A catalog of bacterial reference genomes from cultivated human oral bacteria

Wenxi Li; Hewei Liang; Xiaoqian Lin; Tongyuan Hu; Zhinan Wu; Wenxin He; Mengmeng Wang; Jiahao Zhang; Zhuye Jie; Xin Jin; Xun Xu; Jian Wang; Huanming Yang; Wenwei Zhang; Karsten Kristiansen; Liang Xiao; Yuanqiang Zou

doi:10.1038/s41522-023-00414-3

A catalog of bacterial reference genomes from cultivated human oral bacteria

Wenxi Li, Hewei Liang, Xiaoqian Lin, Tongyuan Hu, Zhinan Wu, Wenxin He, Mengmeng Wang, Jiahao Zhang, Zhuye Jie, Xin Jin, Xun Xu, Jian Wang, Huanming Yang, Wenwei Zhang, Karsten Kristiansen, Liang Xiao^*, Yuanqiang Zou

^*Corresponding author af dette arbejde

Genomforskning og Molekylær Biomedicin

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

10 Citationer (Scopus)

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Abstract

The oral cavity harbors highly diverse communities of microorganisms. However, the number of isolated species and high-quality genomes is limited. Here we present a Cultivated Oral Bacteria Genome Reference (COGR), comprising 1089 high-quality genomes based on large-scale aerobic and anaerobic cultivation of human oral bacteria isolated from dental plaques, tongue, and saliva. COGR covers five phyla and contains 195 species-level clusters of which 95 include 315 genomes representing species with no taxonomic annotation. The oral microbiota differs markedly between individuals, with 111 clusters being person-specific. Genes encoding CAZymes are abundant in the genomes of COGR. Members of the Streptococcus genus make up the largest proportion of COGR and many of these harbor entire pathways for quorum sensing important for biofilm formation. Several clusters containing unknown bacteria are enriched in individuals with rheumatoid arthritis, emphasizing the importance of culture-based isolation for characterizing and exploiting oral bacteria.

Originalsprog	Engelsk
Artikelnummer	45
Tidsskrift	npj Biofilms and Microbiomes
Vol/bind	9
Udgave nummer	1
Antal sider	13
ISSN	2055-5008
DOI	https://doi.org/10.1038/s41522-023-00414-3
Status	Udgivet - 2023

Bibliografisk note

Funding Information:
This work was supported by grants from National Key Research and Development Program of China (No. 2018YFC1313801) and Natural Science Foundation of Guangdong Province, China (No. 2019B020230001). We thank the colleagues at BGI-Shenzhen for sample collection, and bacteria preservation, and China National GeneBank (CNGB) Shenzhen for DNA extraction, library construction, and sequencing. We also thank Xiaohuan Jing from CNGB for his assistance in deposit of bacterial strains. This work was supported by the Henan Supercomputer Center.

Funding Information:
This work was supported by grants from National Key Research and Development Program of China (No. 2018YFC1313801) and Natural Science Foundation of Guangdong Province, China (No. 2019B020230001). We thank the colleagues at BGI-Shenzhen for sample collection, and bacteria preservation, and China National GeneBank (CNGB) Shenzhen for DNA extraction, library construction, and sequencing. We also thank Xiaohuan Jing from CNGB for his assistance in deposit of bacterial strains. This work was supported by the Henan Supercomputer Center.

Publisher Copyright:
© 2023, The Author(s).

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10.1038/s41522-023-00414-3Licens: CC BY

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Citationsformater

A catalog of bacterial reference genomes from cultivated human oral bacteria. / Li, Wenxi; Liang, Hewei; Lin, Xiaoqian; Hu, Tongyuan; Wu, Zhinan; He, Wenxin; Wang, Mengmeng; Zhang, Jiahao; Jie, Zhuye; Jin, Xin; Xu, Xun; Wang, Jian; Yang, Huanming; Zhang, Wenwei; Kristiansen, Karsten; Xiao, Liang; Zou, Yuanqiang.

I: npj Biofilms and Microbiomes, Bind 9, Nr. 1, 45, 2023.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

Li, Wenxi ; Liang, Hewei ; Lin, Xiaoqian ; Hu, Tongyuan ; Wu, Zhinan ; He, Wenxin ; Wang, Mengmeng ; Zhang, Jiahao ; Jie, Zhuye ; Jin, Xin ; Xu, Xun ; Wang, Jian ; Yang, Huanming ; Zhang, Wenwei ; Kristiansen, Karsten ; Xiao, Liang ; Zou, Yuanqiang. / A catalog of bacterial reference genomes from cultivated human oral bacteria. I: npj Biofilms and Microbiomes. 2023 ; Bind 9, Nr. 1.

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abstract = "The oral cavity harbors highly diverse communities of microorganisms. However, the number of isolated species and high-quality genomes is limited. Here we present a Cultivated Oral Bacteria Genome Reference (COGR), comprising 1089 high-quality genomes based on large-scale aerobic and anaerobic cultivation of human oral bacteria isolated from dental plaques, tongue, and saliva. COGR covers five phyla and contains 195 species-level clusters of which 95 include 315 genomes representing species with no taxonomic annotation. The oral microbiota differs markedly between individuals, with 111 clusters being person-specific. Genes encoding CAZymes are abundant in the genomes of COGR. Members of the Streptococcus genus make up the largest proportion of COGR and many of these harbor entire pathways for quorum sensing important for biofilm formation. Several clusters containing unknown bacteria are enriched in individuals with rheumatoid arthritis, emphasizing the importance of culture-based isolation for characterizing and exploiting oral bacteria.",

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AU - Lin, Xiaoqian

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AU - He, Wenxin

AU - Wang, Mengmeng

AU - Zhang, Jiahao

AU - Jie, Zhuye

AU - Jin, Xin

AU - Xu, Xun

AU - Wang, Jian

AU - Yang, Huanming

AU - Zhang, Wenwei

AU - Kristiansen, Karsten

AU - Xiao, Liang

AU - Zou, Yuanqiang

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AB - The oral cavity harbors highly diverse communities of microorganisms. However, the number of isolated species and high-quality genomes is limited. Here we present a Cultivated Oral Bacteria Genome Reference (COGR), comprising 1089 high-quality genomes based on large-scale aerobic and anaerobic cultivation of human oral bacteria isolated from dental plaques, tongue, and saliva. COGR covers five phyla and contains 195 species-level clusters of which 95 include 315 genomes representing species with no taxonomic annotation. The oral microbiota differs markedly between individuals, with 111 clusters being person-specific. Genes encoding CAZymes are abundant in the genomes of COGR. Members of the Streptococcus genus make up the largest proportion of COGR and many of these harbor entire pathways for quorum sensing important for biofilm formation. Several clusters containing unknown bacteria are enriched in individuals with rheumatoid arthritis, emphasizing the importance of culture-based isolation for characterizing and exploiting oral bacteria.

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