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Liu C, Zhou N, Du MX, Sun YT, Wang K, Wang YJ, Li DH, Yu HY, Song Y, Bai BB, Xin Y, Wu L, Jiang CY, Feng J, Xiang H, Zhou Y, Ma J, Wang J, Liu HW, Liu SJ. The Mouse Gut Microbial Biobank expands the coverage of cultured bacteria. Nat Commun 2020; 11:79. [PMID: 31911589 PMCID: PMC6946648 DOI: 10.1038/s41467-019-13836-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 11/25/2019] [Indexed: 02/07/2023] Open
Abstract
Mice are widely used as experimental models for gut microbiome (GM) studies, yet the majority of mouse GM members remain uncharacterized. Here, we report the construction of a mouse gut microbial biobank (mGMB) that contains 126 species, represented by 244 strains that have been deposited in the China General Microorganism Culture Collection. We sequence and phenotypically characterize 77 potential new species and propose their nomenclatures. The mGMB includes 22 and 17 species that are significantly enriched in ob/ob and wild-type C57BL/6J mouse cecal samples, respectively. The genomes of the 126 species in the mGMB cover 52% of the metagenomic nonredundant gene catalog (sequence identity ≥ 60%) and represent 93-95% of the KEGG-Orthology-annotated functions of the sampled mouse GMs. The microbial and genome data assembled in the mGMB enlarges the taxonomic characterization of mouse GMs and represents a useful resource for studies of host-microbe interactions and of GM functions associated with host health and diseases.
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Affiliation(s)
- Chang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
- Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
- Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
| | - Meng-Xuan Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
| | - Yu-Tong Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
| | - Kai Wang
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
| | - Yu-Jing Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Dan-Hua Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
| | - Hai-Ying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
| | - Yuqin Song
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
- Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
| | - Bing-Bing Bai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
| | - Yuhua Xin
- Microbial Resources and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
| | - Linhuan Wu
- Microbial Resources and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
- Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
- Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
| | - Yuguang Zhou
- Microbial Resources and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
| | - Juncai Ma
- Microbial Resources and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
| | - Jun Wang
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China
| | - Hong-Wei Liu
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China.
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China.
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China.
- Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichenxi Road, Chaoyang District, Beijing, 100101, P. R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China.
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