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Introduction: When infants cannot consume breast milk, the most commonly available alternative milk formula is cow milk-based. Due to a rise in the prevalence of cow milk protein allergy (CMPA) among children, this study aimed to assess the biofilm formation and acidogenicity of cow milk-based formulas as well as milk formulas suggested for children with CMPA. Methods: Cow milk-based formulas with 0%, 10%, or 18% sucrose added, partially hydrolyzed formula (pHF), extensively hydrolyzed formula (eHF), amino acid-based formula (AAF), and soy-based formulas with 0%, or 11% sucrose added were evaluated. Streptococcus mutans was used as a representative microorganism associated with caries. The acidogenicity after 24-h incubation was assessed by the pH of the formed biofilm and lactic acid formation. Biofilm formation was quantified using crystal violet staining. Additionally, the biofilm characteristics were determined using confocal laser scanning microscopy (CLSM). Comparisons were made among formulas without added sucrose to observe protein-based differences. Furthermore, formulas with different sucrose percentages were compared to explore the impact of sucrose content. Results: When comparing the formulas without added sucrose, the biofilm formation in the cow milk-based formula and pHF were significantly greater than the soy-based formula, eHF, and AAF. In the presence of S. mutans, all formulas reduced the biofilm pH below the critical enamel pH. The cow milk-based formula and AAF showed a significantly lower biofilm pH than the pHF, soy-based, and eHF groups, while the lactic acid production was markedly higher in the cow milk-based formula, pHF and AAF, compared with the eHF and soy-based formula. Adding sucrose into the cow milk-based and soy-based formulas substantially increased biofilm mass. The biofilm pH of the cow milk-based formulas, with or without sucrose, was significantly lower than that of the soy-based formulas. The CLSM indicated distinct biofilm characteristics among the different protein-based formulas, with sucrose supplementation promoting S. mutans aggregation in cow milk-based formula biofilm and increased density and intact biofilm in the soy-based formula. Conclusion: All assessed milk formulas had caries-inducing factors, including those without supplemental sucrose. Among them, the eHF demonstrated the least caries-inducing factors, attributed to its minimal biofilm formation and the highest biofilm pH.

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