Towards standards for human fecal sample processing in metagenomic studies
Towards standards for human fecal sample processing in metagenomic studies
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DOI：
10.1038/nbt.3960
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发表时间：
2017-11-01
影响因子：
46.9
通讯作者：
Bork, Peer
中科院分区：
文献类型：
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作者：
Costea, Paul I.;Zeller, Georg;Bork, Peer
宏基因组分析中的技术差异必须最小化，以自信地评估微生物群对人类健康的贡献。在这里，我们测试了21个代表性的DNA提取方案，对相同的粪便样本和定量的差异，观察到的微生物群落组成。我们将它们与由于文库制备和样品储存而产生的差异进行了比较，并将其与同一标本内或个体内随时间推移观察到的生物学变异进行了对比。我们发现DNA提取对宏基因组分析的结果影响最大。为了对DNA提取方案进行排名，我们考虑了产生的DNA数量和质量，并确定了社区多样性估计值以及革兰氏阳性和革兰氏阴性细菌之间的比率的偏差。我们推荐一种用于人类粪便样本的标准化DNA提取方法，建立了跨实验室的可转移性，并使用已知组成的模拟社区进行了进一步的基准测试。它的采用将提高人类肠道微生物组研究的可比性，并促进荟萃分析。
Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. We found that DNA extraction had the largest effect on the outcome of metagenomic analysis. To rank DNA extraction protocols, we considered resulting DNA quantity and quality, and we ascertained biases in estimates of community diversity and the ratio between Gram-positive and Gram-negative bacteria. We recommend a standardized DNA extraction method for human fecal samples, for which transferability across labs was established and which was further benchmarked using a mock community of known composition. Its adoption will improve comparability of human gut microbiome studies and facilitate meta-analyses.