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Nat Biotechnol. 2019 Feb;37(2):179-185. doi: 10.1038/s41587-018-0008-8. Epub 2019 Feb 4.

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses.

Zou Y1,2,3, Xue W1,2, Luo G1,2,4, Deng Z1,2, Qin P1,2,5, Guo R1,2, Sun H1,2, Xia Y1,2,5, Liang S1,2,6, Dai Y1,2, Wan D1,2, Jiang R1,2, Su L1,2, Feng Q1,2, Jie Z1,2, Guo T1,2, Xia Z1,2, Liu C1,2,6, Yu J1,2, Lin Y1,2, Tang S1,2, Huo G4, Xu X1,2, Hou Y1,2, Liu X1,2,7, Wang J1,8, Yang H1,8, Kristiansen K1,2,3,9, Li J10,11,12, Jia H13,14,15, Xiao L16,17,18,19,20.

Author information

1
BGI-Shenzhen, Shenzhen, China.
2
China National Genebank, BGI-Shenzhen, Shenzhen, China.
3
Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
4
Key Laboratory of Dairy Science, College of Food Sciences, Northeast Agricultural University, Harbin, Heilongjiang, China.
5
BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.
6
Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China.
7
BGI-Qingdao, BGI-Shenzhen, Qingdao, China.
8
James D. Watson Institute of Genome Sciences, Hangzhou, China.
9
Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China.
10
BGI-Shenzhen, Shenzhen, China. lijunhua@genomics.cn.
11
China National Genebank, BGI-Shenzhen, Shenzhen, China. lijunhua@genomics.cn.
12
School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China. lijunhua@genomics.cn.
13
BGI-Shenzhen, Shenzhen, China. jiahuijue@genomics.cn.
14
China National Genebank, BGI-Shenzhen, Shenzhen, China. jiahuijue@genomics.cn.
15
Macau University of Science and Technology, Taipa, Macau, China. jiahuijue@genomics.cn.
16
BGI-Shenzhen, Shenzhen, China. xiaoliang@genomics.cn.
17
China National Genebank, BGI-Shenzhen, Shenzhen, China. xiaoliang@genomics.cn.
18
Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China. xiaoliang@genomics.cn.
19
Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China. xiaoliang@genomics.cn.
20
Department of Digestive Diseases, Huashan Hospital of Fudan University, Shanghai, China. xiaoliang@genomics.cn.

Abstract

Reference genomes are essential for metagenomic analyses and functional characterization of the human gut microbiota. We present the Culturable Genome Reference (CGR), a collection of 1,520 nonredundant, high-quality draft genomes generated from >6,000 bacteria cultivated from fecal samples of healthy humans. Of the 1,520 genomes, which were chosen to cover all major bacterial phyla and genera in the human gut, 264 are not represented in existing reference genome catalogs. We show that this increase in the number of reference bacterial genomes improves the rate of mapping metagenomic sequencing reads from 50% to >70%, enabling higher-resolution descriptions of the human gut microbiome. We use the CGR genomes to annotate functions of 338 bacterial species, showing the utility of this resource for functional studies. We also carry out a pan-genome analysis of 38 important human gut species, which reveals the diversity and specificity of functional enrichment between their core and dispensable genomes.

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PMID:
30718868
PMCID:
PMC6784896
DOI:
10.1038/s41587-018-0008-8
[Indexed for MEDLINE]
Free PMC Article

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