Comparative genomics reconciliations of genus Streptococcus resolves its taxonomy and elucidates biotechnological importance of their constituent species

Abstract

The current taxonomy of Streptococcus is primarily based on low-resolution methods such as biochemical analysis, single housekeeping gene-based phylogeny, or conserved sequence identity of species groups resulting in various amendments in the taxonomic positioning of their constituent species.. We reported genome similarities assessment and phylogeny using several methods to provide a robust taxonomic framework with inclusion of 115 type strains and 23 unclassified species. Phylogeny based on the 16S rRNA gene suggests no integrity of the earlier classified species groups, which cannot be used for taxonomic classification. The whole genome phylogeny does not support the existence of the earlier defined species groups. Genome similarity assessment suggests the presence of sixteen novel genomospecies, including some of the amendments in the earlier classified species and subspecies. A highly stringent antibiotic resistance gene search resulted in widespread fluoroquinolones resistance. It is noteworthy that among the 42 genomes analyzed, which include strains of probiotic significance such as S. thermophilus NCTC 12958T and S. salivarius NCTC 8618T, no properly curated antibiotic resistance genes were discovered. However, the presence of partial hits for resistance genes in such strains requires further experimental validation before their downstream application.