Assessing the Unseen Bacterial Diversity in Microbial Communities.
Assessing the Unseen Bacterial Diversity in Microbial Communities.
复制标题
DOI：
10.1093/gbe/evv234
复制
发表时间：
2015-11-27
影响因子：
3.3
通讯作者：
Ochman H
中科院分区：
文献类型：
--
作者：
Caro-Quintero A;Ochman H
由于历史和技术的原因，16 S核糖体RNA一直是用于分析微生物群落内容的最常见的分子标记。然而，其缓慢的进化速度阻碍了对密切相关的细菌个体16 S-DNA类型的解析，特别是当以97%的序列同一性聚类时，隐藏了大量的物种和菌株水平的变异。蛋白质编码基因进化更快，可用于区分最近分化的谱系，但它们的应用因难以设计低冗余引物而复杂化，所述引物扩增来自远亲类群的同源区域。鉴于现在普遍的做法是复用数百个样品，采用新基因通常需要合成大量的条形码引物。为了规避与使用蛋白质编码基因来调查微生物群落相关的问题，我们开发了一种方法，称为引物设计，提供了一个自动化的解决方案，可以很容易地适应于目标不同的分类群体和/或不同的蛋白质编码区。我们应用这种方法分析了大猩猩肠道微生物组的多样性，并回收了数百种在16 S rDNA扩增子深度测序后未被检测到的菌株。PhyloTAG为恢复微生物群落内精细水平的多样性以及研究细菌种群的稳定性和动态提供了一种强有力的方法。
For both historical and technical reasons, 16S ribosomal RNA has been the most common molecular marker used to analyze the contents of microbial communities. However, its slow rate of evolution hinders the resolution of closely related bacteria—individual 16S-phylotypes, particularly when clustered at 97% sequence identity, conceal vast amounts of species- and strain-level variation. Protein-coding genes, which evolve more quickly, are useful for differentiating among more recently diverged lineages, but their application is complicated by difficulties in designing low-redundancy primers that amplify homologous regions from distantly related taxa. Given the now-common practice of multiplexing hundreds of samples, adopting new genes usually entails the synthesis of large sets of barcoded primers. To circumvent problems associated with use of protein-coding genes to survey microbial communities, we develop an approach—termed phyloTAGs—that offers an automatic solution for primer design and can be easily adapted to target different taxonomic groups and/or different protein-coding regions. We applied this method to analyze diversity within the gorilla gut microbiome and recovered hundreds of strains that went undetected after deep-sequencing of 16S rDNA amplicons. PhyloTAGs provides a powerful way to recover the fine-level diversity within microbial communities and to study stability and dynamics of bacterial populations.