Genome sequence analyses show that Neisseria oralis is the same species as 'Neisseria mucosa var. heidelbergensis'

Abstract

Phylogenies generated from whole genome sequence (WGS) data provide definitive means of bacterial isolate characterization for typing and taxonomy. The species status of strains recently defined with conventional taxonomic approaches as representing Neisseria oralis was examined by the analysis of sequences derived from WGS data, specifically: (i) 53 Neisseria ribosomal protein subunit (rps) genes (ribosomal multi-locus sequence typing, rMLST); and (ii) 246 Neisseria core genes (core genome MLST, cgMLST). These data were compared with phylogenies derived from 16S and 23S rRNA gene sequences, demonstrating that the N. oralis strains were monophyletic with strains described previously as representing 'Neisseria mucosa var. heidelbergensis' and that this group was of equivalent taxonomic status to other well-described species of the genus Neisseria. Phylogenetic analyses also indicated that Neisseria sicca and Neisseria macacae should be considered the same species as Neisseria mucosa and that Neisseria flavescens should be considered the same species as Neisseria subflava. Analyses using rMLST showed that some strains currently defined as belonging to the genus Neisseria were more closely related to species belonging to other genera within the family; however, whole genome analysis of a more comprehensive selection of strains from within the family Neisseriaceae would be necessary to confirm this. We suggest that strains previously identified as representing 'N. mucosa var. heidelbergensis' and deposited in culture collections should be renamed N. oralis. Finally, one of the strains of N. oralis was able to ferment lactose, due to the presence of β-galactosidase and lactose permease genes, a characteristic previously thought to be unique to Neisseria lactamica, which therefore cannot be thought of as diagnostic for this species; however, the rMLST and cgMLST analyses confirm that N. oralis is most closely related to N. mucosa.

Fig. 1.

Neighbour-joining tree reconstructed from concatenated ribosomal protein gene sequences. Type strains are indicated with superscript T. Only bootstrap values of 70 % or greater are shown. Suggested species reclassifications are indicated by brackets. Bar, 0.02 substitutions per nucleotide position. ID numbers are the strain identifiers used in the PubMLST Neisseria database (http://pubmlst.org/neisseria/) or the rMLST database (http://pubmlst.org/rmlst/).

Fig. 2.

Neighbour-joining tree reconstructed from 246 concatenated core gene sequences. Type strains are indicated with superscript T. Only bootstrap values of 70 % or greater are shown. Suggested species reclassifications are indicated by brackets. Bar, 0.02 substitutions per nucleotide position. ID numbers are the strain identifiers used in the PubMLST Neisseria database (http://pubmlst.org/neisseria/).