Re-evaluation of boundaries of and and demonstration of multiple later synonyms of and description of subsp. subsp. nov. and emended description of .

The commensal species and are genetically diverse to a degree that challenges traditional definitions of species. This causes automatic identification based on DNA sequences or cellular extract profiles problematic. Based on an initial analysis of 266 genomes, we subjected a subset of 100 representative genomes to detailed phylogenetic, pairwise distance and gene pattern analyses. and constitute a continuum of clones that are genetically unique. To recognize most isolates as separate species is biologically and practically meaningless. We recommend bending the proposed similarity borders to accommodate the biological reality. Accordingly, we conclude that , , , and are later heterotypic synonyms of . Type strains of effectively but not validly published '', '' and '' belong in and are later synonyms of is a later synonym of subsp. , and the type of '' belongs in subsp. . The genome sequence of the type of the recently proposed '' is based on a mixed culture. Phylogenetic results and the pattern of presence/absence of accessory genes support the distinction of two subspecies of , i.e. subsp subsp. nov. (type strain is NCTC 12261) and subsp. subsp. nov. (type strain is SK608=CCUG 55085=LMG 33510). The special population structure of the complex renders automated classification of isolates based on average nucleotide identity or digital DNA-DNA hybridization values problematic. As an alternative, for initial taxonomic assignment, we present a whole-genome phylogeny-based method that enables phylogenetic comparison of new isolates in the context of a set of 117 well-characterized reference strains assigned to the Mitis/Sanguinis group.