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).