Harmonized multi-cohort analysis of oral microbiome development during early lifetime

Early-life assembly of the oral microbiome may influence oral and systemic health, yet developmental patterns are difficult to compare across studies because of differences in sampling and analytical workflows. We conducted a harmonized cross-cohort re-analysis of longitudinal pediatric 16S rRNA datasets spanning birth to early childhood.

Five publicly available longitudinal cohorts from birth to seven years were curated and independently reprocessed using QIIME 2 and R. Taxonomy was assigned using the Human Oral Microbiome Database (HOMD). Alpha and beta diversity, taxonomic composition, and species-level temporal dynamics were evaluated. Age was harmonized to months and summarized into three developmental intervals: birth-12 months, 12-36 months, and >36 months. Temporal clustering used fuzzy c-means clustering (TCseq).

Alpha diversity increased rapidly during the first year, plateaued between one and three years, and increased gradually thereafter. Beta diversity showed the greatest compositional shifts during infancy, followed by relative stabilization. Taxonomic profiling revealed reproducible succession from Streptococcus and Staphylococcus to Haemophilus, Neisseria, and Veillonella, followed by Prevotella and Campylobacter after three years. Temporal clustering identified three developmental groups corresponding to early, transitional, and later-expanding taxa.

This harmonized analysis of five longitudinal cohorts demonstrates a reproducible three-phase trajectory of oral microbiome maturation during early childhood. The most pronounced microbial restructuring occurred during infancy, followed by community stabilization and gradual maturation. These findings provide a framework for understanding age-associated microbial succession and identifying developmental windows for preventive interventions in pediatric oral health.