Integrated salivary microbiome and metabolome profiling reveals ecological and functional alterations in severe early childhood caries.

BACKGROUND: Early childhood caries (ECC), particularly severe early childhood caries (S-ECC), remains a prevalent chronic disease, significantly affecting children's health and quality of life. Despite extensive research, the detailed ecological and metabolic shifts underlying S-ECC pathogenesis are still poorly characterized. Integrating microbial and metabolic profiling of saliva may provide crucial insights and identify novel biomarkers and therapeutic targets. METHODS: We performed high-throughput 16S rRNA gene sequencing and untargeted metabolomics to comprehensively profile the salivary microbiome and metabolome in children with S-ECC (n = 30) compared to caries-free (CF) controls (n = 30). Differential microbial taxa and metabolites were identified, and their functional implications were explored through KEGG pathway enrichment analysis. Furthermore, integrated correlation analysis was conducted to uncover interactions between key microbial taxa and metabolites. RESULTS: Microbial community analysis revealed significant ecological alterations in the saliva of children with S-ECC, characterized by enrichment of potentially cariogenic taxa, including Rothia, Lautropia, Lactobacillus, Achromobacter, as well as Streptococcus mutans, Prevotella histicola, and Lachnoanaerobaculum saburreum. Conversely, health-associated genera such as Bergeyella and Acinetobacter were more abundant in CF children. Metabolomics identified a total of 4,325 salivary metabolites, among which 1,226 differed significantly between groups. Notably, metabolites involved in amino acid metabolism pathways-phenylalanine, tyrosine, D-amino acids, aminobenzoate, arginine, and proline-were upregulated in S-ECC saliva. Integrated analysis further revealed strong positive correlations between key cariogenic bacteria (S. mutans, P. histicola, L. saburreum) and multiple metabolites, including succinic acid, 2-piperidone, D-3-phenyllactic acid, 5-aminovaleric acid, L-malic acid, 2-hydroxypalmitic acid, LPE (16:0), vitamin K1 2,3-epoxide, leucylproline, and L-valine. CONCLUSIONS: Our findings demonstrate distinct ecological and functional signatures in the salivary microbiome and metabolome associated with S-ECC. The identified microbial and metabolic alterations, particularly in amino acid metabolism, provide novel insights into the pathogenesis of S-ECC and highlight potential biomarkers for early detection and targeted intervention. However, the cross-sectional design and single time-point saliva collection limit the ability to assess longitudinal dynamics. Future longitudinal studies are warranted to track microbial and metabolomic changes during disease progression and intervention.