Oralgen Database, Genome Science Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Mol Oral Microbiol. 2010 Dec;25(6):391-405. doi: 10.1111/j.2041-1014.2010.00587.x.
Human dental plaque is a complex microbial community containing an estimated 700 to 19,000 species/phylotypes. Despite numerous studies analysing species richness in healthy and diseased human subjects, the true genomic composition of the human dental plaque microbiota remains unknown. Here we report a metagenomic analysis of a healthy human plaque sample using a combination of second-generation sequencing platforms. A total of 860 million base pairs of non-human sequences were generated. Various analysis tools revealed the presence of 12 well-characterized phyla, members of the TM-7 and BRC1 clade, and sequences that could not be classified. Both pathogens and opportunistic pathogens were identified, supporting the ecological plaque hypothesis for oral diseases. Mapping the metagenomic reads to sequenced reference genomes demonstrated that 4% of the reads could be assigned to the sequenced species. Preliminary annotation identified genes belonging to all known functional categories. Interestingly, although 73% of the total assembled contig sequences were predicted to code for proteins, only 51% of them could be assigned a functional role. Furthermore, ~2.8% of the total predicted genes coded for proteins involved in resistance to antibiotics and toxic compounds, suggesting that the oral cavity is an important reservoir for antimicrobial resistance.
人类牙菌斑是一种复杂的微生物群落，其中估计包含 700 到 19,000 个物种/类群。尽管有许多研究分析了健康和患病人体中的物种丰富度，但人类牙菌斑微生物组的真实基因组组成仍不清楚。在这里，我们使用第二代测序平台的组合报告了对健康人牙菌斑样本的宏基因组分析。共产生了 8.6 亿个非人类序列的碱基对。各种分析工具揭示了 12 个特征明确的门，TM-7 和 BRC1 分支的成员，以及无法分类的序列。病原体和机会性病原体均被鉴定，支持口腔疾病的生态菌斑假说。将宏基因组读映射到测序的参考基因组上表明，4%的读可以分配给测序的物种。初步注释确定了属于所有已知功能类别的基因。有趣的是，尽管总组装的连续序列的 73%被预测为编码蛋白质，但其中只有 51%可以分配功能作用。此外，~2.8%的总预测基因编码与抗生素和有毒化合物抗性相关的蛋白质，表明口腔是抗微生物抗性的重要储库。
