Zhu Jie, Tian Liu, Chen Peishan, Han Mo, Song Liju, Tong Xin, Sun Xiaohuan, Yang Fangming, Lin Zhipeng, Liu Xing, Liu Chuan, Wang Xiaohan, Lin Yuxiang, Cai Kaiye, Hou Yong, Xu Xun, Yang Huanming, Wang Jian, Kristiansen Karsten, Xiao Liang, Zhang Tao, Jia Huijue, Jie Zhuye
BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China.
BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen 518083, China.
Genomics Proteomics Bioinformatics. 2022 Apr;20(2):246-259. doi: 10.1016/j.gpb.2021.05.001. Epub 2021 Sep 4.
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.
每个人的口腔中都存在着数百种细菌。虽然已经使用基于培养的表征方法以及扩增子测序对口腔疾病的分类群进行了研究，但与粪便微生物组相比，宏基因组和基因组信息仍然匮乏。在这里，我们使用来自3346个口腔宏基因组样本以及808个已发表样本的宏基因组鸟枪法数据，获得了56213个宏基因组组装基因组（MAG），并且在3589个物种水平基因组箱（SGB）中，超过64%没有公开可用的基因组。所得的基因组集合代表了世界各地的样本，并且包含许多来自缺乏纯培养的候选门辐射（CPR）的基因组。此外，它还能够发现新的分类群，例如无胆甾原体科内的一个暂定属——候选比格等离子体属。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分类群（如卟啉单胞菌属和奈瑟菌属）的菌株。口腔微生物编码的基因可能具有药物代谢潜力。除了这些发现外，还鉴定出一种在男性中显著富集的弯曲杆菌属物种。与粪便样本相比，口腔样本的采集对用户来说更加方便，并且具有疾病诊断的潜力。因此，这些数据为未来对人类口腔微生物组的研究奠定了基因组框架。
