Key Species and Functional Traits Across Stages of Early Childhood Caries

Early childhood caries (ECC) involves complex shifts in oral microbial communities, yet the microbial and functional distinctions across severity stages remain underexplored, especially regarding the role and mechanisms of key species within these communities. Saliva samples were collected from 60 ECC patients with varying severities (classified by dmfs score) and 20 healthy controls. DNA extracted from the samples underwent shotgun analysis to compare the changes in microbial characteristics such as diversity, functional potential and gene co-expression patterns across different groups. Zi-Pi analysis helped identify key species, while the least absolute shrinkage and selection operator (LASSO) logistic regression models were constructed to distinguish ECC of different severity. Alpha diversity showed significant differences only between the healthy group and the severe ECC group at the genus level (p < 0.05), while beta diversity differed significantly between the mild and severe ECC groups (p < 0.05), indicating a shift in community composition during disease progression. Key species, such as Streptococcus parasanguinis and Pandoraea pneumonica showed significant changes in abundance across groups (p < 0.05). Weighted gene co-expression network analysis (WGCNA) of key species identified two major gene modules, each associated with a distinct ECC severity level. Functional annotation of the corresponding KEGG Orthology (KO) genes revealed upregulated activities in pathways such as carbohydrate metabolism, quorum sensing, and amino sugar biosynthesis with increasing disease severity, indicating enhanced acidogenic capacity and microbial structural adaptation. Moreover, diagnostic models constructed based on species and genes demonstrated high accuracy in differentiating ECC severity stages, underscoring their potential utility for early risk stratification. In conclusion, these findings offer novel insights into the structures and functions of ECC-associated microbiota and highlight key microbial targets for early ECC detection and personalized interventions.