Objective To analyze the oral and gut microbial composition in preschool children during the deciduous and mixed dentition stages, and to investigate the characteristics of microbiota across different dentition stages.

Methods  Using 16S rRNA gene-based third-generation sequencing, this study analyzed saliva and fecal samples collected from 10 children with deciduous dentition and 10 with mixed dentition. The composition and differences in oral and gut microbiota between the two groups were compared.

Results The differences in microbial richness (Chao1 index) and evenness (Shannon index) between the oral cavity and intestine were statistically significant (P = 0.001). Firmicutes, Proteobacteria, and Bacteroidetes were the three dominant phyla at both sites. At the genus level, Neisseria and Streptococcus were abundant in the oral cavity, while Bacteroides and Faecalibacterium predominated in the gut. o_Lactobacillus (LDA = 5.04, P < 0.001) was identified as a marker genus in the oral cavity during the deciduous dentition period, while g_Neisseria (LDA = 5.15, P < 0.001) served as an oral marker genus in children with mixed dentition. In the gut, marker genera during the deciduous dentition period included o_Bacteroides (LDA = 5.17, P < 0.001) and f_Lachnospiraceae (LDA = 5.16, P < 0.001), whereas f_Ruminococcus (LDA = 5.09, P < 0.001) and g_Faecalibacterium (LDA = 5.03, P < 0.001) were marker genera during the mixed dentition period. Upregulation of pathways including lactose degradation and nitrate reduction was observed in the oral microbiota, in contrast to the gut microbiota, where enhanced activity of the methanogenesis from acetate pathway was noted.

Conclusion The composition of oral and gut microbiota varies among children at different dentition stages. As dentition changes, the structural diversity and metabolic functions of both oral and gut microbiota also change.