Re-evaluation of the taxonomy of the Mitis group of the genus Streptococcus based on whole genome phylogenetic analyses, and proposed reclassification of Streptococcus dentisani as Streptococcus oralis subsp. dentisani comb. nov., Streptococcus tigurinus as Streptococcus oralis subsp. tigurinus comb. nov., and Streptococcus oligofermentans as a later synonym of Streptococcus cristatus

Abstract

The Mitis group of the genus Streptococcus currently comprises 20 species with validly published names, including the pathogen S. pneumoniae. They have been the subject of much taxonomic confusion, due to phenotypic overlap and genetic heterogeneity, which has hampered a full appreciation of their clinical significance. The purpose of this study was to critically re-examine the taxonomy of the Mitis group using 195 publicly available genomes, including designated type strains for phylogenetic analyses based on core genomes, multilocus sequences and 16S rRNA gene sequences, combined with estimates of average nucleotide identity (ANI) and in silico and in vitro analyses of specific phenotypic characteristics. Our core genomic phylogenetic analyses revealed distinct clades that, to some extent, and from the clustering of type strains represent known species. However, many of the genomes have been incorrectly identified adding to the current confusion. Furthermore, our data show that 16S rRNA gene sequences and ANI are unsuitable for identifying and circumscribing new species of the Mitis group of the genus Streptococci. Based on the clustering patterns resulting from core genome phylogenetic analysis, we conclude that S. oligofermentans is a later synonym of S. cristatus. The recently described strains of the species Streptococcus dentisani includes one previously referred to as 'S. mitis biovar 2'. Together with S. oralis, S. dentisani and S. tigurinus form subclusters within a coherent phylogenetic clade. We propose that the species S. oralis consists of three subspecies: S. oralis subsp. oralis subsp. nov., S. oralis subsp. tigurinus comb. nov., and S. oralis subsp. dentisani comb. nov.

Health-Associated Niche Inhabitants as Oral Probiotics: The Case of Streptococcus dentisani

“…Production of ammonia from urea or arginine by several oral bacteria has been shown to efficiently buffer salivary pH and has been associated to a reduction in caries risk (Reyes et al, 2014; Moncada et al, 2015). The analysis of the genome of Streptococcus dentisani revealed all genes from the arginolytic pathway, including the arginine deiminase and the carbamate kinase, a feature which appears to be common to all members of the cluster (Jensen et al, 2016). In addition, the agmatine deiminase gene, involved in the production of ammonia (Liu et al, 2012) was also present in both analyzed strains.…”

“…There are currently six isolates for which the genome sequence is available and that robust phylogenomic analysis include within the dentisani cluster (Jensen et al, 2016). This cluster forms part of the S. oralis clade and differs from the S. oralis and S. tigurinus clusters mainly in their ability to hydrolyze arginine (Jensen et al, 2 016).…”

Capsular Polysaccharide Expression in CommensalStreptococcusSpecies: Genetic and Antigenic Similarities to Streptococcus pneumoniae

“…The remaining strains were from our own or national bacterial culture collections. The identity of the strains was according to the most recent taxonomic updates based on core genome analyses (63). The streptococcus strains were cultured on either 5% blood agar plates (Statens Serum Institut, Copenhagen, Denmark) or in Todd-Hewitt broth (CM189; Oxoid) overnight at 35°C in a 5% CO 2 incubator.…”

Biology of Oral Streptococci

“…Species within the mitis group have been challenging to differentiate based on 16S RNA sequence alone, particularly S. oralis and S. mitis . Recent efforts to re-classify many of the species within this group indicate there are many strains that have been misclassified and new species descriptions may soon emerge (14). …”