Dental caries, the most common chronic infectious disease worldwide, has a complex etiology involving the interplay of microbial and host factors that are not completely understood. In this study, the oral microbiome and 38 host cytokines and chemokines were analyzed across 23 children with caries and 24 children with healthy dentition. De novo assembly of metagenomic sequencing obtained 527 metagenome-assembled genomes (MAGs), representing 150 bacterial species. Forty-two of these species had no genomes in public repositories, thereby representing novel taxa. These new genomes greatly expanded the known pangenomes of many oral clades, including the enigmatic Saccharibacteria clades G3 and G6, which had distinct functional repertoires compared to other oral Saccharibacteria. Saccharibacteria are understood to be obligate epibionts, which are dependent on host bacteria. These data suggest that the various Saccharibacteria clades may rely on their hosts for highly distinct metabolic requirements, which would have significant evolutionary and ecological implications. Across the study group, Rothia, Neisseria, and Haemophilus spp. were associated with good dental health, whereas Prevotella spp., Streptococcus mutans, and Human herpesvirus 4 (Epstein-Barr virus [EBV]) were more prevalent in children with caries. Finally, 10 of the host immunological markers were significantly elevated in the caries group, and co-occurrence analysis provided an atlas of potential relationships between microbes and host immunological molecules. Overall, this study illustrated the oral microbiome at an unprecedented resolution and contributed several leads for further study that will increase the understanding of caries pathogenesis and guide therapeutic development.

中文翻译：

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深度宏基因组学检查龋齿期间的口腔微生物组，揭示新的分类群以及与宿主分子的共存

龋齿是世界上最常见的慢性传染病，其病因复杂，涉及尚未完全了解的微生物和宿主因素的相互作用。在这项研究中，对 23 名龋齿儿童和 24 名健康牙列儿童的口腔微生物组和 38 种宿主细胞因子和趋化因子进行了分析。宏基因组测序的从头组装获得了 527 个宏基因组组装的基因组 (MAG)，代表了 150 种细菌。其中 42 个物种在公共存储库中没有基因组，因此代表了新的分类群。这些新的基因组极大地扩展了许多口腔进化枝的已知泛基因组，包括神秘的糖杆菌进化枝 G3 和 G6，与其他口腔糖杆菌相比，它们具有不同的功能库。糖杆菌被理解为专性外生菌，它们依赖于宿主细菌。这些数据表明，各种糖杆菌进化枝可能依赖其宿主来满足高度不同的代谢需求，这将具有重大的进化和生态意义。在整个学习小组中，Rothia、奈瑟菌和嗜血杆菌属。与良好的牙齿健康有关，而普氏菌属、变形链球菌和人类疱疹病毒 4（爱泼斯坦-巴尔病毒 [EBV]）在儿童龋病中更为普遍。最后，有 10 个宿主免疫标志物在龋齿组中显着升高，共现分析提供了微生物与宿主免疫分子之间潜在关系的图谱。总体而言，这项研究以前所未有的分辨率说明了口腔微生物组，并为进一步研究提供了一些线索，这将增加对龋病发病机制的理解并指导治疗发展。