Background: This study integrated 16S ribosomal ribonucleic acid sequencing and untargeted metabolomics to investigate the mechanisms by which oral microorganisms and Lacticaseibacillus rhamnosus (LGG) influence dental caries development in rats.

Methods: A rat caries model was established to examine the effects of different interventions, including healthy dental plaque suspension (NC_R), caries-associated plaque suspension (M_R), and the probiotic LGG, on oral microbial composition, metabolic profiles, and caries severity.

Results: The caries model group exhibited ecological dysbiosis, characterized by a significant increase in the abundance of cariogenic bacteria such as Streptococcus mutans and a decrease in health-associated genera like Veillonella. Metabolomic analysis identified 105 significantly differential metabolites between the Model and Normal Control (NC) groups. Kyoto Encyclopedia of Genes and Genomes pathway enrichment classification revealed that carbohydrate metabolism pathways were significantly enriched in the Model group, whereas lipid metabolism and cofactor metabolism pathways exhibited higher activity in the NC group. Notably, the sphingolipid metabolism pathway showed the highest significance in differential metabolite enrichment. Probiotic intervention, particularly the combined application of LGG and NC_R, substantially reversed the levels of abnormal metabolites, improved enamel surface area, volume, and mineral density (p < 0.05), and reduced caries scores (p < 0.05).

Conclusion: By integrating microbiome and metabolomics analyses, this study elucidates the interplay between microbial dysbiosis and metabolic dysregulation in the pathogenesis of dental caries. It further reveals a novel anti-caries mechanism of probiotics through their modulation of oral microecological balance and host metabolic networks, particularly via key pathways such as sphingolipid metabolism. This provides experimental evidence for the development of precise caries prevention and control strategies based on microecological regulation.