Advancing our understanding of the human microbiome using QIIME

José A. Navas-Molina, Juan M. Peralta-Sánchez, Antonio González, Paul J. McMurdie, Yoshiki Vázquez-Baeza, Zhenjiang Xu, Luke K. Ursell, Christian Lauber, Hongwei Zhou, Se Jin Song, James Huntley, Gail L. Ackermann, Donna Berg-Lyons, Susan Holmes, J. Gregory Caporaso, Rob Knight

Research output: Chapter in Book/Report/Conference proceedingChapter

434 Scopus citations


High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding of the human microbiome. QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics software package designed for microbial community analysis based on DNA sequence data, which provides a single analysis framework for analysis of raw sequence data through publication-quality statistical analyses and interactive visualizations. In this chapter, we demonstrate the use of the QIIME pipeline to analyze microbial communities obtained from several sites on the bodies of transgenic and wild-type mice, as assessed using 16S rRNA gene sequences generated on the Illumina MiSeq platform. We present our recommended pipeline for performing microbial community analysis and provide guidelines for making critical choices in the process. We present examples of some of the types of analyses that are enabled by QIIME and discuss how other tools, such as phyloseq and R, can be applied to expand upon these analyses.

Original languageEnglish (US)
Title of host publicationMicrobial Metagenomics, Metatranscriptomics, and Metaproteomics
PublisherAcademic Press Inc.
Number of pages74
ISBN (Print)9780124078635
StatePublished - 2013

Publication series

NameMethods in Enzymology
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988


  • Highthroughput sequencing
  • Microbial community analyses
  • Microbial ecology
  • Microbiome

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology


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