微生物群
基因组
生物
数据科学
计算生物学
计算机科学
生物信息学
遗传学
基因
作者
Rob Knight,Alison Vrbanac,Bryn C. Taylor,Alexander A. Aksenov,Chris Callewaert,Justine W. Debelius,Antonio González,Tomasz Kościółek,Laura-Isobel McCall,Daniel McDonald,Alexey V. Melnik,James T. Morton,J.I. Navas,Robert A. Quinn,Jon G. Sanders,Austin D. Swafford,Luke Thompson,Anupriya Tripathi,Zhenjiang Zech Xu,Jesse Zaneveld,Qiyun Zhu,J. Gregory Caporaso,Pieter C. Dorrestein
标识
DOI:10.1038/s41579-018-0029-9
摘要
Complex microbial communities shape the dynamics of various environments, ranging from the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies and data analysis have provided drastic improvements in microbiome analyses, for example, in taxonomic resolution, false discovery rate control and other properties, over earlier methods. In this Review, we discuss the best practices for performing a microbiome study, including experimental design, choice of molecular analysis technology, methods for data analysis and the integration of multiple omics data sets. We focus on recent findings that suggest that operational taxonomic unit-based analyses should be replaced with new methods that are based on exact sequence variants, methods for integrating metagenomic and metabolomic data, and issues surrounding compositional data analysis, where advances have been particularly rapid. We note that although some of these approaches are new, it is important to keep sight of the classic issues that arise during experimental design and relate to research reproducibility. We describe how keeping these issues in mind allows researchers to obtain more insight from their microbiome data sets.
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