Advancing Our Understanding of the Human Microbiome Using QIIME

High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding ofthe human microbiome. QIIME (Quantitative Insights Into Microbial Ecology) is an opensource bioinformatics software package designed for microbial community analysisbased on DNA sequence data, which provides a single analysis framework for analysisof raw sequence data through publication-quality statistical analyses and interactivevisualizations. In this chapter, we demonstrate the use of the QIIME pipeline to analyzemicrobial communities obtained from several sites on the bodies of transgenic andwild-type mice, as assessed using 16S rRNA gene sequences generated on the IlluminaMiSeq platform. We present our recommended pipeline for performing microbial community analysis and provide guidelines for making critical choices in the process. Wepresent 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 theseanalyses.