Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing.
Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing.
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DOI：
10.1016/j.bbrc.2015.12.083
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发表时间：
2016-01-22
影响因子：
3.1
通讯作者：
Perkins DL
中科院分区：
文献类型：
--
作者：
Ranjan R;Rani A;Metwally A;McGee HS;Perkins DL
人类微生物组已成为调节人类健康和疾病的主要参与者。微生物组的翻译研究有可能表明临床应用，如粪便移植和益生菌。然而，一个主要问题是准确识别构成微生物群的微生物。微生物组的研究经常利用保守的16S核糖体RNA（rRNA）基因的测序。我们提出了一种替代方法，使用鸟枪全基因组测序（WGS）的比较研究。在本研究中，我们分析了人类粪便微生物组，使用多种测序方法和平台从单个样本中编译了总计194.1×106个读数。具体而言，在通过广泛的多重化建立我们的方法的再现性之后，我们比较了：1）16S rRNA扩增子与WGS方法，2）Illumina HiSeq与MiSeq平台，3）读段与从头组装的重叠群的分析，以及4）较短与较长读段的影响。我们的研究表明，鸟枪全基因组测序与16S扩增子方法相比具有多个优势，包括增强细菌物种的检测，增加多样性的检测和增加基因的预测。此外，由于更长的读段或重叠群的组装而增加的长度提高了物种检测的准确性。
The human microbiome has emerged as a major player in regulating human health and disease. Translation studies of the microbiome have the potential to indicate clinical applications such as fecal transplants and probiotics. However, one major issue is accurate identification of microbes constituting the microbiota. Studies of the microbiome have frequently utilized sequencing of the conserved 16S ribosomal RNA (rRNA) gene. We present a comparative study of an alternative approach using shotgun whole genome sequencing (WGS). In the present study, we analyzed the human fecal microbiome compiling a total of 194.1×106 reads from a single sample using multiple sequencing methods and platforms. Specifically, after establishing the reproducibility of our methods with extensive multiplexing, we compared: 1) The 16S rRNA amplicon versus the WGS method, 2) the Illumina HiSeq versus MiSeq platforms, 3) the analysis of reads versus de novo assembled contigs, and 4) the effect of shorter versus longer reads. Our study demonstrates that shotgun whole genome sequencing has multiple advantages compared with the 16S amplicon method including enhanced detection of bacterial species, increased detection of diversity and increased prediction of genes. In addition, increased length, either due to longer reads or the assembly of contigs, improved the accuracy of species detection.