ConStrains identifies microbial strains in metagenomic datasets.
ConStrains identifies microbial strains in metagenomic datasets.
复制标题
DOI：
10.1038/nbt.3319
复制
发表时间：
2015-10
影响因子：
46.9
通讯作者：
Gevers D
中科院分区：
文献类型：
--
作者：
Luo C;Knight R;Siljander H;Knip M;Xavier RJ;Gevers D
菌株个体性是微生物多样性的重要组成部分，因此鉴定同种细菌菌株对于提高对微生物群落功能的理解至关重要。生物信息学和测序技术的局限性迄今为止已经排除了菌株鉴定，这是由于难以对短读段进行定相以忠实地恢复具有高度相似序列的原始菌株水平基因型。我们提出了约束，一个开源的算法，确定同种菌株从宏基因组序列数据和重建这些菌株在微生物群落中的同源性。该算法使用一组通用基因中的单核苷酸多态性（SNP）模式来推断代表菌株的种内结构。将约束应用于模拟和宿主衍生的数据集，可以深入了解微生物群落动态。
An important fraction of microbial diversity is harbored in strain individuality, so identification of conspecific bacterial strains is imperative for improved understanding of microbial community functions. Limitations in bioinformatics and sequencing technologies have to date precluded strain identification owing to difficulties in phasing short reads to faithfully recover the original strain-level genotypes, which have highly similar sequences. We present ConStrains, an open-source algorithm that identifies conspecific strains from metagenomic sequence data and reconstructs the phylogeny of these strains in microbial communities. The algorithm uses single-nucleotide polymorphism (SNP) patterns in a set of universal genes to infer within-species structures that represent strains. Applying ConStrains to simulated and host-derived data sets provides insights into microbial community dynamics.