Complete genome sequence of Streptococcus sp. strain KHUD_013 isolated from the human buccal mucosa

The genus Streptococcus constitutes a major component of the human oral microbiome and exhibits substantial genomic diversity at the species level. However, complete and high-quality reference genomes remain limited for many closely related oral streptococci, constraining accurate comparative and taxonomic analyses. The objective of this Data Note was to generate and report a complete genome sequence of Streptococcus sp. strain KHUD_013, isolated from the human buccal mucosa, and to provide a genomic context for comparison with closely related species.

Long-read sequencing using the PacBio Revio platform generated 89,500 high-fidelity (HiFi) reads with a mean read length of 6,960 bp. Genome assembly produced a single circular chromosome of 1,988,919 bp with a G + C content of 42.5%. Genome annotation identified 1,827 protein-coding genes, four ribosomal RNA operons (5 S, 16 S, and 23 S), and 62 transfer RNA genes, with an estimated completeness of 98.8%. Average Nucleotide Identity (ANI) analysis indicated that strain KHUD_013 is most closely related to the Streptococcus ilei type strain (GCA_000479335.1), with a value of 94.39% and an alignment coverage of 86.55%, consistent with genomic divergence at the species boundary. Comparative genomic analysis with four publicly available S. ilei genomes identified 179 gene clusters unique to KHUD_013, predominantly associated with replication, recombination, and repair, as well as cell wall and membrane biogenesis and transcription. This genome sequence provides a valuable resource for strain-level comparative and taxonomic studies of oral streptococci.