Comparative evaluation of 16S rRNA sequencing strategies reveals superior resolution of the healthy Korean salivary microbiome by full-length sequencing

Although next-generation sequencing has elucidated complex microbial networks within the human oral cavity, current analyses remain predominantly limited to genus-level resolution, and most of the human oral microbiome landscape is based on Western population datasets. Because the oral microbial network is sensitive to environmental and dietary factors, mitigating this population bias is important for understanding oral microbial ecology. Building upon our previous findings, we aimed to refine the species-level resolution of the healthy Korean salivary microbiome. Using the same 112 salivary metagenomic DNA samples, we performed 16S full-length sequencing (16S FL platform) and compared it with our previous 16S V3V4 dataset. Distinct and shared bacterial taxa were evenly distributed on the 16S FL platform, whereas the 16S V3V4 data were skewed toward shared taxa. In both groups, the proportion of taxa with ambiguous nomenclature (‘unclear taxa’) was much lower on the 16S FL platform. The 16S FL platform also improved species-level assignment for Streptococcus and Haemophilus , the dominant genera of the healthy Korean oral microbiome, reducing from more than a third of the community to about 5% the fraction that the short-read platform reported only as an unnamed member of these genera. These results provide a high-resolution reference dataset for Korean-specific oral microbiome research.