Phylo-taxonogenomic reconciliations of genus Streptococcus reveals the existence of sixteen novel genomospecies

Abstract Over two centuries, genus Streptococcus has been extensively explored in clinical and industrial settings. However, its taxonomy is based on low-resolution methods such as biochemical, housekeeping genes, or conserved sequence identity of species groups resulting in various amendments. In the current study, we have used genome similarities and phylogeny to provide a robust taxonomic framework of 115 type strains and 23 unclassified species. Phylogeny based on 16S rRNA suggests no integrity of the earlier classified species groups, which cannot be used as a taxonomic classification. Whole genome phylogeny counter supports the non-existence of the earlier defined species groups. Genome similarity assessment suggest the existence of sixteen novel genomospecies including some of the amendments in the earlier classified species and subspecies. Highly stringent antibiotic resistance genes search resulted in widespread of fluoroquinolones resistance. Interestingly, no well-curated antibiotic resistance genes were not found in 42 genomes, including strains of probiotic importance like S. thermophilus NCTC 12958 (T) and S. salivarius NCTC 8618 (T), etc. However, presence of partial hits for resistance genes in such strains requires further experimental validation before their downstream application.