Characterization of the gut microbiome in epidemiologic studies: the multiethnic cohort experience.
Characterization of the gut microbiome in epidemiologic studies: the multiethnic cohort experience.
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DOI：
10.1016/j.annepidem.2016.02.009
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发表时间：
2016-05
影响因子：
5.6
通讯作者：
Lampe JW
中科院分区：
文献类型：
--
作者：
Fu BC;Randolph TW;Lim U;Monroe KR;Cheng I;Wilkens LR;Le Marchand L;Hullar MA;Lampe JW
下一代测序和伴随的生物信息学工具的发展已经彻底改变了微生物群落的特征。随着人们对人类微生物组在健康和疾病中的作用越来越感兴趣，对动力充足、设计严密的流行病学研究的需求也在增加。在这里，我们讨论了在肠道微生物组研究中可能出现的偏见来源。综述了肠道微生物样品的标本采集、保存、处理和分析方法的比较研究。虽然选择的研究主要基于肠道，但许多相同的原则也适用于来自其他解剖部位的样本。还描述了在正在进行的基于人群的研究中实施的参与者招募和肠道微生物组采样的方法，即多种族队列（MEC）。方法上的差异会影响人类微生物组研究的结果。为了帮助减少偏差，应在方案中采用样品均质化、添加内部标准和质量过滤等技术。在MEC中，参与者对粪便样本收集的反应率与其他研究相当，并且在家中收集粪便样本可以为肠道微生物组分析提供足够的高质量DNA。在人类微生物组研究中应用标准化和质量控制的方法是保证数据质量和研究之间可比性的必要条件。
Development of next-generation sequencing and accompanying bioinformatics tools has revolutionized characterization of microbial communities. As interest grows in the role of the human microbiome in health and disease, so does the need for well-powered, robustly designed epidemiologic studies. Here, we discuss sources of bias that can arise in gut microbiome research. Research comparing methods of specimen collection, preservation, processing, and analysis of gut microbiome samples is reviewed. While selected studies are primarily based on the gut, many of the same principles are applicable to samples derived from other anatomical sites. Methods for participant recruitment and sampling of the gut microbiome implemented in an ongoing population-based study, the Multiethnic Cohort (MEC), are also described. Variation in methodologies can influence the results of human microbiome studies. To help minimize bias, techniques such as sample homogenization, addition of internal standards, and quality filtering should be adopted in protocols. Within the MEC, participant response rates to stool sample collection were comparable to other studies, and in-home stool sample collection yields sufficient high-quality DNA for gut microbiome analysis. Application of standardized and quality controlled methods in human microbiome studies is necessary to ensure data quality and comparability among studies.