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)

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

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)

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

Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

Prokaryotic systematics provides the fundamental framework for microbiological research but remains a discipline that relies on a labour- and time-intensive polyphasic taxonomic approach, including DNA-DNA hybridization, variation in 16S rRNA gene sequence and phenotypic characteristics. These techniques suffer from poor resolution in distinguishing between closely related species and often result in misclassification and misidentification of strains. Moreover, guidelines are unclear for the delineation of bacterial genera. Here, we have applied an innovative phylogenetic and taxogenomic approach to a heterogeneous actinobacterial taxon, Rhodococcus, to identify boundaries for intrageneric and supraspecific classification. Seven species-groups were identified within the genus Rhodococcus that are as distantly related to one another as they are to representatives of other mycolic acid containing actinobacteria and can thus be equated with the rank of genus. It was also evident that strains assigned to rhodococcal species-groups are underspeciated with many misclassified using conventional taxonomic criteria. The phylogenetic and taxogenomic methods used in this study provide data of theoretical value for the circumscription of generic and species boundaries and are also of practical significance as they provide a robust basis for the classification and identification of rhodococci of agricultural, industrial and medical/veterinary significance

Verrucosispora fiedleri sp. nov., an actinomycete isolated from a fjord sediment which synthesizes proximicins

A novel filamentous actinobacterial organism, designated strain MG-37T, was isolated from a Norwegian fjord sediment and examined using a polyphasic taxonomic approach. The organism was determined to have chemotaxonomic and morphological properties consistent with its classification in the genus Verrucosispora and formed a distinct phyletic line in the Verrucosispora 16S rRNA gene tree. It was most closely related to Verrucosispora maris DSM 45365T (99.5 % 16S rRNA gene similarity) and Verrucosispora gifhornensis DSM 44337T (99.4 % 16S rRNA gene similarity) but was distinguished from these strains based on low levels of DNA:DNA relatedness (~56 and ~50 %, respectively). It was readily delineated from all of the type strains of Verrucosispora species based on a combination of phenotypic properties. Isolate MG-37T (=NCIMB 14794T = NRRL-B-24892T) should therefore be classified as the type strain of a novel species of Verrucosispora for which the name Verrucosispora fiedleri is proposed

Mycolicibacterium stellerae sp. nov., a rapidly growing scotochromogenic strain isolated from Stellera chamaejasme

A polyphasic study was undertaken to establish the taxonomic provenance of a rapidly growing Mycolicibacterium strain, CECT 8783T, recovered from the plant Stellera chamaejasme L. in Yunnan Province, China. Phylogenetic analyses based upon 16S rRNA and whole-genome sequences showed that the strain formed a distinct branch within the evolutionary radiation of the genus Mycolicibacterium . The strain was most closely related to Mycolicibacterium moriokaense DSM 44221T with 98.4 % 16S rRNA gene sequence similarity, but was distinguished readily from this taxon by a combination of chemotaxonomic and phenotypic features and by low average nucleotide identity and digital DNA–DNA hybridization values of 79.5 and 21.1 %, respectively. Consequently, the strain is considered, to represent a novel species of Mycolicibacterium for which the name Mycolicibacterium stellerae sp. nov is proposed; the type strain is I10A-01893T (=CECT 8783T=KCTC 19843T=DSM 45590T)