特异性基因探针杂交捕获16S rRNA基因 具有更强的多样性

Title：
Hybridization capture reveals microbial diversity missed using current profiling methods

DOI：
10.1186/s40168-018-0442-3

Abstract：
Microorganisms comprise the majority of living organisms on our planet. For many years, exploration of the composition of microbial communities has been performed through the PCR-based study of the small subunit rRNA gene due to its high conservation across the domains of life. The application of this method has resulted in the discovery of many unexpected evolutionary lineages. However, amplicon sequencing is subject to numerous biases, with some taxa being missed, and is limited by the read length of second-generation sequencing platforms, which drastically reduces the phylogenetic resolution.Here, we describe a hybridization capture strategy that allows the enrichment of 16S rRNA genes from metagenomic samples and enables an exhaustive identification and a complete reconstruction of the biomarker. Applying this approach to a microbial mock community and a soil sample, we demonstrated that hybridization capture is able to reveal greater microbial diversity than 16S rDNA amplicon sequencing and shotgun sequencing. The reconstruction of full-length 16S rRNA genes facilitated the improvement of phylogenetic resolution and the discovery of novel prokaryotic taxa.Our results demonstrate that hybridization capture can lead to major breakthroughs in our understanding of microbial diversity, overcoming the limitations of conventional 16S rRNA gene studies. If applied to a broad range of environmental samples, this innovative approach could reveal the undescribed diversity of the still underexplored microbial communities and could provide a better understanding of ecosystem function.

All Authors：
Cyrielle Gasc,Pierre Peyret

First Authors：
Pierre Peyret

Correspondence：
Pierre Peyret

摘要：

      现有的物种多样性分析方法主要基于rRNA基因的扩增子和测序，扩增过程偏差、二代测序读长都限制了其分辨率；现在有一种新的通过杂交捕获的策略富集宏基因组样本中的16S rRNA基因，并在此基础上建库测序分析的方法；即是将特异性16S rRNA基因探针组含15个标记的DNA，通过体外转录得到RNA，用RNA探针捕获样品中的16S rRNA基因，捕获得到的DNA使用MiSeq方法建库测序；对比MiSeq直接测序，特别是16S rRNA扩增子测序结果，此种方法显示出更复杂的多样性。