Prescottia equi gen. nov., comb. nov.: a new home for an old pathogen

The taxonomic status of Rhodococcus equi, originally isolated from foal specimens, has been the subject of discussion for a number of years. The chequered history of the taxon has prompted this polyphasic analysis of R. equi strains, close members of the genus Rhodococcus and representatives of other genera classified in the order Corynebacteriales, to establish the taxonomic position of this taxon. Thirty one R. equi strains, including the type strain, were examined for genotypic and numerical taxonomic properties. The resultant data are consistent with their classification in the order Corynebacteriales but the R. equi strains formed a distinct phyletic clade away from representatives of other members of the genus Rhodococcus in the 16S rRNA gene tree. Representatives of this clade shared their highest pairwise 16S rRNA gene sequence similarities with the type strain of Rhodococcus kunmingensis (95.2–98.1 %). However, the R. equi taxon was readily distinguished from R. kunmingensis and from the other members of the order Corynebacteriales using a combination of genotypic, chemotypic and phenotypic properties. On the basis of these data the R. equi strains are considered to represent a new genus. The name proposed for this taxon is Prescottia gen. nov., with Prescottia equi comb. nov. as the type species containing the type strain, C 7T (= ATCC 25729T = ATCC 6939T = CCUG 892T = CIP 54.72T = DSM 20307T = HAMBI 2061T = NBRC 14956T = JCM 1311T = JCM 3209T = LMG 18452T = NBRC 101255T = NCTC 1621T = NRRL B-16538T = VKM Ac-953T)

Williamsia faeni sp. nov., an actinomycete isolated from a hay meadow

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)

Dietzia papillomatosis sp. nov., a novel actinomycete isolated from the skin of an immunocompetent patient with confluent and reticulated papillomatosis

An actinomycete isolated from an immunocompetent patient suffering from confluent and reticulated papillomatosis was characterized using a polyphasic taxonomic approach. The organism had chemotaxonomic and morphological properties that were consistent with its assignment to the genus Dietzia and it formed a distinct phyletic line within the Dietzia 16S rRNA gene tree. It shared a 16S rRNA gene sequence similarity of 98.3 % with its nearest neighbour, the type strain of Dietzia cinnamea, and could be distinguished from the type strains of all Dietzia species using a combination of phenotypic properties. It is apparent from genotypic and phenotypic data that the organism represents a novel species in the genus Dietzia. The name proposed for this taxon is Dietzia papillomatosis; the type strain is N 1280T (=DSM 44961T=NCIMB 14145T)

Genomic analyses confirm close relatedness between Rhodococcus defluvii and Rhodococcus equi (Rhodococcus hoagii)

Rhodococcus defluvii strain Ca11T was isolated from a bioreactor involved in extensive phosphorus removal. We have sequenced the whole genome of this strain and our comparative genomic and phylogenetic analyses confirm its close relatedness with Rhodococcus equi (Rhodococcus hoagii) strains, which share >80% of the gene content. The R. equi virulence plasmid is absent though most of the chromosomal R. equi virulence-associated genes are present in R. defluvii Ca11T. These data suggest that although R. defluvii is an environmental organism, it has the potential to colonise animal hosts

Hydricity Of 3d transition metal complexes from density functional theory : a benchmarking study

A range of modern density functional theory (DFT) functionals have been benchmarked against experimentally determined metal hydride bond strengths for three first-row TM hydride complexes. Geometries were found to be produced sufficiently accurately with RI-BP86-D3(PCM)/def2-SVP and further single-point calculations with PBE0-D3(PCM)/def2-TZVP were found to reproduce the experimental hydricity accurately, with a mean absolute deviation of 1.4 kcal/mol for the complexes studied.Publisher PDFPeer reviewe

Nocardia aciditolerans sp. nov., isolated from a spruce forest soil

Actinomycetes growing on acidified starch-casein agar seeded with suspensions of litter and mineral soil from a spruce forest were provisionally assigned to the genus Nocardia based upon colonial properties. Representative isolates were found to grow optimally at pH 5.5, have chemotaxonomic and morphological features consistent with their assignment to the genus Nocardia and formed two closely related subclades in the Nocardia 16S rRNA gene tree. DNA:DNA relatedness assays showed that representatives of the subclades belong to a single genomic species. The isolates were distantly associated with their nearest phylogenetic neighbour, the type strain of Nocardia kruczakiae, and were distinguished readily from the latter based on phenotypic properties. On the basis of these data it is proposed that the isolates merit recognition as a new species, Nocardia aciditolerans sp. nov. The type strain is isolate CSCA68(T) (=KACC 17155(T) = NCIMB 14829(T) = DSM 45801(T)). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10482-013-9887-3) contains supplementary material, which is available to authorized users

Nocardia kroppenstedtii sp. nov., a novel actinomycete isolated from a lung transplant patient with a pulmonary infection

An actinomycete, strain N1286T, isolated from a lung transplant patient with a pulmonary infection, was provisionally assigned to the genus Nocardia. The strain had chemotaxonomic and morphological properties typical of members of the genus Nocardia and formed a distinct phyletic line in the Nocardia 16S rRNA gene tree. It was most closely related to Nocardia farcinica DSM 43665T (99.8% gene similarity) but was distinguished from the latter by a low level of DNA:DNA relatedness. These strains were also distinguished by a broad range of phenotypic properties. On the basis of these data, it is proposed that isolate N1286T (=DSM 45810T = NCTC 13617T) should be classified as the type strain of a new Nocardia species for which the name Nocardia kroppenstedtii is proposed

Comparative Genomic and Phylogenomic Analyses Clarify Relationships Within and Between Bacillus cereus and Bacillus thuringiensis: Proposal for the Recognition of Two Bacillus thuringiensis Genomovars

The present study was designed to clarify the taxonomic status of two species classified as Bacillus cereus sensu lato, namely B. cereus sensu stricto and Bacillus thuringiensis. To this end, nearly 900 whole genome sequences of strains assigned to these taxa were the subject of comparative genomic and phylogenomic analyses. A phylogenomic tree based on core gene sequences showed that the type strains of B. cereus and B. thuringiensis formed a well-supported monophyletic clade that was clearly separated from corresponding clades composed of the remaining validly published species classified as B. cereus sensu lato. However, since average nucleotide identity and digital DNA-DNA hybridization similarities between the two types of Bacillus were slightly higher than the thresholds used to distinguish between closely related species we conclude that B. cereus and B. thuringiensis should continue to be recognized as validly published species. The B. thuringiensis strains were assigned to two genomically distinct groups, we propose that these taxa be recognized as genomovars, that is, as B. thuringiensis gv. thuringiensis and B. thuringiensis gv. cytolyticus. The extensive comparative genomic data clearly show that the distribution of pesticidal genes is irregular as strains identified as B. thuringiensis were assigned to several polyphyletic groups/subclades within the B. cereus-B. thuringiensis clade. Consequently, we recommend that genomic or equivalent molecular systematic features should be used to identify B. thuringiensis strains as the presence of pesticidal genes cannot be used as a diagnostic marker for this species. Comparative taxonomic studies are needed to find phenotypic properties that can be used to distinguish between the B. thuringiensis genomovars and between them and B. cereus.