The oral cavity contains one of the most intricate bacterial ecosystems in humans. Yet, the processes through which newborns first obtain these microorganisms are still not well understood. This work tracked shifts in oral microbial communities among healthy infants and assessed how the maternal oral flora contributes to microbial acquisition in early life. We proposed that oral microbial diversity in infants would rise as they age. A total of 116 whole-saliva samples were obtained from 32 healthy infant–mother pairs at postpartum, 9 months, and 15 months. Bacterial DNA was isolated and analyzed using Human Oral Microbe Identification through Next Generation Sequencing (HOMINGS). Microbial diversity within each dyad (alpha diversity) was quantified with the Shannon index. Differences between infant and maternal microbiomes (beta diversity) were evaluated using weighted Bray–Curtis distances in QIIME 1.9.1. Core microbiome profiles were examined via MicrobiomeAnalyst, and linear discriminant analysis with effect size was employed to detect taxa distinguishing the two groups. Sequencing generated 6,870,571 16S rRNA reads from matched saliva samples. Infant and maternal microbial communities differed significantly (p < 0.001). Infant salivary microbial diversity increased over time, whereas mothers displayed a largely consistent core microbiome throughout. Neither breastfeeding nor infant sex influenced diversity patterns. Infants exhibited higher proportions of Firmicutes and lower levels of Actinobacteria, Bacteroidetes, Fusobacteria, and Proteobacteria compared with mothers. SparCC analysis revealed ongoing shifts in infants’ microbial interaction networks (p < 0.05). Findings indicate that infants begin life with an oral microbiota distinct from that of adults. During the first year, microbial composition and diversity undergo substantial change, and by the period preceding age two, infant oral communities may resemble those of their mothers.
