Abstract
Dental caries in children is a disease of oral microbial dysbiosis, yet interventional strategies that target the ecological balance of the oral microbiome remain underexplored. The dietary flavonoids hesperetin (Hesp) and naringenin (Nar) have demonstrated antimicrobial and biofilm-modulating properties in single-species models, but their effects on the complex, polymicrobial oral community in the context of childhood caries have not been characterized at the metagenomic level. Using an in vitro model with saliva from 11 caries-affected children, we employed metagenomic sequencing. This study is exploratory and hypothesis-generating in nature. Comprehensive bioinformatics analyses were performed, including de novo assembly, non-redundant gene catalog construction, and multi-database functional annotation. Taxonomic composition, alpha diversity, and beta diversity were assessed to evaluate community-level restructuring. Both flavonoids were associated with substantial remodeling in this pilot cohort of the oral metagenome. On average, 39% of annotated genes exhibited abundance alterations exceeding 70% relative to controls, with Hesp demonstrating a consistently broader regulatory effect than Nar across most sample groups. Functional annotation revealed treatment-associated shifts in carbohydrate-active enzyme profiles. Beta diversity analyses revealed clear compositional separation between flavonoid-treated samples and controls at both taxonomic and functional levels. Notably, Hesp and Nar were associated with distinct ecological directions in ordination space, suggesting that subtle structural differences between these flavonoids may translate into divergent metagenomic outcomes. These hypothesis-generating findings provide a foundational genomic resource for future studies exploring flavonoid-based ecological modulation of the caries-associated oral microbiome in children.