A human gut bacterial genome and culture collection for improved metagenomic analyses
A human gut bacterial genome and culture collection for improved metagenomic analyses
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DOI：
10.1038/s41587-018-0009-7
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发表时间：
2019-02-01
影响因子：
46.9
通讯作者：
Lawley, Trevor D.
中科院分区：
文献类型：
--
作者：
Forster, Samuel C.;Kumar, Nitin;Lawley, Trevor D.
了解肠道微生物组功能需要培养细菌进行实验验证和参考细菌基因组序列来解释宏基因组数据集并指导功能分析。我们展示了人类胃肠道细菌培养物保藏中心 (HBC)，这是一套综合的 737 个全基因组测序细菌分离株，代表人类胃肠道微生物群中发现的 31 个科的 273 个物种（105 个新物种）。 HBC 使源自人类胃肠道微生物群的细菌基因组数量增加了 37%。由此产生的全球人类胃肠道细菌基因组集合 (HGG) 根据丰度对 13,490 个鸟枪法测序的宏基因组样本中的 83% 的属进行了分类，与人类微生物组计划 (HMP) 基因组集合相比，分类学分类提高了 61%，并且对近 50% 的序列实现了亚种级分类。胃肠道细菌参考序列资源的改进避免了对宏基因组从头组装的依赖，并能够对人类胃肠道微生物群进行准确且具有成本效益的鸟枪式宏基因组分析。
Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets and guide functional analyses. We present the Human Gastrointestinal Bacteria Culture Collection (HBC), a comprehensive set of 737 whole-genome-sequenced bacterial isolates, representing 273 species (105 novel species) from 31 families found in the human gastrointestinal microbiota. The HBC increases the number of bacterial genomes derived from human gastrointestinal microbiota by 37%. The resulting global Human Gastrointestinal Bacteria Genome Collection (HGG) classifies 83% of genera by abundance across 13,490 shotgun-sequenced metagenomic samples, improves taxonomic classification by 61% compared to the Human Microbiome Project (HMP) genome collection and achieves subspecies-level classification for almost 50% of sequences. The improved resource of gastrointestinal bacterial reference sequences circumvents dependence on de novo assembly of metagenomes and enables accurate and cost-effective shotgun metagenomic analyses of human gastrointestinal microbiota.