Combined quantitative and relative microbiome profiling reveals key salivary bacteriome shifts associated with periodontal health and different stages of periodontitis

Aim

To characterize the salivary microbiota in subjects with periodontal health (PH), stage I-II periodontitis (moderate periodontitis, MP), and stage III-IV periodontitis (severe periodontitis, SP) by integrating quantitative microbiome profiling (QMP) and relative microbiome profiling (RMP) approaches.

Methodology

This cross-sectional study involved the collection of 74 saliva samples, categorized into PH (n = 25), MP (n = 25), and SP (n = 24) groups, based on the 2018 Classification of Periodontal and Peri-Implant Diseases and Conditions. Samples were processed using absolute quantitative high-throughput sequencing technologies (Illumina NovaSeq). Alpha diversity, beta diversity, taxonomic shifts, bacterial types, and co-occurrence networks were compared across groups using QMP and RMP.

Results

Significant differences in microbial composition and microbial load were observed in the salivary microbiota across the PH, MP, and SP groups. With increasing periodontitis severity, salivary microbiota showed decreased alpha diversity but increased total abundance. Gram-negative anaerobic pathogens (e.g., Porphyromonas, Prevotella, Treponema, Fusobacterium) increased in both absolute and relative abundances. Conversely, aerobic and facultative anaerobic commensals (e.g., Streptococcus, Haemophilus, Neisseria, Rothia) showed increased absolute but decreased relative abundances. Additionally, co-occurrence networks constructed using QMP contained more species and connections compared to those constructed using RMP.

Conclusion

A strong association between increasing periodontitis severity and both elevated total microbial load and microbial dysbiosis, characterized by increased relative abundance of periodontal pathogens, was detected in the salivary microbiota. The combined QMP and RMP approach proved essential for capturing these complex microbial dynamics.

Clinical Relevance

Effective periodontitis management requires a dual approach: mechanical debridement to reduce microbial load and disrupt pathogenic ecological niches by decreasing pocket depth and inflammation, combined with targeted therapies to correct dysbiotic microbial communities and restore health-associated microbiota composition.