Microbiome composition and metabolic pathways in shallow and deep periodontal pockets

In periodontal diseases, a dysbiotic subgingival microbiome interacts complexly with the host immune response and is strongly considered a risk factor for various systemic conditions. The high prevalence of both periodontal and systemic diseases in older adults highlights the importance of characterizing the subgingival microbiome in this age group. This study specifically characterizes the composition of the subgingival microbiome and investigates the interactions between microbial niches in shallow and deep periodontal pockets in individuals in their early 70s. We collected 1928 samples from 1287 participants, all born between 1950 and 1951. Participants had either shallow (≤ 4 mm) periodontal pockets or both shallow and deep (≥ 5 mm) periodontal pockets. Distinct microbial patterns were observed in shallow and deep periodontal pockets within the same oral cavity. Deep pockets exhibited a significantly higher abundance of species from genera such as Prevotella, Centipeda, Treponema, and Fusobacterium, while shallow pockets were enriched with species from Actinomyces, Pauljensenia, Streptococcus, and Gemella. The top significant species associated with deep pockets included Fretibacterium fastidiosum, Tannerella forsythia, and Treponema denticola, whereas shallow pockets were predominantly associated with Actinomyces species and Rothia dentocariosa. Additionally, shallow pockets in individuals with both pocket types showed a positive association with Tannerella forsythia, Porphyromonas gingivalis, and Fusobacterium nucleatum compared to shallow pockets in individuals with only shallow pockets. Metabolic pathways showed significant variation with pocket depth, with pathways such as lipopolysaccharide metabolism, lipid metabolism, and polyamine biosynthesis being positively associated with deep pockets. Overall, this study provides comprehensive microbiome analyses of periodontal pockets in aging adults, contributing to a better understanding of periodontal health and its potential impact on reducing systemic health risks in aging populations. © The Author(s) 2025.