Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease

The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Through the sequencing of the 16S rRNA gene and of whole community DNA we provide a glimpse at the global genetic, metabolic, and ecological changes associated with periodontitis in 15 subgingival plaque samples, four from each of two periodontitis patients, and the remaining samples from three healthy individuals. We also demonstrate the power of whole-metagenome sequencing approaches in characterizing the genomes of key players in the oral microbiome, including an unculturable TM7 organism. We reveal the disease microbiome to be enriched in virulence factors, and adapted to a parasitic lifestyle that takes advantage of the disrupted host homeostasis. Furthermore, diseased samples share a common structure that was not found in completely healthy samples, suggesting that the disease state may occupy a narrow region within the space of possible configurations of the oral microbiome. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. Despite a modest level of sequencing (∼2 lanes Illumina 76 bp PE) and high human DNA contamination (up to ∼90%) we were able to partially reconstruct several oral microbes and to preliminarily characterize some systems-level differences between the healthy and diseased oral microbiomes.

口腔微生物组（oral microbiome）是栖息于人类口腔的复杂微生物生态系统，蕴含数千种细菌类群。口腔内致病菌的增殖会引发牙周炎（periodontitis），这种炎症性疾病同时被证实为心血管疾病的风险因素。尽管学界对与发病机制相关的单个菌种已有较多了解，但从健康状态向疾病状态转变的系统层面机制仍知之甚少。本研究通过对16S rRNA基因及全群落DNA进行测序，分析了15份龈下菌斑样本中与牙周炎相关的全局遗传、代谢与生态变化，其中两份牙周炎患者各提供4份样本，剩余样本来自3名健康个体。本研究还证实了全宏基因组测序（whole-metagenome sequencing）方法在表征口腔微生物组关键菌种基因组方面的优势，包括一种尚未实现体外培养的TM7生物体。研究发现，疾病相关的口腔微生物组富集毒力因子，并适应了利用宿主稳态失衡的寄生生活方式。此外，患病样本共享一套健康样本中不存在的共同结构特征，这表明疾病状态可能仅占据口腔微生物组可能配置空间中的狭窄区域。本先导研究证明了高通量测序作为解析口腔微生物组在牙周疾病中作用的工具的价值。尽管本次测序规模适中（约2条Illumina 76 bp双端测序泳道）且存在高比例的人类DNA污染（最高约90%），本研究仍成功部分重建了数种口腔微生物，并初步表征了健康与患病口腔微生物组之间的部分系统层面差异。