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      Best practices for analysing microbiomes

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          Abstract

          <p class="first" id="d6651406e350">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. </p>

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          Author and article information

          Journal
          Nature Reviews Microbiology
          Nat Rev Microbiol
          Springer Nature
          1740-1526
          1740-1534
          May 23 2018
          Article
          10.1038/s41579-018-0029-9
          29795328
          7d57ad9d-9a21-4f9d-ad05-f6a9c7278b10
          © 2018

          http://www.springer.com/tdm

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