Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

Daryl M. Gohl, Pajau Vangay, John Garbe, Allison MacLean, Adam Hauge, Aaron Becker, Trevor J. Gould, Jonathan B. Clayton, Timothy J. Johnson, Ryan Hunter, Dan Knights, Kenneth B. Beckman

Research output: Contribution to journalArticle

186 Scopus citations

Abstract

Amplicon-based marker gene surveys form the basis of most microbiome and other microbial community studies. Such PCR-based methods have multiple steps, each of which is susceptible to error and bias. Variance in results has also arisen through the use of multiple methods of next-generation sequencing (NGS) amplicon library preparation. Here we formally characterized errors and biases by comparing different methods of amplicon-based NGS library preparation. Using mock community standards, we analyzed the amplification process to reveal insights into sources of experimental error and bias in amplicon-based microbial community and microbiome experiments. We present a method that improves on the current best practices and enables the detection of taxonomic groups that often go undetected with existing methods.

Original languageEnglish (US)
Pages (from-to)942-949
Number of pages8
JournalNature Biotechnology
Volume34
Issue number9
DOIs
StatePublished - Sep 1 2016

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Molecular Medicine
  • Biomedical Engineering

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    Gohl, D. M., Vangay, P., Garbe, J., MacLean, A., Hauge, A., Becker, A., Gould, T. J., Clayton, J. B., Johnson, T. J., Hunter, R., Knights, D., & Beckman, K. B. (2016). Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies. Nature Biotechnology, 34(9), 942-949. https://doi.org/10.1038/nbt.3601