Description and genomic characterization of Streptococcus symci sp. nov., isolated from a child’s oropharynx

Using the culturomics approach, we isolated a new Streptococcus species, strain C17(T), from the oropharynx mucosa sample of a healthy 5-year-old child living in Shenyang, China. We studied the phenotypic, phylogenetic, and genomic characteristics of strain C17(T), which was identified as a Gram-positive, coccus-shaped, non-motile, aerobic, catalase-negative bacteria. Its growth temperatures ranged from 20 to 42 °C, with optimal growth at 37 °C. Acid production could be inhibited by two sugars, trehalose and raffinose. In C17(T), the reactions for enzyme lipase (C14) were confirmed to be negative, whereas those for alkaline phosphatase, α-glucosidase, and hippuric acid hydrolysis were positive. The C17(T) genome contained 2,189,419 base pairs (bp), with an average G+C content of 39.95%, encoding 2092 genes in total. The 16S ribosomal RNA sequence showed 99.8% similarity with the newly identified Streptococcus pseudopneumoniae ATCC BAA-960(T). The main fatty acid components in C17(T) were C16:0, C18:1 w7c, C18:0, and C18:1 w9c, all of which can be found in other species of the Streptococcus genus. Strain C17(T) showed high susceptibility to clindamycin, linezolid, vancomycin, chloramphenicol, and cefepime, and moderate susceptibility to erythromycin. The obtained dDDH value between strain C17(T) and the closest species was 52.9%. In addition, the whole genome sequence of strain C17(T) had an 82.21–93.40% average nucleotide identity (ANI) with those strains of closely related Streptococcus species, indicating that the strain C17(T) was unique among all Streptococcus species. Based on these characteristics, we determine that C17(T) is a novel species, named Streptococcus symci sp. nov. (= GDMCC 1.1633 = JCM 33582).