Oliveira Simone G de, Jardim Rodrigo, Kotowski Nelson, Dávila Alberto M R, Sampaio-Filho Hélio R, Ruiz Karina G S, Aguiar Flávio H B
Piracicaba School of Dentistry, Campinas State University, Piracicaba 13414-903, SP, Brazil.
School of Dentistry, State University of Rio de Janeiro, Rio de Janeiro 13414-903, RJ, Brazil.
Biomedicines. 2025 Feb 26;13(3):583. doi: 10.3390/biomedicines13030583.
Dental caries remains a prevalent chronic disease globally, driven by complex interactions between the host, diet, and microbial communities. This study employs a metatranscriptomic RNA-Seq analysis to explore the functional dynamics of the dentin microbiome in both healthy and carious teeth. By examining the transcriptional activity of bacterial communities, we aimed to identify key microbial species and molecular functions associated with caries progression. Samples from six patients (three healthy and three decayed teeth) were analyzed using the Illumina NovaSeq 2000 platform, with data processed through the SAMSA2 pipeline for taxonomic and functional annotation. The differential expression analysis revealed significant upregulation of and species, including , , and , in carious samples, highlighting their roles in acid production and carbohydrate metabolism. Additionally, species, known for their biofilm-forming capabilities and acid tolerance, were upregulated in decayed teeth. The Gene Ontology (GO) enrichment analysis identified unique molecular functions and biological processes in carious teeth, such as carbohydrate metabolism, oxidative stress response, and bacterial cell wall biogenesis, which are critical for microbial survival in acidic environments. In contrast, healthy teeth exhibited functions related to homeostasis and nutrient acquisition, reflecting a balanced microbial community. The study underscores the polymicrobial nature of dental caries, with multiple bacterial species contributing to disease progression through diverse metabolic and stress-response mechanisms. These findings provide deeper insights into the ecological shifts within the oral microbiome during caries development, emphasizing the importance of a functional metatranscriptomic analysis in understanding the pathogenesis of dental caries.
龋齿仍然是全球普遍存在的慢性疾病，由宿主、饮食和微生物群落之间的复杂相互作用驱动。本研究采用宏转录组RNA测序分析来探索健康牙齿和龋坏牙齿中牙本质微生物群的功能动态。通过检查细菌群落的转录活性，我们旨在确定与龋齿进展相关的关键微生物物种和分子功能。使用Illumina NovaSeq 2000平台对6名患者的样本（3颗健康牙齿和3颗龋坏牙齿）进行分析，数据通过SAMSA2管道进行分类和功能注释处理。差异表达分析显示，在龋坏样本中，包括变形链球菌、远缘链球菌和血链球菌在内的多种物种显著上调，突出了它们在产酸和碳水化合物代谢中的作用。此外，以形成生物膜能力和耐酸性而闻名的某些物种在龋坏牙齿中上调。基因本体（GO）富集分析确定了龋坏牙齿中独特的分子功能和生物学过程，如碳水化合物代谢、氧化应激反应和细菌细胞壁生物合成，这些对于微生物在酸性环境中的生存至关重要。相比之下，健康牙齿表现出与体内平衡和营养获取相关的功能，反映了微生物群落的平衡。该研究强调了龋齿的多微生物性质，多种细菌物种通过不同的代谢和应激反应机制促进疾病进展。这些发现为龋齿发展过程中口腔微生物群的生态变化提供了更深入的见解，强调了功能宏转录组分析在理解龋齿发病机制中的重要性。
