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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

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

In: Genomics, Proteomics and Bioinformatics, Vol. 20, No. 2, 2022, p. 246-259.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Zhu, J, Tian, L, Chen, P, Han, M, Song, L, Tong, X, Sun, X, Yang, F, Lin, Z, Liu, X, Liu, C, Wang, X, Lin, Y, Cai, K, Hou, Y, Xu, X, Yang, H, Wang, J, Kristiansen, K, Xiao, L, Zhang, T, Jia, H & Jie, Z 2022, 'Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa', Genomics, Proteomics and Bioinformatics, vol. 20, no. 2, pp. 246-259. https://doi.org/10.1016/j.gpb.2021.05.001

APA

Zhu, J., Tian, L., Chen, P., Han, M., Song, L., Tong, X., Sun, X., Yang, F., Lin, Z., Liu, X., Liu, C., Wang, X., Lin, Y., Cai, K., Hou, Y., Xu, X., Yang, H., Wang, J., Kristiansen, K., ... Jie, Z. (2022). Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa. Genomics, Proteomics and Bioinformatics, 20(2), 246-259. https://doi.org/10.1016/j.gpb.2021.05.001

Vancouver

Zhu J, Tian L, Chen P, Han M, Song L, Tong X et al. Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa. Genomics, Proteomics and Bioinformatics. 2022;20(2):246-259. https://doi.org/10.1016/j.gpb.2021.05.001

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. / Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa. In: Genomics, Proteomics and Bioinformatics. 2022 ; Vol. 20, No. 2. pp. 246-259.

Bibtex

@article{dc787848f1f24645806b9e1cb8691e72,
title = "Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa",
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.",
keywords = "Gender, Genome catalog, Human oral microbiome, Metagenome-assembly genome, Metagenomics",
author = "Jie Zhu and Liu Tian and Peishan Chen and Mo Han and Liju Song and Xin Tong and Xiaohuan Sun and Fangming Yang and Zhipeng Lin and Xing Liu and Chuan Liu and Xiaohan Wang and Yuxiang Lin and Kaiye Cai and Yong Hou and Xun Xu and Huanming Yang and Jian Wang and Karsten Kristiansen and Liang Xiao and Tao Zhang and Huijue Jia and Zhuye Jie",
note = "Funding Information: This work is supported by the National Key Program for Infectious Diseases of China (Grant No. 2018ZX10714-002 ). We gratefully acknowledge Dr. Junkun Niu, Dr. Yang Sun, and Dr. Yinglei Miao from the First Affiliated Hospital of Kunming Medical University for Yunnan sample collection. And we also thank colleagues at BGI-Shenzhen and CNGB, Shenzhen for sample collection, DNA extraction, library construction, sequencing, and discussions. Funding Information: This work is supported by the National Key Program for Infectious Diseases of China (Grant No. 2018ZX10714-002). We gratefully acknowledge Dr. Junkun Niu, Dr. Yang Sun, and Dr. Yinglei Miao from the First Affiliated Hospital of Kunming Medical University for Yunnan sample collection. And we also thank colleagues at BGI-Shenzhen and CNGB, Shenzhen for sample collection, DNA extraction, library construction, sequencing, and discussions. Publisher Copyright: {\textcopyright} 2022",
year = "2022",
doi = "10.1016/j.gpb.2021.05.001",
language = "English",
volume = "20",
pages = "246--259",
journal = "Genomics, Proteomics and Bioinformatics",
issn = "1672-0229",
publisher = "Elsevier",
number = "2",

}

RIS

TY - JOUR

T1 - Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa

AU - Zhu, Jie

AU - Tian, Liu

AU - Chen, Peishan

AU - Han, Mo

AU - Song, Liju

AU - Tong, Xin

AU - Sun, Xiaohuan

AU - Yang, Fangming

AU - Lin, Zhipeng

AU - Liu, Xing

AU - Liu, Chuan

AU - Wang, Xiaohan

AU - Lin, Yuxiang

AU - Cai, Kaiye

AU - Hou, Yong

AU - Xu, Xun

AU - Yang, Huanming

AU - Wang, Jian

AU - Kristiansen, Karsten

AU - Xiao, Liang

AU - Zhang, Tao

AU - Jia, Huijue

AU - Jie, Zhuye

N1 - Funding Information: This work is supported by the National Key Program for Infectious Diseases of China (Grant No. 2018ZX10714-002 ). We gratefully acknowledge Dr. Junkun Niu, Dr. Yang Sun, and Dr. Yinglei Miao from the First Affiliated Hospital of Kunming Medical University for Yunnan sample collection. And we also thank colleagues at BGI-Shenzhen and CNGB, Shenzhen for sample collection, DNA extraction, library construction, sequencing, and discussions. Funding Information: This work is supported by the National Key Program for Infectious Diseases of China (Grant No. 2018ZX10714-002). We gratefully acknowledge Dr. Junkun Niu, Dr. Yang Sun, and Dr. Yinglei Miao from the First Affiliated Hospital of Kunming Medical University for Yunnan sample collection. And we also thank colleagues at BGI-Shenzhen and CNGB, Shenzhen for sample collection, DNA extraction, library construction, sequencing, and discussions. Publisher Copyright: © 2022

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

KW - Gender

KW - Genome catalog

KW - Human oral microbiome

KW - Metagenome-assembly genome

KW - Metagenomics

U2 - 10.1016/j.gpb.2021.05.001

DO - 10.1016/j.gpb.2021.05.001

M3 - Journal article

C2 - 34492339

AN - SCOPUS:85140206600

VL - 20

SP - 246

EP - 259

JO - Genomics, Proteomics and Bioinformatics

JF - Genomics, Proteomics and Bioinformatics

SN - 1672-0229

IS - 2

ER -

ID: 324378420