1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses
1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses
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来自培养的人类肠道细菌的 1,520 个参考基因组可实现功能性微生物组分析
DOI：
10.1038/s41587-018-0008-8
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发表时间：
2019-02-01
影响因子：
46.9
通讯作者：
Xiao, Liang
中科院分区：
文献类型：
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作者：
Zou, Yuanqiang;Xue, Wenbin;Xiao, Liang
参考基因组对于宏基因组分析和人类肠道微生物群的功能表征至关重要。我们推出了可培养基因组参考 (CGR)，它是从健康人类粪便样本中培养的超过 6,000 种细菌生成的 1,520 个非冗余、高质量基因组草图的集合。在 1,520 个基因组中，这些基因组被选择覆盖人类肠道中的所有主要细菌门和属，其中 264 个基因组没有出现在现有的参考基因组目录中。我们表明，参考细菌基因组数量的增加将宏基因组测序读数的作图率从 50% 提高到 > 70%，从而能够对人类肠道微生物组进行更高分辨率的描述。我们使用 CGR 基因组注释 338 个细菌物种的功能，展示了该资源在功能研究中的实用性。我们还对 38 个重要的人类肠道物种进行了泛基因组分析，揭示了其核心基因组和非必需基因组之间功能富集的多样性和特异性。
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.