Streptomyces corynorhini sp. nov., isolated from Townsend's big-eared bats (Corynorhinus townsendii).

Four bacterial strains, with the capability of inhibiting Pseudogymnoascus destructans, the causative agent of white-nose syndrome, were isolated from male Townsend's big-eared bats (Corynorhinus townsendii, Family: Vespertilionidae) in New Mexico. Isolates AC161, AC162, AC208, and AC230 were characterised as a novel clade using morphological, phenotypic and phylogenetic analysis. A draft genome of the type strain was completed to determine its taxonomy and secondary metabolite biosynthetic potential.

Discovery of the Tyrobetaine Natural Products and Their Biosynthetic Gene Cluster via Metabologenomics.

Natural products (NPs) are a rich source of medicines, but traditional discovery methods are often unsuccessful due to high rates of rediscovery. Genetic approaches for NP discovery are promising, but progress has been slow due to the difficulty of identifying unique biosynthetic gene clusters (BGCs) and poor gene expression. We previously developed the metabologenomics method, which combines genomic and metabolomic data to discover new NPs and their BGCs.

Entomopathogen ID: a curated sequence resource for entomopathogenic fungi.

We report the development of a publicly accessible, curated nucleotide sequence database of hypocrealean entomopathogenic fungi. The goal is to provide a platform for users to easily access sequence data from taxonomic reference strains. The database can be used to accurately identify unknown entomopathogenic fungi based on sequence data for a variety of phylogenetically informative loci.

Streptomyces odonnellii sp. nov., a proteolytic streptomycete isolated from soil under cerrado (savanna) vegetation cover.

A novel streptomycete, strain 594, isolated from Brazilian soil collected under cerrado (savanna) vegetation cover is described. Strain 594 produced thermophilic chitinolytic proteases in assays containing feather meal and corn steep liquor as sole sources of carbon and nitrogen. The strain produced white to grey aerial mycelium and spiral chains of spiny-surfaced spores on the aerial mycelium and did not produce diffusible pigments.

Streptomyces asenjonii sp. nov., isolated from hyper-arid Atacama Desert soils and emended description of Streptomyces viridosporus Pridham et al. 1958.

A polyphasic study was undertaken to establish the taxonomic status of Streptomyces strains isolated from hyper-arid Atacama Desert soils. Analysis of the 16S rRNA gene sequences of the isolates showed that they formed a well-defined lineage that was loosely associated with the type strains of several Streptomyces species. Multi-locus sequence analysis based on five housekeeping gene alleles showed that the strains form a homogeneous taxon that is closely related to the type strains of Streptomyces ghanaensis and Streptomyces viridosporus.

Streptomyces aridus sp. nov., isolated from a high altitude Atacama Desert soil and emended description of Streptomyces noboritoensis Isono et al. 1957.

A polyphasic study was undertaken to determine the taxonomic status of a Streptomyces strain which had been isolated from a high altitude Atacama Desert soil and shown to have bioactive properties. The strain, isolate H9, was found to have chemotaxonomic, cultural and morphological properties that place it in the genus Streptomyces. 16S rRNA gene sequence analyses showed that the isolate forms a distinct branch at the periphery of a well-delineated subclade in the Streptomyces 16S rRNA gene tree together with the type strains of Streptomyces crystallinus, Streptomyces melanogenes and Streptomyces noboritoensis.

Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis.

The family Streptomycetaceae, notably species in the genus Streptomyces, have long been the subject of investigation due to their well-known ability to produce secondary metabolites. The emergence of drug resistant pathogens and the relative ease of producing genome sequences has renewed the importance of Streptomyces as producers of new natural products and resulted in revived efforts in isolating and describing strains from novel environments. A previous large study of the phylogeny in the Streptomycetaceae based on 16S rRNA gene sequences provided a useful framework for the relationships among species, but did not always have sufficient resolution to provide definitive identification.

Western Bats as a Reservoir of Novel Streptomyces Species with Antifungal Activity.

At least two-thirds of commercial antibiotics today are derived from , more specifically from the genus Antibiotic resistance and new emerging diseases pose great challenges in the field of microbiology. Cave systems, in which actinobacteria are ubiquitous and abundant, represent new opportunities for the discovery of novel bacterial species and the study of their interactions with emergent pathogens. White-nose syndrome is an invasive bat disease caused by the fungus , which has killed more than six million bats in the last 7 years.

Quinovosamycins: new tunicamycin-type antibiotics in which the α, β-1″,11'-linked N-acetylglucosamine residue is replaced by N-acetylquinovosamine.

Tunicamycins (TUN) are potent inhibitors of polyprenyl phosphate N-acetylhexosamine 1-phosphate transferases (PPHP), including essential eukaryotic GPT enzymes and bacterial HexNAc 1-P translocases. Hence, TUN blocks the formation of eukaryotic N-glycoproteins and the assembly of bacterial call wall polysaccharides. The genetic requirement for TUN production is well-established.

Taxonomic evaluation of species in the Streptomyces hirsutus clade using multi-locus sequence analysis and proposals to reclassify several species in this clade.

Previous phylogenetic analysis of species of the genus Streptomyces based on 16S rRNA gene sequences resulted in a statistically well-supported clade (100 % bootstrap value) containing eight species that exhibited very similar gross morphology in producing open looped (Retinaculum-Apertum) to spiral (Spira) chains of spiny- to hairysurfaced, dark green spores on their aerial mycelium. The type strains of the species in this clade, specifically Streptomyces bambergiensis, Streptomyces cyanoalbus, Streptomyces emeiensis, Streptomyces hirsutus, Streptomyces prasinopilosus and Streptomyces prasinus, were subjected to multi-locus sequence analysis (MLSA) utilizing partial sequences of the housekeeping genes atpD, gyrB, recA, rpoB and trpB to clarify their taxonomic status. The type strains of several recently described species with similar gross morphology, including Streptomyces chlorus, Streptomyces herbaceus, Streptomyces incanus, Streptomyces pratens and Streptomyces viridis, were also studied along with six unidentified green-spored Streptomyces strains from the ARS Culture Collection.

Taxonomic evaluation of putative Streptomyces scabiei strains held in the ARS Culture Collection (NRRL) using multi-locus sequence analysis.

Multi-locus sequence analysis has been demonstrated to be a useful tool for identification of Streptomyces species and was previously applied to phylogenetically differentiate the type strains of species pathogenic on potatoes (Solanum tuberosum L.). The ARS Culture Collection (NRRL) contains 43 strains identified as Streptomyces scabiei deposited at various times since the 1950s and these were subjected to multi-locus sequence analysis utilising partial sequences of the house-keeping genes atpD, gyrB, recA, rpoB and trpB.

Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes.

Although natural products have been a particularly rich source of human medicines, activity-based screening results in a very high rate of rediscovery of known molecules. Based on the large number of natural product biosynthetic genes in microbial genomes, many have proposed "genome mining" as an alternative approach for discovery efforts; however, this idea has yet to be performed experimentally on a large scale. Here, we demonstrate the feasibility of large-scale, high-throughput genome mining by screening a collection of over 10,000 actinomycetes for the genetic potential to make phosphonic acids, a class of natural products with diverse and useful bioactivities.

A roadmap for natural product discovery based on large-scale genomics and metabolomics.

Actinobacteria encode a wealth of natural product biosynthetic gene clusters, whose systematic study is complicated by numerous repetitive motifs. By combining several metrics, we developed a method for the global classification of these gene clusters into families (GCFs) and analyzed the biosynthetic capacity of Actinobacteria in 830 genome sequences, including 344 obtained for this project. The GCF network, comprising 11,422 gene clusters grouped into 4,122 GCFs, was validated in hundreds of strains by correlating confident mass spectrometric detection of known small molecules with the presence or absence of their established biosynthetic gene clusters.

Streptomyces leeuwenhoekii sp. nov., the producer of chaxalactins and chaxamycins, forms a distinct branch in Streptomyces gene trees.

A polyphasic study was carried out to establish the taxonomic status of an Atacama Desert isolate, Streptomyces strain C34(T), which synthesises novel antibiotics, the chaxalactins and chaxamycins. The organism was shown to have chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Streptomyces. Analysis of 16S rRNA gene sequences showed that strain C34(T) formed a distinct phyletic line in the Streptomyces gene tree that was very loosely associated with the type strains of several Streptomyces species.

Diversity and abundance of phosphonate biosynthetic genes in nature.

Phosphonates, molecules containing direct carbon-phosphorus bonds, compose a structurally diverse class of natural products with interesting and useful biological properties. Although their synthesis in protozoa was discovered more than 50 y ago, the extent and diversity of phosphonate production in nature remains poorly characterized. The rearrangement of phosphoenolpyruvate (PEP) to phosphonopyruvate, catalyzed by the enzyme PEP mutase (PepM), is shared by the vast majority of known phosphonate biosynthetic pathways.

An investigation of a recent outbreak of nocardioform placentitis caused abortions in horses.

Nocardioform placentitis associated with gram positive branching actinomycetes caused a record number of abortions in mares diagnosed by the University of Kentucky Veterinary Diagnostic Laboratory (UKVDL) affecting the 2011 foal crop (2011 foal crop: the cohort of foals conceived during the 2010 breeding season). The goal of the present study is to make a comprehensive analysis of this outbreak in terms of frequencies of the bacteria causing nocardioform placentitis mediated abortions and to investigate the ages of fetuses, abortion months and breeding times. In the present study, characteristic slow-growing, pungent/soil odor gram positive branching actinomycetes were recovered in high numbers in placental specimens in 76 abortion cases diagnosed as nocardioform placentitis by pathologists.

Reassessment of the status of Streptomyces setonii and reclassification of Streptomyces fimicarius as a later synonym of Streptomyces setonii and Streptomyces albovinaceus as a later synonym of Streptomyces globisporus based on combined 16S rRNA/gyrB gene sequence analysis.

The 16S rRNA and gyrB genes of 22 Streptomyces strains belonging to the Streptomyces griseus cluster were sequenced, and their taxonomic positions were re-evaluated. For correct analysis, all of the publicly available sequences of the species were collected and compared with those obtained in this study. Species for which no consensus sequence could be identified were excluded from the phylogenetic analysis.

Genome sequences of three tunicamycin-producing Streptomyces Strains, S. chartreusis NRRL 12338, S. chartreusis NRRL 3882, and S. lysosuperificus ATCC 31396.

We announce the sequencing of Streptomyces chartreusis NRRL 12338 and NRRL 3882 and Streptomyces lysosuperificus ATCC 31396. These are producers of tunicamycins, chartreusins, cephalosporins, holomycins, and calcimycin. The announced genomes, together with the published Streptomyces clavuligerus genome, will facilitate data mining of these secondary metabolites.

A proteomic survey of nonribosomal peptide and polyketide biosynthesis in actinobacteria.

Actinobacteria such as streptomycetes are renowned for their ability to produce bioactive natural products including nonribosomal peptides (NRPs) and polyketides (PKs). The advent of genome sequencing has revealed an even larger genetic repertoire for secondary metabolism with most of the small molecule products of these gene clusters still unknown. Here, we employed a "protein-first" method called PrISM (Proteomic Investigation of Secondary Metabolism) to screen 26 unsequenced actinomycetes using mass spectrometry-based proteomics for the targeted detection of expressed nonribosomal peptide synthetases or polyketide synthases.

Multilocus sequence analysis of phytopathogenic species of the genus Streptomyces.

The identification and classification of species within the genus Streptomyces is difficult because there are presently 576 species with validly published names and this number increases every year. The value of multilocus sequence analysis applied to the systematics of Streptomyces species has been well demonstrated in several recently published papers. In this study the sequence fragments of four housekeeping genes, atpD, recA, rpoB and trpB, were determined for the type strains of 10 known phytopathogenic species of the genus Streptomyces, including Streptomyces scabiei, Streptomyces acidiscabies, Streptomyces europaeiscabiei, Streptomyces luridiscabiei, Streptomyces niveiscabiei, Streptomyces puniciscabiei, Streptomyces reticuliscabiei, Streptomyces stelliscabiei, Streptomyces turgidiscabies and Streptomyces ipomoeae, as well as six uncharacterized phytopathogenic Streptomyces isolates.

Kroppenstedtia eburnea gen. nov., sp. nov., a thermoactinomycete isolated by environmental screening, and emended description of the family Thermoactinomycetaceae Matsuo et al. 2006 emend. Yassin et al. 2009.

A Gram-positive, spore-forming, aerobic, filamentous bacterium, strain JFMB-ATE(T), was isolated in 2008 during environmental screening of a plastic surface in grade C in a contract manufacturing organization in southern Germany. The isolate grew at temperatures of 25-50 °C and at pH 5.0-8.

Reclassification of 'Dactylosporangium variesporum' as Saccharothrix variisporea corrig. (ex Tomita et al. 1977) sp. nov., nom. rev.

In the course of a polyphasic study it was observed that 'Dactylosporangium variesporum' NRRL B-16296 is misclassified in the genus Dactylosporangium as it exhibits properties consistent with its assignment to the genus Saccharothrix. Phylogenetic analyses based on 16S rRNA gene sequences show that the strain falls within the evolutionary radiation of the genus Saccharothrix, a result which is supported by corresponding chemotaxonomic and morphological markers. The strain is phylogenetically most closely, albeit loosely, related to Saccharothrix espanaensis, but can be readily distinguished from this and other species of the genus Saccharothrix with validly described names by using a range of phenotypic properties.

Paenibacillus tundrae sp. nov. and Paenibacillus xylanexedens sp. nov., psychrotolerant, xylan-degrading bacteria from Alaskan tundra.

Eight psychrotolerant, xylan-degrading strains of bacteria that were catalase-positive, oxidase-negative and able to reduce nitrate to nitrite were isolated from soil beneath moist non-acidic and acidic tundra in northern Alaska. The DNA G+C contents for the strains ranged from 46.4-50.

The Streptomyces violaceusniger clade: a home for Streptomycetes with rugose ornamented spores.

The taxonomic status of 16 strains received as Streptomyces hygroscopicus, Streptomyces melanosporofaciens, Streptomyces sparsogenes, Streptomyces sporoclivatus and Streptomyces violaceusniger was evaluated in a polyphasic study. Eleven of the organisms formed a distinct clade in the Streptomyces 16S rRNA gene tree with the type strains of Streptomyces asiaticus, Streptomyces cangkringensis, Streptomyces indonesiensis, Streptomyces javensis, Streptomyces malaysiensis, Streptomyces rhizosphaericus, Streptomyces yatensis and Streptomyces yogyakartensis, the members of this group produced rugose ornamented spores in spiral spore chains. The eleven strains were assigned to three established and four novel species, namely Streptomyces albiflaviniger sp.

Evaluation of microbial strains for linoleic acid hydroxylation and reclassification of strain ALA2.

In previous studies, a new microbial strain ALA2 was isolated which produced many new products from linoleic acid [Gardner H.W., Hou C.