Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing
Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing
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DOI：
10.1038/s42003-019-0540-1
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发表时间：
2019-08-05
影响因子：
5.9
通讯作者：
Sorensen, Soren J.
中科院分区：
文献类型：
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作者：
Gupta, Shashank;Mortensen, Martin S.;Sorensen, Soren J.
16S rRNA基因的下一代测序（NGS）是目前研究中最广泛使用的应用之一，用于研究任何给定身体部位的微生物群。由于NGS比传统培养方法（TCM）更敏感，许多研究认为它们可以取代TCM。然而，我们真的为这种转变做好了准备吗？在这里，我们使用大量样本（n = 1，748粪便和n = 1，790下咽），在不同时间点的健康儿童中比较两种方法的诊断效率。在这里，我们表明，由NGS鉴定的细菌代表了每个样品中培养的独特细菌种类的75.70%，而TCM仅鉴定了通过扩增子测序发现的细菌种类的23.86%。我们讨论了这两种方法的优点和缺点，并提供了如何在临床环境中有效地实施NGS的观点。
Next-Generation Sequencing (NGS) of 16S rRNA gene is now one of the most widely used application to investigate the microbiota at any given body site in research. Since NGS is more sensitive than traditional culture methods (TCMs), many studies have argued for them to replace TCMs. However, are we really ready for this transition? Here we compare the diagnostic efficiency of the two methods using a large number of samples (n = 1,748 fecal and n = 1,790 hypopharyngeal), among healthy children at different time points. Here we show that bacteria identified by NGS represented 75.70% of the unique bacterial species cultured in each sample, while TCM only identified 23.86% of the bacterial species found by amplicon sequencing. We discuss the pros and cons of both methods and provide perspective on how NGS can be implemented effectively in clinical settings.