A catalog of bacterial reference genomes from cultivated human oral bacteria
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 anaero...
| Main Authors: | , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-07-01
|
| Series: | npj Biofilms and Microbiomes |
| Online Access: | https://doi.org/10.1038/s41522-023-00414-3 |
| _version_ | 1797784754920095744 |
|---|---|
| author | 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 |
| author_facet | 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 |
| author_sort | Wenxi Li |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-13T00:44:24Z |
| format | Article |
| id | doaj.art-4d05566d767c49aebaad8fa088497b31 |
| institution | Directory Open Access Journal |
| issn | 2055-5008 |
| language | English |
| last_indexed | 2024-03-13T00:44:24Z |
| publishDate | 2023-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Biofilms and Microbiomes |
| spelling | doaj.art-4d05566d767c49aebaad8fa088497b312023-07-09T11:07:59ZengNature Portfolionpj Biofilms and Microbiomes2055-50082023-07-019111310.1038/s41522-023-00414-3A catalog of bacterial reference genomes from cultivated human oral bacteriaWenxi Li0Hewei Liang1Xiaoqian Lin2Tongyuan Hu3Zhinan Wu4Wenxin He5Mengmeng Wang6Jiahao Zhang7Zhuye Jie8Xin Jin9Xun Xu10Jian Wang11Huanming Yang12Wenwei Zhang13Karsten Kristiansen14Liang Xiao15Yuanqiang Zou16BGI-ShenzhenBGI-ShenzhenBGI-ShenzhenBGI-ShenzhenBGI-ShenzhenBGI-ShenzhenBGI-ShenzhenBGI-ShenzhenBGI-ShenzhenBGI-ShenzhenBGI-ShenzhenBGI-ShenzhenBGI-ShenzhenBGI-ShenzhenLaboratory of Genomics and Molecular Biomedicine, Department of Biology, University of CopenhagenBGI-ShenzhenBGI-ShenzhenAbstract 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.https://doi.org/10.1038/s41522-023-00414-3 |
| spellingShingle | 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 A catalog of bacterial reference genomes from cultivated human oral bacteria npj Biofilms and Microbiomes |
| title | A catalog of bacterial reference genomes from cultivated human oral bacteria |
| title_full | A catalog of bacterial reference genomes from cultivated human oral bacteria |
| title_fullStr | A catalog of bacterial reference genomes from cultivated human oral bacteria |
| title_full_unstemmed | A catalog of bacterial reference genomes from cultivated human oral bacteria |
| title_short | A catalog of bacterial reference genomes from cultivated human oral bacteria |
| title_sort | catalog of bacterial reference genomes from cultivated human oral bacteria |
| url | https://doi.org/10.1038/s41522-023-00414-3 |
| work_keys_str_mv | AT wenxili acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT heweiliang acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT xiaoqianlin acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT tongyuanhu acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT zhinanwu acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT wenxinhe acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT mengmengwang acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT jiahaozhang acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT zhuyejie acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT xinjin acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT xunxu acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT jianwang acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT huanmingyang acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT wenweizhang acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT karstenkristiansen acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT liangxiao acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT yuanqiangzou acatalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT wenxili catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT heweiliang catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT xiaoqianlin catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT tongyuanhu catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT zhinanwu catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT wenxinhe catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT mengmengwang catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT jiahaozhang catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT zhuyejie catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT xinjin catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT xunxu catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT jianwang catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT huanmingyang catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT wenweizhang catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT karstenkristiansen catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT liangxiao catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria AT yuanqiangzou catalogofbacterialreferencegenomesfromcultivatedhumanoralbacteria |