Exploring Intra-individual Oral Microbiome diversity and Streptococcal Colonisation Patterns

Aims We have investigated bacterial colonisation and site-specific distribution across hard and soft oral tissues focusing on both intra- and inter-individual patterns of Streptococcus clonality and overall microbial composition. Methods and Results Thirty samples were collected from five healthy adults, covering six oral sites (buccal mucosa, tongue dorsum, maxillary central incisors, mandibular molar fissure, and saliva). Repetitive sequence-based PCR (rep-PCR) assessed Streptococcus clonality, while 16S rRNA gene sequencing characterised broader microbial communities. Among 98 Streptococcus isolates, 67.3% were clonal and frequently recovered from multiple sites within individuals. Identical S. vestibularis clones were detected across all sampled sites in one participant and across several sites in others, indicating shared intra-oral reservoirs. Amplicon sequencing revealed distinct microbial compositions across oral sites, with saliva displaying the highest alpha diversity (Shannon index) and significant beta-diversity differences between most sites, except saliva and tongue. Firmicutes predominated overall, and Streptococcus was the most abundant genus. Differential-abundance testing (ANCOM-BC2) identified 26 genera varying significantly across sites, with lower abundance generally observed on soft tissues. Conclusions These findings suggest that while microbial communities vary by oral site, certain streptococcal clones, including S. vestibularis, occur across multiple habitats. This suggests potential intra-oral reservoirs that may contribute to microbiome stability.