Best practices for analysing microbiomes

Details

• Journal Title:
  Nature Reviews Microbiology
• Personal Author:
  Knight, Rob ; Vrbanac, Alison ; Taylor, Bryn C. ; Aksenov, Alexander ; Callewaert, Chris ; Debelius, Justine ; Gonzalez, Antonio ; Kosciolek, Tomasz ; McCall, Laura-Isobel ; McDonald, Daniel ; Melnik, Alexey V. ; Morton, James T. ; Navas, Jose ; Quinn, Robert A. ; Sanders, Jon G. ; Swafford, Austin D. ; Thompson, Luke R. ; Tripathi, Anupriya ; Xu, Zhenjiang Z. ; Zaneveld, Jesse R. ; Zhu, Qiyun ; Caporaso, J. Gregory ; Dorrestein, Pieter C.
• NOAA Program & Office:
  OAR (Oceanic and Atmospheric Research) ; AOML (Atlantic Oceanographic and Meteorological Laboratory) ; NGI (Northern Gulf Institute)
• Description:
  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.
• Keywords:
  Experimental Design Microorganisms Experimental Design
• Source:
  Nature Reviews Microbiology, 16(7), 410-422
• DOI:
  https://doi.org/10.1038/s41579-018-0029-9
• Document Type:
  Journal Article
• Rights Information:
  Accepted Manuscript
• Rights Statement:
  The NOAA IR provides access to this content under the authority of the government's retained license to distribute publications and data resulting from federal funding. While users may legally access this content, the copyright owners retain rights that govern the reproduction, redistribution, and re-use of this work. The user is solely responsible for complying with applicable copyright law.
• Compliance:
  Submitted
• Main Document Checksum:
  urn:sha-512:713aa71b551b3a3d6621d3f498a2b0b8328bfc2394f7b273f3865bc72e22e32d20205b89f1b2a7c236b6695437ac847fc074568aee3cbda352c0e1bd5862c455
• Download URL:
  https://repository.library.noaa.gov/view/noaa/28862/noaa_28862_DS1.pdf
• File Type:
  [PDF - 1023.71 KB ]