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2. Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa

Author

Jie Zhu, Liu Tian, Peishan Chen, Mo Han, Liju Song, Xin Tong, Xiaohuan Sun, Fangming Yang, Zhipeng Lin, Xing Liu, Chuan Liu, Xiaohan Wang, Yuxiang Lin, Kaiye Cai, Yong Hou, Xun Xu, Huanming Yang, Jian Wang, Karsten Kristiansen, Liang Xiao, Tao Zhang, Huijue Jia, and Zhuye Jie

Subjects
Metagenomics, Human oral microbiome, Metagenome-assembly genome, Genome catalog, Gender, Biology (General), QH301-705.5, Computer applications to medicine. Medical informatics, R858-859.7
Abstract

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.

Published
2022
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3. Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa

Author

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, 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, and Jie, Zhuye

Abstract

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) which 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.

Published
2022

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