized. A number of genes have been cloned in Streptomyces and some preliminary results characterizing the gene for a Streptomyces-derived beta-galactosidase-like activity were described.

Actinomyces↗
PubMed1974

Susceptibility of pathogenic actinomycetes to antimicrobial compounds.

Current interest in antimicrobial susceptibility testing of anaerobic pathogens and recent recognition that actinomycetes other than Actinomyces israelii may cause actinomycosis in man prompted this in vitro survey of 74 strains of actinomycetes, representing seven species. Minimum inhibitory concentrations (MICs) for 24 antimicrobials were determined by inhibition of gross colonial enlargement in semisolid antibiotic agar after incubation at 37 C for 48 h under anaerobic conditions. Erythromycin and rifampin were the most active drugs in vitro (MICs of 0.008 to 0.25 mug/ml), although a small number of non-israelii strains were conspicuously more resistant to the latter (MICs >0.5 mug/ml). Penicillin G, cephaloridine, minocycline, and clindamycin were also very active in vitro (MICs of 0.03 to 1.0 mug/ml); for a few non-israelii strains the MICs of clindamycin were 2.0 to 8.0 mug/ml. MICs of cephalothin, ampicillin, lincomycin, tetracycline, doxycycline, and chloramphenicol were well within a therapeutic range for all strains of A. israelii and most other species, although the MIC of lincomycin against a few non-israelii strains and of tetracycline and doxycycline against the majority of these strains was 2.0 to 8.0 mug/ml. Oxacillin, dicloxacillin, and cephalexin were less active in vitro, particularly against strains other than A. israelii. Most non-israelii species were not suppressed by 125 mug of metronidazole per ml, which concentration inhibited all strains of A. israelii; otherwise, there were no antimicrobial susceptibility differences among the species tested. Aminoglycoside activity was negligible.

Actinomyces↗
PubMed2006

Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora.

Here we report associations between secondary metabolite production and phylogenetically distinct but closely related marine actinomycete species belonging to the genus Salinispora. The pattern emerged in a study that included global collection sites, and it indicates that secondary metabolite production can be a species-specific, phenotypic trait associated with broadly distributed bacterial populations. Associations between actinomycete phylotype and chemotype revealed an effective, diversity-based approach to natural product discovery that contradicts the conventional wisdom that secondary metabolite production is strain specific. The structural diversity of the metabolites observed, coupled with gene probing and phylogenetic analyses, implicates lateral gene transfer as a source of the biosynthetic genes responsible for compound production. These results conform to a model of selection-driven pathway fixation occurring subsequent to gene acquisition and provide a rare example in which demonstrable physiological traits have been correlated to the fine-scale phylogenetic architecture of an environmental bacterial community.

Micromonosporaceae↗
PubMed1984

Use of a computer to group actinomycetes for studies on the ecology of soil microorganisms.

A computer program has been prepared for grouping soil actinomycetes into cluster groups based on the presence or absence of aerial mycelium, the color of soluble pigment, and the shade of color of surface and reverse mycelium. The program automatically condenses cultures with wide ranges of characteristics into a limited number of groups and provides a permanent record so that comparisons can be made among experiments performed over a span of time. The program permits the grouping of large numbers of cultures with minimal laboratory effort and has proven useful in defining some of the ecological factors that lead to changed actinomycete populations in soils.

Actinomycetales↗
PubMed1988

Identification and characteristics of actinomycetes useful for semicontinuous treatment of domestic animal feces.

Selected strains of actinomycetes useful for practicing semicontinuous treatment of swine and poultry feces were identified as Streptomyces antibioticus S-4, S. puniceus N-50-2, S. nigrifaciens N-9-3, Thermoactinomyces vulgaris HIR-60, and Thermomonospora viridis HIR-50. These five obligately aerobic strains grew preferably on nonsterilized fresh swine feces in 24 h without any additives. They assimilated offensive volatile fatty acids in the swine and poultry feces. Cultures of these five strains were mixed and used as seed for the practical treatments of 1 ton of swine feces over the wide temperature range of 15 to 60 degrees C. Strain HIR-50 grew most predominantly on both fresh swine and poultry feces at 50 to 55 degrees C and decomposed uric acid. For the efficient penetration of mycelia into the feces, manures were mixed once a day so as not to break the solid mass, and the dehydration rate of feces had to be controlled in proportion to the mycelial growth rate. The actinomycete biofertilizer thus manufactured in 10 days was odorless and promotive of plant growth.

Journal Article↗