Periodontitis Severity and Subgingival Microbiome Variation in Postmenopausal Women: A Stratified Case–Control Study

Background: This study aimed to determine whether osteoporosis is associated with differences in the subgingival microbiome of postmenopausal women, stratified by periodontitis stage. Methods: In this observational, stratified case–control study, 166 postmenopausal women were assigned to six strata defined by bone status (osteoporosis vs. normal BMD) and periodontal category (no periodontitis, Stage I–II, Stage III–IV). Standardized pooled subgingival samples were profiled by 16S rRNA gene sequencing. Community structure was evaluated using Bray–Curtis dissimilarity and tested with PERMANOVA (9999 permutations) and prespecified contrasts comparing osteoporosis versus normal BMD within each periodontal category (Holm adjustment). Alpha diversity (Shannon) was assessed using two-way ANOVA. Results: Periodontal category was strongly associated with community structure (PERMANOVA R² = 0.514, pseudo-F = 86.681, p < 0.0001), whereas bone status (R² = 0.004, p = 0.178) and the bone status × periodontal category interaction (R² = 0.007, p = 0.294) were not. None of the three prespecified within-category contrasts reached significance after Holm adjustment. Shannon diversity differed by periodontal category (p = 1.93 × 10⁻²⁴) but not by bone status (p = 0.200), with similar distributions between osteoporosis and normal BMD within each periodontal category. Conclusions: In postmenopausal women, periodontitis severity dominates variation in the subgingival microbiome, and osteoporosis does not confer an additional community-level or taxonomic signature when periodontal status is held constant. Longitudinal and multi-omic studies incorporating host-response biomarkers and therapy exposures are warranted to clarify whether osteoporosis influences periodontal susceptibility and progression primarily through host-mediated mechanisms.