@inbook{cc6d86c7956740678b554bc806934eec,
title = "Advancing our understanding of the human microbiome using QIIME",
abstract = "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.",
keywords = "Highthroughput sequencing, Microbial community analyses, Microbial ecology, Microbiome, QIIME",
author = "Navas-Molina, {Jos{\'e} A.} and Peralta-S{\'a}nchez, {Juan M.} and Antonio Gonz{\'a}lez and McMurdie, {Paul J.} and Yoshiki V{\'a}zquez-Baeza and Zhenjiang Xu and Ursell, {Luke K.} and Christian Lauber and Hongwei Zhou and Song, {Se Jin} and James Huntley and Ackermann, {Gail L.} and Donna Berg-Lyons and Susan Holmes and Caporaso, {J. Gregory} and Rob Knight",
note = "Funding Information: We thank William A. Walters and Jessica Metcalf for productive discussion and their useful comments about QIIME. We also acknowledge Manuel Lladser for helping collect the dataset and allowing us to use it, and the IQBio IGERT grant for funding data collection. J.A.N.M. is supported by a graduate scholarship funded jointly by the Balsells Foundation and by the University of Colorado at Boulder. S.H. is partially supported by NIH Grant R01 GM086884. This work was partially supported by the Howard Hughes Medical Institute.",
year = "2013",
doi = "10.1016/B978-0-12-407863-5.00019-8",
language = "English (US)",
isbn = "9780124078635",
series = "Methods in Enzymology",
publisher = "Academic Press Inc.",
pages = "371--444",
booktitle = "Microbial Metagenomics, Metatranscriptomics, and Metaproteomics",
address = "United States",
}