Oral microbiome insights: Tracing acidic culprits in dental caries with functional metagenomics

Dental caries in the human population are caused by teeth demineralization and the subsequent deterioration of tooth structure due to bacterial contamination. Acidogenic oral microbes metabolize carbohydrates, thereby generating acid, which in turn leads to the demineralization of tooth enamel (Kleinberg, 1967; Bretz et al., 2005). Due to the production of acid by bacterial glycolysis within dental biofilms, the tooth enamel undergoes demineralization. The dissolution of phosphate and calcium in hydroxyapatite crystal structure is a consequence of acid formation by cariogenic bacteria. The process of decalcification is also influenced by acid formation by plaque microflora, the concentration of carbon source, the rate of salivary flow, and the characteristics of the tooth surface (Nishimura et al., 2012). Acidification takes place when acid-producing bacteria are prevalent, resulting in an increase in the acidogenic flora and a subsequent decrease in the pH level. This process ultimately leads to the demineralization of the enamel and the acceleration of caries formation (Burne & Marquis, 2000; Van Houte, Lopman et al., 1994).

Dental biofilms are comprised of aciduric and acidogenic bacteria that establish colonization through co-agglutination on the surface of the tooth. Dental caries are caused by various acid-producing microorganisms such as Streptococcus sanguis, Streptococcus mutans, Actinomyces viscosus, Actinomyces naeslundii, Streptococcus sanguis, and Lactobacillus acidophilus (Kara & İpek, 2024). These biofilms exist in a constantly changing equilibrium with the defensive mechanisms of the host (Bradshaw & Marsh, 1998; Burne et al., 2009). The influence of glucose on biofilm pH promotes acid-producing bacteria and damages tooth surfaces by reducing alkaline-dependent bacteria (Schlafer et al., 2018; Wade, 2021; Ealla et al., 2024). High salivary glucose levels increase the biomass and viability of Candida albicans and the adherence ability of Streptococcus mutans, enhancing biofilm formation (Brito et al., 2021). Enterococcus faecalis forms more biofilm with 2 % glucose in culture media (T. Chen et al., 2020). while Pseudomonas aeruginosa shows inhibited quorum sensing and biofilm formation with hypertonic glucose. The core microbiota of early childhood caries including Fusobacterium nucleatum and Veillonella parvula, supports biofilm formation and enhances the development of several cariogenic species (Chen et al., 2021, pp. 11083638; Spatafora et al., 2024).

Dental caries infection is an infection that originates from within the body, and it occurs when the resident microorganisms outcompete other species and alter the optimal condition of the biofilm. Streptococcus mutants have been identified as the most transmissible, acid-resistant, and acid-producing pathogen primarily accountable for dental caries in human individuals (Hamada & Slade, 1980; Loesche, 1986). Streptococcus mutants have the capacity to generate a greater amount of non-soluble glucan, aiding the bacteria in adhering to the surfaces of teeth and thereby contributing to the formation of caries (Hamada & Slade, 1980). Subsequently, it was determined that dental caries can occur even in the absence of Streptococcus mutans (Bowden, 1997; Aas et al., 2008). Certain bacteria, such as Actinomyces, that are able to withstand acid and produce acid have been identified as potential pathogens in the initiation of dental caries (Van Houte, 1994; Van Houte et al., 1996). Recent research has provided evidence that newly discovered phylotypes, including Actinomyces israelii, Actinomyces naeslundii, and Actinomyces gerencseriae, as well as bacteria, can potentially be attributed to the development of caries (Takahashi & Nyvad, 2008). Additionally, a diverse range of Veillonela species and non-Streptococcus mutants have the potential to induce dental caries in the absence of a direct association between dental caries and Streptococcus mutans (Takahashi & Nyvad, 2008). Non-Streptococcus mutans in particular strains like Streptococcus gordonii, Streptococcus oralis, Streptococcus mitis, and Streptococcus anginosus are more rapid acid producers than Streptococcus mutans strains (Van Houte, 1994). According to a study conducted in Japan on dental caries, statistical analysis showed that children with Lactobacillus salivarius had a greater frequency of dental caries than children with Streptococcus mutants. The research findings indicate a positive link between the growing capability of Lactobacillus salivarius in acidic environments and individual caries scores. Furthermore, salivary-induced agglutination in Lactobacillus salivarius was found to positively correlate with caries scores (SHIMADA et al., 2015). In the presence or absence of Streptococcus mutans, Scardovia wiggsiae, or Veillonella parvula, is a very recently recognized species that has been found in caries in multiple instances from severe early childhood caries (Tanner, Kent et al., 2011; Tanner, Mathney et al., 2011). Adult dental caries have been discovered to be related to Bifidobacteriaceae, which are typically acidogenic and tolerant (Modesto et al., 2006; Becker et al., 2002). Based on existing reports, dental caries is initiated and progresses due to the colonization of a supragingival biofilm by Lactococcus lactis, Streptococcus salivarius, Aureodontolyticus, and Leuconostoc citreum (SHIMADA et al., 2015). In the world of dental science and healthcare, there is an ongoing dispute on the precise relationship between a particular group of bacteria and dental caries. This lack of clarity creates difficulties for both the use of probiotic therapies to prevent caries and the use of antibiotics to treat existing caries.

The Embden Meyerhof-Parnas route converts carbohydrate molecules to pyruvate, which is the first step in the formation of acid that causes dental caries (Detman et al., 2019). A vital component of cellular metabolism, pyruvate can be directed through various metabolic pathways found in certain bacteria to produce lactic, acetic, butyric, and propionic acids. These pathways have unique roles in bacterial metabolism and physiology. Hence, gaining insights into the group of microorganisms responsible for generating these acids becomes a critical aspect in the treatment and prevention of dental caries. The prevalence of periodontal disease and caries can be traced back to ancient times, although full tissue recovery from either condition has not yet been accomplished. The available treatment aims to slow the progression of the illness to relieve symptoms or restore tissue using artificial materials. Also, caries treatment is expensive, and only symptomatic therapy is provided. There is no effective preventative treatment based on the inhibiting bacterial growth responsible for tooth decay and periodontal diseases (Loesche, 1986) Since adult human teeth cannot be spontaneously replaced, methods must be developed for preventing the disease in terms of developing probiotics and treating this disease.

Metagenomic analyses have linked dental caries with Leptotrichia buccalis, Streptococcus gordonii, Actinomyces gerencseriae, Veillonella parvula, Hallella multisaccharivorax, Parascardovia denticolens, and Propionibacterium acidifaciens (Pang et al., 2021; Luo et al., 2024). Recent culture-independent studies have expanded the diversity of acid-producing bacteria linked to dental caries beyond the traditionally recognized Streptococcus mutans. Research has identified various bacteria, including non-mutans streptococci, Bifidobacterium, Actinomyces, Lactobacillus, Veillonella, Propionibacterium, Atopobium, and Selenomonas, associated with different stages of carious lesions (Kianoush et al., 2014). Richards et al. and Zhang et al. found Lactobacillus salivarius, Streptococcus mutans, Parascardovia denticolens, and Scardovia wiggsiae in dentin caries (Richards et al., 2017Zhang et al., 2022), while Caufield et al. identified several Lactobacillus species linked to severe early-childhood caries (Caufield et al., 2015). Wen et al. emphasized the significant role of lactobacilli in dental caries through acid production (Wen et al., 2022). Previous research identified a few of these as pathogenic and acid producers, while our study has found acid producers in the Indian population that can be responsible for causing caries.