Supplementary Material for: A Tissue-Dependent Hypothesis of Dental Caries

Current understanding of dental caries considers this disease a demineralization of the tooth tissues due to the acid produced by sugar-fermenting microorganisms. Thus, caries is considered a diet- and pH-dependent process. We present here the first metagenomic analysis of the bacterial communities present at different stages of caries development, with the aim of determining whether the bacterial composition and biochemical profile are specific to the tissue affected. The data show that microbial composition at the initial, enamel-affecting stage of caries is significantly different from that found at subsequent stages, as well as from dental plaque of sound tooth surfaces. Although the relative proportion of <i>Streptococcus mutans</i> increased from 0.12% in dental plaque to 0.72% in enamel caries, <i>Streptococcus mitis</i> and <i>Streptococcus sanguinis</i> were the dominant streptococci in these lesions. The functional profile of caries-associated bacterial communities indicates that genes involved in acid stress tolerance and dietary sugar fermentation are overrepresented only at the initial stage (enamel caries), whereas other genes coding for osmotic stress tolerance as well as collagenases and other proteases enabling dentin degradation are significantly overrepresented in dentin cavities. The results support a scenario in which pH and diet are determinants of the disease during the degradation of enamel, but in dentin caries lesions not only acidogenic but also proteolytic bacteria are involved. We propose that caries disease is a process of varying etiology, in which acid-producing bacteria are the vehicle to penetrate enamel and allow dentin degrading microorganisms to expand the cavity.

当前学界对龋齿的认知将该疾病定义为：致龋微生物发酵糖类产生酸性物质，进而引发牙体组织脱矿病变。因此，龋齿被视为依赖饮食与pH值的病理过程。本研究首次针对龋齿发展不同阶段的细菌群落开展宏基因组（metagenomic）分析，旨在明确细菌组成与生化特征是否因受侵害的牙体组织而异。分析数据显示，龋齿初始阶段（侵害牙釉质阶段）的微生物群落组成，与后续阶段的群落组成及健康牙面的牙菌斑均存在显著差异。尽管变形链球菌（Streptococcus mutans）的相对占比从牙菌斑中的0.12%升至牙釉质龋损中的0.72%，但轻型链球菌（Streptococcus mitis）与血链球菌（Streptococcus sanguinis）才是此类病损中的优势链球菌属物种。龋相关细菌群落的功能特征分析表明，参与酸性应激耐受与膳食糖类发酵的基因仅在初始阶段（牙釉质龋）中显著富集；而编码渗透压应激耐受、胶原酶及其他可介导牙本质降解的蛋白酶的基因，则在牙本质龋洞中显著富集。本研究结果支持如下病理机制：在牙釉质脱矿阶段，pH值与饮食是龋齿发生的决定性因素；而在牙本质龋损中，参与致病的不仅有产酸菌，还有蛋白水解菌。我们据此提出：龋齿是一类病因具有异质性的病理过程，产酸菌作为媒介穿透牙釉质，随后使牙本质降解微生物得以扩增龋洞。