RESULTS:

The genus Ochrobactrum belongs to the family Brucellaceae and its members are known to be adapted to a wide range of ecological niches. Ochrobactrum anthropi ATCC 49188T and Ochrobactrum lupini LUP21T are strains isolated from human clinical and plant root nodule samples respectively which share high similarity for phylogenetic markers (i.e 100 % for 16S rRNA 99.9 % for dnaK and 99.35 % for rpoB). In this work multiple genome average nucleotide identity (ANI) approaches digital DNA–DNA hybridization (dDDH) and phylogenetic analysis were performed in order to investigate the taxonomic relationship between O. anthropi ATCC 49188T O. lupini LUP21T and other five type strains from the genus Ochrobactrum . Whole-genome comparisons demonstrated that O. lupini LUP21T and the Ochrobactrum genus type species O. anthropi ATCC 49188T share 97.55 % of ANIb 98.25 % of ANIm 97.99 % of gANI 97.94 % of OrthoANI and 83.9 % of dDDH which exceed the species delineation thresholds. These strains are also closely related in phylogenies reconstructed from a concatenation of 1193 sequences from single-copy ortholog genes. A review of their profiles revealed that O. anthropi ATCC 49188T and O. lupini LUP21T do not present pronounced differences at phenotypic and chemotaxonomic levels. Considering phylogenetic genomic phenotypic and chemotaxonomic data O. lupini should be considered a later heterotypic synonym of O. anthropi .

Over recent years genomic information has increasingly been used for prokaryotic species definition and classification. Genome sequence-based alternatives to the gold standard DNA–DNA hybridization (DDH) relatedness have been developed notably average nucleotide identity (ANI) which is one of the most useful measurements for species delineation in the genomic era. However the strictly intracellar lifestyle the few measurable phenotypic properties and the low level of genetic heterogeneity made the current standard genomic criteria for bacterial species definition inapplicable to Rickettsia species. We evaluated a range of whole genome sequence (WGS)-based taxonomic parameters to develop guidelines for the classification of Rickettsia isolates at genus and species levels. By comparing the degree of similarity of 74 WGSs from 31 Rickettsia species and 61 WGSs from members of three closely related genera also belonging to the order Rickettsiales ( Orientia 11 genomes; Ehrlichia 22 genomes; and Anaplasma 28 genomes) using digital DDH (dDDh) and ANI by orthology (OrthoANI) parameters we demonstrated that WGS-based taxonomic information which is easy to obtain and use can serve for reliable classification of isolates within the Rickettsia genus and species. To be classified as a member of the genus Rickettsia a bacterial isolate should exhibit OrthoANI values with any Rickettsia species with a validly published name of ≥83.63 %. To be classified as a new Rickettsia species an isolate should not exhibit more than any of the following degrees of genomic relatedness levels with the most closely related species: >92.30 and >99.19 % for the dDDH and OrthoANI values respectively. When applied to four rickettsial isolates of uncertain status the above-described thresholds enabled their classification as new species in one case. Thus we propose WGS-based guidelines to efficiently delineate Rickettsia species with OrthoANI and dDDH being the most accurate for classification at the genus and species levels respectively.

Phylogenetic analyses based on 16S rRNA gene sequences of members of the family Staphylococcaceae showed the presence of para- and polyphyletic genera. This finding prompted a thorough investigation into the taxonomy of the Staphylococcaceae family by analysing their core genome phylogeny complemented with genome-based indices such as digital DNA–DNA hybridization average nucleotide identity and average amino acid identity. The resulting data suggested the following proposals: Auricoccus indicus was reduced in taxonomic rank as a later heterotypic synonym of Abyssicoccus albus ; Staphylococcus petrasii subsp. jettensis as a later heterotypic synonym of Staphylococcus petrasii subsp. petrasii ; the unification of Staphylococcus aureus subsp. anaerobius and Staphylococcus aureus subsp. aureus as Staphylococcus aureus ; the unification of Staphylococcus carnosus subsp. utilis and Staphylococcus carnosus subsp. carnosus as Staphylococcus carnosus ; the unification of Staphylococcus saprophyticus subsp. bovis and Staphylococcus saprophyticus subsp. saprophyticus as Staphylococcus saprophyticus ; Staphylococcus succinis subsp. casei as the novel species Staphylococcus casei; Staphylococcus schleiferi subsp. coagulans as the novel species Staphylococcus coagulans; Staphylococcus petrasii subsp. croceilyticus as the novel species Staphylococcus croceilyticus; Staphylococcus petrasii subsp. pragensis as the novel species Staphylococcus pragensis; Staphylococcus cohnii subsp. urealyticus as the novel species Staphylococcus urealyticus; the reassignment of Staphylococcus sciuri Staphylococcus fleurettii Staphylococcus lentus Staphylococcus stepanovicii and Staphylococcus vitulinus to the novel genus Mammaliicoccus with Mammaliicoccus sciuri as the type species; and the formal assignment of Nosocomiicoccus as a member of the family Staphylococcaceae .

A strain of the recently validated species Faecalibacterium hominis shares 99.0 % 16S rRNA gene sequence similarity with the type strain of Faecalibacterium duncaniae . The aim of this study was to evaluate the taxonomic relationship between F. hominis and F. duncaniae. F. duncaniae JCM 31915T showed 73.0 % digital DNA–DNA hybridization (dDDH) value with F. hominis JCM 39347T. The average nucleotide identity (ANI) value between these two strains was 96.7 %. These results indicate that F. duncaniae JCM 31915T and F. hominis JCM 39347T represent members of the same species. Based on these data we propose Faecalibacterium hominis as a later heterotypic synonym of Faecalibacterium duncaniae . An emended description is provided.

The status Candidatus was introduced to bacterial taxonomy in the 1990s to accommodate uncultured taxa defined by analyses of DNA sequences. Here I review the strengths weaknesses opportunities and threats (SWOT) associated with the status Candidatus in the light of a quarter century of use twinned with recent developments in bacterial taxonomy and sequence-based taxonomic discovery. Despite ambiguities as to its scope philosophical objections to its use and practical problems in implementation the status Candidatus has now been applied to over 1000 taxa and has been widely adopted by journals and databases. Although lacking priority under the International Code for Nomenclature of Prokaryotes many Candidatus names have already achieved de facto standing in the academic literature and in databases via description of a taxon in a peer-reviewed publication alongside deposition of a genome sequence and there is a clear path to valid publication of such names on culture. Continued and increased use of Candidatus names provides an alternative to the potential upheaval that might accompany creation of a new additional code of nomenclature and provides a ready solution to the urgent challenge of naming many thousands of newly discovered but uncultured species.