Genomic insights support the taxonomic differentiation of Streptococcus thermophilus Orla-Jensen 1919 (Approved Lists 1980) and Streptococcus salivarius Andrewes and Horder 1906 (Approved Lists 1980) as individual species.

Streptococcus thermophilus is widely used as a starter culture in the production of cheese, yoghurt and various cultured dairy products, which holds considerable significance in both research and practical applications within the food industry. Throughout history, the taxonomy of S. thermophilus has undergone several adjustments and revisions. In 1984, based on the result of DNA-DNA hybridization, S. thermophilus was reclassified as Streptococcus salivarius subsp. thermophilus. Subsequently, in 1991, Schleifer et al. proposed the revival of the species S. thermophilus also relying on a DNA-DNA hybridization study conducted under stringent conditions. At present, both the taxonomic names, S. thermophilus and S. salivarius subsp. thermophilus, are considered as synonyms and adopted within scientific research, regulatory oversight and relevant industries, leading to a certain degree of confusion. A precise and scientifically accurate taxonomic status is imperative as a foundational prerequisite for a strain evaluation and its application in food manufacture and regulatory contexts. In this study, we utilized whole-genome sequencing to evaluate the genetic relationship of S. thermophilus and S. salivarius. At the gene level, phylogenetic analyses were conducted on 52 S. thermophilus strains and 63 S. salivarius strains based on sequences of both the 16S rRNA gene and the housekeeping gene, recA. Additionally, a core-gene phylogeny was inferred using the whole-genome sequencing data of 216 strains within the Streptococcus genus. This analysis facilitated an exhaustive evaluation of the evolutionary interconnections among the studied strains. At the genetic level, average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were used to verify the species identity of S. thermophilus and S. salivarius. The results of phylogenetic analysis, ANI and dDDH all collectively confirm that S. thermophilus and S. salivarius are distinct species. These research results provide sufficient scientific evidence to support the definitive scientific and rational application of the name of S. thermophilus.