Caries Microbiome: Time to Move from Blame to Balance

Advances in next-generation sequencing and multi-omics approaches reinforced the concept of functional diversity within biofilm communities, revealing roles beyond bacterial taxonomy and highlighting metabolic and ecological mechanisms operating at the individual level rather than within isolated caries lesions. Moving toward new clinical solutions will require broader perspectives; to this end, we propose key directions to advance the translational potential of caries microbiome research. We present a perspective that connects ecological theory, molecular evidence, and clinical implications through three central topics: (1) microbial composition, (2) microbial function, and (3) individual-level characteristics.

From a compositional perspective, caries microbiome research should move beyond the search for bacterial culprits and instead consider the broader microbial ecosystem, including low-abundance and nonbacterial members (such as archaea). Within this framework, microbial taxa and functions should not be viewed as inherently "good" or "bad," but rather as context-dependent components of a dynamic ecosystem shaped by sustained environmental pressures. Functionally, the recurrent enrichment of pathways related to carbohydrate metabolism, sugar transport, and acid production likely reflects microbial adaptation to persistent sugar exposure rather than intrinsic virulence traits. This perspective suggests that progress in caries research depends on moving beyond disease-centered models toward understanding how microbial stability preserves oral health. At the individual level, individuals with previous caries experience may retain disease-associated microbial or functional signatures during remission, a phenomenon referred to here as a microbiological dysbiosis scar. This ecological memory may help explain why past caries experience remains one of the strongest predictors of future lesions and highlights the importance of incorporating individual history into the design and interpretation of caries microbiome studies. Integrating detailed clinical metadata with advanced bioinformatic approaches, including artificial intelligence, will be essential for establishing meaningful biological links.

Progress in caries microbiome research depends on refining study design across microbial composition, functional, and individual levels. Strengthening the resilience of the oral microbiome rather than eliminating specific pathogens or the microbiome should be the central goal of caries microbiology. Moving from blame to balance is not merely semantic; it represents a fundamental shift in how we study, prevent, and manage dental caries.