Salivary metagenomic profiling of Neisseria, Dialister, and Filifactor species in periodontal health and disease using next-generation sequencing

Background Periodontal diseases represent a complex dysbiosis-driven inflammatory condition, where the transition from health to gingivitis and periodontitis is accompanied by distinct microbial shifts. Emerging evidence highlights the significance of less-studied genera such as Neisseria , Dialister , and Filifactor in shaping periodontal outcomes. This study aimed to investigate the salivary distribution of Neisseria , Dialister , and Filifactor species across periodontal health, gingivitis, periodontitis, and gingival recession using next-generation sequencing (NGS). Methods Whole saliva samples were collected from 40 participants (10 per group) classified according to the American Academy of Periodontology criteria. Microbial DNA was extracted and subjected to 16S rRNA sequencing (V3–V4 region, Illumina MiSeq). Species-level classification was performed using the Human Oral Microbiome Database. Frequency distributions were compared across groups using Fisher's exact test, with significance set at p < 0.05. Results Distinct patterns were observed. Several commensal Neisseria species, including N. subflava (p = 0.001), N. elongata (p = 0.015), and N. polysaccharea (p = 0.001), showed significantly reduced prevalence in periodontitis compared with health and gingivitis. In contrast, Dialister pneumosintes exhibited a sharp increase in all diseased groups (p = 0.002). Filifactor alocis was markedly enriched in gingivitis, recession, and periodontitis (p = 0.011), suggesting its strong association with disease states. Conclusion The findings demonstrate a characteristic microbial shift in saliva: health-associated Neisseria species decline with disease progression, while anaerobic taxa such as D. pneumosintes and F. alocis expand. These results align with the polymicrobial synergy and dysbiosis model and underscore the potential of these species as salivary biomarkers for early detection and monitoring of periodontal disease.