Life stage shifts in salivary microbiota determinants: a cross-sectional study in twins

Both host genetics and environmental exposures shape the salivary microbiota; however, the relative contributions of these factors from early life to adulthood remain unclear. To address this, we profiled the salivary microbiota of 3387 twin pairs: 939 infant pairs (9-12 months) and 2,448 adult pairs (23-52 years) using full-length 16S rRNA gene sequencing. In infants, the shared environment dominated: richness, diversity, and overall community composition were driven primarily by shared environmental effects, accounting for >50% of variance across key metrics. Host genetics had no detectable effect on community composition or species presence and only modest effects on species abundances and predicted functions. By contrast, in adults, the pattern reversed: shared environment contributed little, while host genetics exerted a broader, stronger influence, explaining 19-45% of variance in core diversity metrics and significantly affecting both species' presence, abundance, and predicted functions. Several clinically relevant oral taxa showed substantial heritability in adults, with roughly one-third of their variance attributable to genetic factors. These results reveal a life-stage shift in determinants of the salivary microbiota and their predicted functions: infancy is largely shaped by environmental exposures, whereas adult communities increasingly reflect host genetic architecture. These findings suggest that interventions to promote healthy oral microbiota may need to be tailored to life-stage.