Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa
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 sh...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-04-01
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| Series: | Genomics, Proteomics & Bioinformatics |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1672022921001765 |
| _version_ | 1797368335904538624 |
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| 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 Zhuye Jie |
| author_facet | 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 Zhuye Jie |
| author_sort | Jie Zhu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-08T17:30:56Z |
| format | Article |
| id | doaj.art-a73efb1a9f7f44109ed2d13227e66d19 |
| institution | Directory Open Access Journal |
| issn | 1672-0229 |
| language | English |
| last_indexed | 2024-03-08T17:30:56Z |
| publishDate | 2022-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Genomics, Proteomics & Bioinformatics |
| spelling | doaj.art-a73efb1a9f7f44109ed2d13227e66d192024-01-02T15:49:59ZengElsevierGenomics, Proteomics & Bioinformatics1672-02292022-04-01202246259Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New TaxaJie Zhu0Liu Tian1Peishan Chen2Mo Han3Liju Song4Xin Tong5Xiaohuan Sun6Fangming Yang7Zhipeng Lin8Xing Liu9Chuan Liu10Xiaohan Wang11Yuxiang Lin12Kaiye Cai13Yong Hou14Xun Xu15Huanming Yang16Jian Wang17Karsten Kristiansen18Liang Xiao19Tao Zhang20Huijue Jia21Zhuye Jie22BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, ChinaBGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, ChinaBGI-Shenzhen, Shenzhen 518083, China; Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen 518083, ChinaBGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen DK-2100, DenmarkBGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, ChinaBGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, ChinaBGI-Shenzhen, Shenzhen 518083, ChinaBGI-Shenzhen, Shenzhen 518083, ChinaBGI-Shenzhen, Shenzhen 518083, ChinaBGI-Shenzhen, Shenzhen 518083, ChinaBGI-Shenzhen, Shenzhen 518083, ChinaBGI-Shenzhen, Shenzhen 518083, ChinaBGI-Shenzhen, Shenzhen 518083, ChinaBGI-Shenzhen, Shenzhen 518083, ChinaBGI-Shenzhen, Shenzhen 518083, ChinaBGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, ChinaBGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, ChinaBGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, ChinaBGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen DK-2100, DenmarkBGI-Shenzhen, Shenzhen 518083, China; Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen 518083, China; BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, ChinaBGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen DK-2100, DenmarkBGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China; Corresponding authors.BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark; Corresponding authors.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.http://www.sciencedirect.com/science/article/pii/S1672022921001765MetagenomicsHuman oral microbiomeMetagenome-assembly genomeGenome catalogGender |
| spellingShingle | 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 Zhuye Jie Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa Genomics, Proteomics & Bioinformatics Metagenomics Human oral microbiome Metagenome-assembly genome Genome catalog Gender |
| title | Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa |
| title_full | Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa |
| title_fullStr | Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa |
| title_full_unstemmed | Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa |
| title_short | Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa |
| title_sort | over 50 000 metagenomically assembled draft genomes for the human oral microbiome reveal new taxa |
| topic | Metagenomics Human oral microbiome Metagenome-assembly genome Genome catalog Gender |
| url | http://www.sciencedirect.com/science/article/pii/S1672022921001765 |
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