Extensive strain-level copy-number variation across human gut microbiome species.
Extensive strain-level copy-number variation across human gut microbiome species.
复制标题
DOI：
10.1016/j.cell.2014.12.038
复制
发表时间：
2015-02-12
期刊：
影响因子：
64.5
通讯作者：
Borenstein E
中科院分区：
文献类型：
--
作者：
Greenblum S;Carr R;Borenstein E
在每个细菌物种中，不同的菌株可能在它们编码的基因组或这些基因的拷贝数方面有所不同。然而，人类微生物群的分类学特征通常限于物种水平或先前测序的菌株，因此，种内变异的流行程度、其功能作用及其与宿主健康的关系仍不清楚。在这里，我们提出了第一个全面的大规模分析肠道微生物组中的物种内拷贝数变异，引入了严格的计算管道，用于直接从鸟枪宏基因组数据中检测这种变异。我们发现了大量的可变基因在许多物种，并证明这种变化具有显着的功能和临床相关的影响。我们还推断物种内的组成概况，确定人口结构的变化和尚未表征的变体的存在。我们的结果强调了微生物组组成和功能能力之间的复杂关系，将宏基因组水平的组成变化与菌株水平的变异联系起来。
Within each bacterial species, different strains may vary in the set of genes they encode or in the copy number of these genes. Yet, taxonomic characterization of the human microbiota is often limited to the species level or to previously sequenced strains, and accordingly, the prevalence of intra-species variation, its functional role, and its relation to host health remain unclear. Here we present a first comprehensive large-scale analysis of intra-species copy number variation in the gut microbiome, introducing a rigorous computational pipeline for detecting such variation directly from shotgun metagenomic data. We uncover a large set of variable genes in numerous species and demonstrate that this variation has significant functional and clinically-relevant implications. We additionally infer intra-species compositional profiles, identifying population structure shifts and the presence of yet uncharacterized variants. Our results highlight the complex relationship between microbiome composition and functional capacity, linking metagenome-level compositional shifts to strain-level variation.