This study was conducted as a narrative review aimed at summarizing current evidence regarding the role of oral microbiota modulation in the prevention of dental caries. The review focused on ecological mechanisms of cariogenesis, microbiota-based preventive strategies, and emerging diagnostic technologies relevant to oral microbial dysbiosis.

A comprehensive literature search was performed using the electronic databases PubMed/MEDLINE, Scopus, Web of Science, and Google Scholar. Articles published in English between January 2000 and March 2026 were considered. The search strategy combined Medical Subject Headings (MeSH) terms and free-text keywords, including: “dental caries,” “oral microbiota,” “oral microbiome,” “cariogenic bacteria,” “biofilm,” “Streptococcus mutans,” “acidogenic bacteria,” “aciduric bacteria,” “probiotics,” “prebiotics,” “synbiotics,” “salivary microbiome,” “metabolomics,” “quorum sensing,” and “artificial intelligence.” Boolean operators (“AND” and “OR”) were used to optimize the search. Reference lists of relevant articles were additionally screened to identify supplementary studies.

Articles were included if they investigated mechanisms associated with cariogenic microbial dysbiosis, examined microbiota-targeted preventive or therapeutic approaches for dental caries, evaluated diagnostic or predictive tools related to the oral microbiome, or provided clinically and biologically relevant insights into oral microbial ecology and caries prevention. Original research articles, clinical studies, systematic reviews, meta-analyses, and significant experimental studies were considered eligible for inclusion. Non-English publications, conference abstracts without available full texts, duplicate records, and studies not directly related to oral microbiota or caries prevention were excluded from the review.

Relevant information from eligible studies was extracted and organized according to thematic categories, including cariogenic microbiota, ecological shifts, biofilm formation, microbiota-based preventive interventions, salivary diagnostics, metabolomics, and artificial intelligence-assisted predictive models. The findings were narratively synthesized to provide an integrated overview of current evidence and emerging perspectives in microbiota-centered caries prevention.

Dental caries is a polymicrobial ecological disease characterized by dysbiosis within the oral biofilm. Among the best-characterized cariogenic bacteria, Streptococcus mutans plays a major role through its acidogenicity, aciduricity, and production of exopolysaccharides (EPSs) [12,13]. However, cariogenicity arises from coordinated interactions among multiple microbial species that collectively promote biofilm maturation and acidification [14]. These bacteria possess mechanisms that not only enable them to thrive in acidic environments created by the fermentation of dietary sugars but also facilitate their adhesion to dental surfaces, contributing to biofilm formation [12]. For instance, Streptococcus mutans synthesizes glucan-type EPSs, which enhance the biofilm’s stability and cohesion, creating a habitat where other cariogenic species can proliferate [15]. The biochemical nature of these biofilms, primarily reflected in their EPS composition, significantly influences their cariogenic potential. The major cariogenic bacterial species and their pathogenic characteristics are summarized in Table 1. Studies have illustrated that biofilms rich in insoluble glucans demonstrate a higher propensity to lower the pH in the dental environment, which is critical for enamel demineralization [16].

Moreover, the ecological dynamics of cariogenic microbiota highlight its polymicrobial nature, where species such as Lactobacillus spp. and Actinomyces also contribute to caries progression by enhancing acidogenic potential [20]. The interplay among these species, including Rothia sp., indicates a complex biofilm community that exhibits traits associated with cariogenicity, including acid tolerance and EPS production [7,12]. Such interactions between various bacteria underscore the necessity for a multifaceted approach in understanding cariogenic mechanisms and developing therapeutic strategies. For example, treatments targeting the biofilm’s microenvironment to regulate pH levels and inhibit EPS formation have emerged as promising areas for future research [10,24]. Through these multifarious interactions and metabolic events, cariogenic microbiota poses significant challenges to oral health, necessitating continued exploration for effective preventative and therapeutic interventions.

Cariogenic microbiota, particularly in the context of dental caries, exhibit adaptations that enhance their acidogenicity and aciduricity [3,25]. Acidogenic bacteria, most notably mutans streptococci such as Streptococcus mutans, are capable of metabolizing sugars to produce organic acids that lower the pH of the oral environment, promoting the demineralization of dental enamel [26,27]. This process is critical in initiating carious lesions, as frequent access to sugars can drive the ecological shift towards a biofilm dominated by acidogenic and aciduric species [22,28]. Aciduric species, which can survive and thrive in acidic conditions, reflect an adaptive response to the carious environment, indicating a balance alteration within the biofilm community [29]. For instance, non-mutans streptococci and lactobacilli also contribute to acid production and have been shown to increase in proportion following episodes of sugar consumption [14,30]. Research has demonstrated that bacterial adaptation to low pH involves complex physiological changes. For instance, Streptococcus oralis exhibits adaptive responses under acidic conditions that support survival and metabolic activity within cariogenic biofilms [31,32]. Furthermore, studies indicate that acid-adapted bacterial strains exhibit higher rates of growth and acid production when re-exposed to acidic environments, reinforcing the idea that the dental biofilm can become progressively more aciduric in response to dietary habits and local pH fluctuations [33]. The dynamics of these microbial communities illustrate that mixed species interactions can optimize their collective acidogenic potential, thereby maintaining a detrimental environment conducive to caries development [19]. Over time, the continuous acidification from these bacteria results in selection pressure favoring more aciduric organisms, ultimately exacerbating the severity of carious lesions [34]. The interplay between acidogenicity and aciduricity within cariogenic microbiota significantly influences the caries process, characterized by a gradual shift towards more acid-tolerant species that enhance tooth demineralization. As these bacteria adapt to the acidic milieu, they not only survive but thrive, furthering their cariogenic potential and perpetuating the cycle of dental decay [21].

The progression of dental caries is closely linked to the architecture of biofilms formed by cariogenic microbes, particularly Streptococcus mutans [15]. EPSs are produced in high quantities during the metabolism of fermentable carbohydrates, particularly sucrose [35]. The resulting biofilm architecture allows for the formation of dense, structured communities that enhance bacterial adhesion to tooth surfaces and facilitate the retention of nutrients, further promoting an environment conducive to cariogenic activity [36]. The mechanisms driving caries progression through EPS production are multifaceted. Enhanced EPS production not only provides structural integrity to the biofilm but also creates localized acidic microenvironments due to the accumulation of metabolic byproducts from acidogenic bacteria [37,38]. The presence of sucrose leads to the synthesis of insoluble glucans, which serve as a scaffold for the biofilm, allowing Streptococcus mutans and other acidogenic species to flourish [39]. This architectural predominance of Streptococcus mutans in biofilms enables the establishment of microcolonies that can thrive in acidic conditions, underscoring their aciduricity, a crucial characteristic for survival in the cariogenic milieu [18]. Moreover, the structural dynamics of these biofilms affect diffusion properties and the availability of essential nutrients, which can inhibit the growth of beneficial bacteria, further tipping the ecological balance toward pathogenic species [40]. As carbohydrate exposure continues, the resulting acidic conditions, partly facilitated by the biofilm architecture, encourage the persistence of aciduric organisms, contributing to the overall virulence of the biofilm and accelerating the demineralization of dental hard tissues [41].

Dental caries develops more rapidly when alkali-producing bacterial species in the oral microbiome are suppressed [42]. Typically, the advancement of caries is associated with an increase in acidogenic bacteria, which thrive in low-pH environments and contribute to the demineralization of tooth structures [29]. Recent studies highlight that a balanced oral microbiome, where alkali-producing species such as Streptococcus sanguinis and other commensal bacteria are prevalent, is crucial for maintaining pH homeostasis and inhibiting caries onset [42,43]. For instance, alkali production from salivary substrates, particularly arginine and urea, serves a protective role by neutralizing the acids generated by cariogenic bacteria through carbohydrate metabolism [42]. This ability to produce ammonia and other basic metabolites directly opposes the acidic milieu fostered by pathogens such as Streptococcus mutans [29,44]. When the population of alkali-producing bacteria declines, the oral environment shifts towards one dominated by aciduric organisms, which exacerbates the acidic conditions and triggers further mineral loss. The data collected by Du et al. illustrate that high sucrose concentrations can preferentially reduce alkali-generating bacteria, thereby disrupting the delicate balance between acid and base producers, thus accelerating caries development [45]. Furthermore, alkali production from biofilm communities has been shown to enhance bioenergetic responses and offer protection against acid-induced damage, which is critical for maintaining dental health [23]. Collectively, these findings suggest that enhancing the presence and metabolic activity of alkali-producing bacterial species could represent a viable strategy for caries management and prevention [46].

The progression of dental caries is critically influenced by various mechanisms, among which quorum sensing (QS) and biofilm resilience are paramount [47]. QS facilitates communication among Streptococcus mutans populations, allowing them to coordinate virulence factor production and biofilm formation in response to the density of their bacterial community [48]. Specifically, the Competing Stimulating Peptide-mediated QS system in Streptococcus mutans regulates multiple virulence-associated traits, such as the production of bacteriocins intended to eliminate competing species and enhance the pathogen’s dominance in dental biofilms [49]. This communal behavior leads to the establishment of robust biofilms that are resistant to external stressors, including antimicrobial agents, as conventional treatments often fail to disrupt these resilient structures effectively [50]. The resilient nature of dental biofilms is attributed to the structural complexity of these microbial communities, which provide a protective environment for Streptococcus mutans, allowing it to thrive in acidic conditions that occur from carbohydrate fermentation [51]. Moreover, the interaction of Streptococcus mutans with other species, including commensal bacteria, contributes to biofilm stability and alters its susceptibility to dental treatments [52]. Strategies aimed at disrupting QS signals, such as quorum quenching with plant-derived compounds, have been proposed as novel therapeutic avenues to counteract Streptococcus mutans biofilm formation and mitigate the persistent threat of dental caries [53].

The development of dental caries is largely driven by how biofilm microbes interact and their acid tolerance, both of which affect oral ecological balance [29]. The “Ecological Plaque Hypothesis” posits that shifts in microbial composition, driven by dietary changes such as increased consumption of fermentable carbohydrates, lead to the proliferation of acidogenic bacteria [54]. Within this framework, the intake of sugars like sucrose not only promotes the growth of cariogenic pathogens, such as Streptococcus mutans, but also disrupts the microecological equilibrium that typically supports non-pathogenic species, thereby enhancing dysbiosis [55]. This dysbiosis is characterized by an abundance of acidogenic bacteria, which thrive in low-pH conditions, exacerbating the acidic microenvironment necessary for dental demineralization [56]. Importantly, acid tolerance mechanisms among cariogenic bacteria reinforce their survival and pathogenic potential. For instance, the persistence of Streptococcus mutans in acidic environments allows for sustained biofilm formation and acid production, which, in turn, promotes further selection of aciduric bacteria [57]. As biofilms age, the biofilm composition often shifts towards aciduric species due to a selective advantage conferred by their acid tolerance, thus perpetuating an environment conducive to carious activity [58]. This ecological advantage is essential; the glucan-rich matrix produced by Streptococcus mutans not only aids in bacterial cohesion but also creates localized acidic microenvironments that are detrimental to tooth enamel [17]. Thus, understanding the synergistic interactions between acidogenic bacteria and the mechanisms of acid tolerance is crucial for developing effective strategies aimed at mitigating or reversing caries progression. The interconnected roles of EPS production, acidogenicity, QS, and biofilm resilience in caries progression are summarized in Figure 2. Figure 2a illustrates the key virulence-associated mechanisms, including EPS production, acidogenicity, QS, and biofilm resilience, whereas Figure 2b depicts the synergistic interactions within cariogenic biofilms leading to enamel destruction and progressive dental caries.

Microbiota-based prevention strategies in dental health emphasize the importance of maintaining a balanced oral microbiota through effective oral hygiene practices, particularly tooth brushing [9,83]. The oral microbiota plays a crucial role in oral and systemic health, with its dysbiosis contributing to various oral diseases such as dental caries and periodontal disease [84]. Regular and effective tooth brushing disrupts pathogenic biofilm formation on teeth, which is essential for preventing these conditions [85]. Research highlights that inadequate oral hygiene can alter the oral microbiota, resulting in increased caries risk due to the proliferation of cariogenic bacteria [86]. The mechanical removal of plaque through brushing is considered the “gold standard” for preventing both caries and periodontal diseases, as it effectively manages biofilm accumulation and maintains a healthier oral environment [87]. Furthermore, interventions addressing oral hygiene education, particularly in children, have proven effective in favorably altering microbiota profiles, thereby decreasing the prevalence of dental caries. This multifaceted approach is bolstered by evidence suggesting that enhancing the presence of beneficial bacteria and managing diet through education can further improve oral health outcomes [88]. Therefore, promoting proper oral hygiene practices, especially tooth brushing, is integral in managing the oral microbiota and preventing dental diseases.

Although microbiota-based preventive strategies have shown considerable promise, the strength of supporting evidence varies substantially among different interventions. Dietary modification, reduction in fermentable carbohydrate intake, fluoride therapy, and xylitol are supported by relatively strong clinical evidence, including randomized controlled trials and systematic reviews, and are currently incorporated into preventive dental practice. In contrast, probiotics, prebiotics, and synbiotics have demonstrated encouraging biological effects in vitro and in animal models, with several clinical studies reporting reductions in Streptococcus mutans levels or modest improvements in caries-related outcomes. However, the overall clinical evidence remains heterogeneous because of differences in probiotic strains, formulations, treatment durations, study populations, and outcome measures. Consequently, current systematic reviews generally conclude that these microbiota-targeted interventions are promising adjunctive approaches but that high-quality, long-term randomized clinical trials are still needed before routine clinical implementation can be broadly recommended.

Similarly, functional dietary agents such as arginine and plant-derived polyphenols exhibit favorable ecological effects by promoting alkali production, suppressing virulence factors, or modulating biofilm composition. Nevertheless, much of the supporting evidence remains preclinical, and additional well-designed clinical studies are required to establish their long-term efficacy and optimal clinical application. Overall, contemporary evidence supports a shift from broad-spectrum antimicrobial approaches toward ecological biofilm modulation. Rather than indiscriminately eliminating oral microorganisms, microbiota-based interventions aim to selectively suppress cariogenic activities while preserving beneficial microbial communities and restoring oral ecological homeostasis. Consequently, these strategies should be regarded as complementary approaches that enhance, rather than replace, established preventive measures [96].

The salivary microbiome has emerged as an important diagnostic and predictive tool in assessing dental caries, particularly due to its noninvasive nature and the rich information it provides about oral health status [114]. Recent studies highlight distinct microbial profiles in saliva associated with dental caries, which could serve as valuable biomarkers for diagnosing and predicting caries progression [29]. For instance, Vieira et al. demonstrated that children with active dental caries exhibited a unique salivary microbiome composition when compared to their caries-free counterparts, reinforcing the potential of salivary profiles in diagnosing caries status [101]. Similarly, Xu et al. reported longitudinal shifts in the oral microbiome of young children transitioning from caries-free to caries-affected, suggesting that changes in microbiota could precede clinical manifestations of dental caries [103]. Furthermore, the interplay between salivary metabolites and microbial diversity has shown promise, with Kim et al. identifying specific metabolic changes linked to caries that may lead to the discovery of novel salivary biomarkers for early detection [99]. The presence of certain bacterial taxa, such as Streptococcus mutans and Prevotella, has been shown to correlate with caries status, potentially enabling targeted interventions based on individual salivary microbiome profiles [97,100]. The integration of advanced analytical techniques, like mass spectrometry, enhances the capacity to explore the salivary proteome, offering insights into protein biomarkers that could aid in personalized monitoring of dental caries [98,102]. Collectively, these developments indicate that salivary microbiome profiling may revolutionize the diagnostic landscape for dental caries, facilitating earlier infection detection and more tailored treatment approaches. Despite its considerable diagnostic potential, routine clinical application of salivary microbiome profiling remains limited by variability in sample collection, sequencing methodologies, and bioinformatic analysis. Further standardization and multicenter clinical validation are required before it can be routinely incorporated into personalized caries-risk assessment.

Recent advancements in metabolomic analyses, particularly through nuclear magnetic resonance and mass spectrometry, have facilitated the identification of potential biomarkers in saliva that correlate with caries status, showcasing the potential for novel diagnostic avenues in dental health management [115,116]. Studies indicate that salivary metabolite profiles, influenced by microbial dysbiosis, can reflect the state of oral health and predict the risk of developing dental caries [107]. For example, specific metabolites have been associated with shifts in the local microbiome, revealing a complex interplay between salivary biochemistry and microbial presence [99]. Moreover, pH levels serve as critical indicators of dental caries activity, with lower salivary pH consistently linked to higher caries prevalence. Research shows that individuals with active dental caries often exhibit notably acidic pH ranges, between 5.0 and 5.8, which are detrimental to enamel health and promote microbial proliferation [23,105]. The role of salivary flow rate and buffering capacity in maintaining optimal pH levels also emerges in the literature as a vital factor in caries susceptibility, providing insight into the mechanistic aspects of salivary influence on oral health [106]. Thus, integrating pH monitoring with metabolic profiling offers a comprehensive approach for early detection and intervention strategies in managing dental caries, underscoring the need for further exploration within this rapidly evolving research domain [104]. However, routine clinical implementation remains limited by high cost, technical complexity, and the lack of standardized analytical protocols. Large-scale clinical validation will be essential before metabolomic biomarkers can be widely adopted in dental practice.

The application of AI in the diagnosis and prediction of dental caries is rapidly gaining momentum, with numerous studies highlighting its potential impact on oral health management [113,117]. AI techniques, particularly deep learning algorithms, have demonstrated accuracy in analyzing dental radiographs, thereby facilitating earlier and more precise detection of carious lesions [118,119]. For example, convolutional neural networks have been reported to achieve accuracy rates of up to 97% with low false positive rates in identifying carious lesions, enhancing diagnostic reliability [108,120]. Such advancements could significantly augment traditional diagnostic methods, thereby improving preventive strategies for conditions like pulpitis and abscess formation that arise from poorly diagnosed caries [110]. Moreover, the speed of AI diagnostic processes often surpasses that of experienced clinicians, allowing for quicker evaluations of radiographic images, which could contribute to improved patient throughput and diagnostic efficiency in dental practices [109]. Additionally, predictive modeling frameworks utilizing extensive datasets are being explored to forecast future caries development, emphasizing the importance of data quality in training these models to ensure reliable outcomes [111]. Although AI has considerable potential to improve personalized caries prediction and diagnostic efficiency, its clinical implementation requires further external validation, standardized datasets, and careful consideration of data privacy, reproducibility, and regulatory issues. At present, AI should be regarded as a complementary tool rather than a replacement for clinical judgment [112].

The development of dental caries is influenced by complex interactions among pathogenic microorganisms, dietary behaviors, and host-related factors [2]. Research shows that changes in tongue microbiota relate to oral health, directly linking microbiome composition with dental caries prevalence [121]. Furthermore, personalized preventive strategies may incorporate dietary modifications and probiotics targeting specific dysbiotic species to restore ecological balance within the oral cavity [122]. Advances in proteomics reveal that salivary proteins interact with oral microbiota, affecting caries risk and offering potential biomarkers for assessment [123]. Understanding the dynamics of oral biofilms and their ecological relationships allows for tailoring interventions that can mitigate the risks associated with dysbiosis [75]. Thus, a microbiota-driven approach toward caries prevention emphasizes not only the reduction in pathogenic organisms but also the promotion of beneficial microbiotic communities as a pathway to enhance oral health.

Dental caries, a common oral disease marked by tooth decay resulting from demineralization caused by acid-producing bacteria, is being increasingly managed with the advancement of smart and responsive materials [124]. These materials are designed to be antibacterial and react to changes in oral pH. For example, the incorporation of smart dental materials that react to local acidic conditions can help inhibit the growth of cariogenic bacteria, thereby reducing the incidence of caries [79]. The ability of these materials to release bioactive ions or antimicrobial agents in response to acidic pH enhances their efficacy in remineralizing enamel and dentin, providing a dual benefit of antibacterial action and mineral restoration [125]. Advancements in this field include the development of innovative coatings and composite materials designed to inhibit biofilm formation, a key factor in caries progression, through mechanisms that either repel bacterial adhesion or exert bactericidal effects upon contact [126]. Furthermore, the integration of nanotechnology into smart dental materials, as seen in the development of metallic and polymeric nanocomposites, has shown promise in improving antibacterial efficacy through multifaceted action [77,78]. These materials not only enhance treatment outcomes but may also lead to a shift toward more preventive and less invasive treatment modalities, aligning with contemporary trends in minimally invasive dentistry [76]. Despite these promising developments, most smart materials remain at the experimental or early clinical stage. Further studies evaluating long-term performance, cost-effectiveness, regulatory approval, and chairside applicability are needed before widespread clinical adoption.

The original contributions presented in this study are included in the article. Further inquiries can be directed to the corresponding authors.