The oral cavity of each person is home to hundreds of bacterial species. While taxa for oral diseases have been studied using culture-based characterization as well as amplicon sequencing, metagenomic and genomic information remains scarce compared to the fecal microbiome. Here, using metagenomic shotgun data for 3346 oral metagenomic samples together with 808 published samples, we obtain 56,213 metagenome-assembled genomes (MAGs), and more than 64% of the 3589 species-level genome bins (SGBs) contain no publicly available genomes. The resulting genome collection is representative of samples around the world and contains many genomes from candidate phyla radiation (CPR) that lack monoculture. Also, it enables the discovery of new taxa such as a genus Candidatus Bgiplasma within the family Acholeplasmataceae. Large-scale metagenomic data from massive samples also allow the assembly of strains from important oral taxa such as Porphyromonas and Neisseria. The oral microbes encode genes that could potentially metabolize drugs. Apart from these findings, a strongly male-enriched Campylobacter species was identified. Oral samples would be more user-friendly collected than fecal samples and have the potential for disease diagnosis. Thus, these data lay down a genomic framework for future inquiries of the human oral microbiome.

每个人的口腔都是数百种细菌的家园。虽然已经使用基于培养的表征和扩增子测序研究了口腔疾病的分类群，但与粪便微生物组相比，宏基因组和基因组信息仍然稀缺。在这里，使用 3346 个口腔宏基因组样本的宏基因组鸟枪法数据和 808 个已发表样本，我们获得了 56,213 个宏基因组组装基因组 (MAG)，并且 3589 个物种级基因组箱 (SGB) 中超过 64% 不包含公开可用的基因组。由此产生的基因组集合代表了世界各地的样本，并包含许多来自缺乏单一培养的候选辐射门 (CPR) 的基因组。此外，它还能发现新的分类单元，例如Candidatus属Bgiplasma 属于 Acholeplasmataceae 科。来自大量样本的大规模宏基因组数据还允许组装来自重要口腔类群的菌株，例如卟啉单胞菌和奈瑟菌。口腔微生物编码可能代谢药物的基因。除了这些发现之外，还发现了一种高度富含雄性的弯曲杆菌。口腔样本比粪便样本更易于收集，并且具有疾病诊断的潜力。因此，这些数据为未来研究人类口腔微生物组奠定了基因组框架。