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 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.
Department of Computer Science, University of Colorado, Boulder, Colorado, USA.
José A
JA
Navas-Molina
Juan M
JM
Peralta-Sánchez
Antonio
A
González
Paul J
PJ
McMurdie
Yoshiki
Y
Vázquez-Baeza
Zhenjiang
Z
Xu
Luke K
LK
Ursell
Christian
C
Lauber
Hongwei
H
Zhou
Se Jin
SJ
Song
James
J
Huntley
Gail L
GL
Ackermann
Donna
D
Berg-Lyons
Susan
S
Holmes
J Gregory
JG
Caporaso
Rob
R
Knight
D000818:Animals; D001419:Bacteria / Q000235:genetics* / Q000472:pathogenicity; D019295:Computational Biology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D051379:Mice; D064307:Microbiota / Q000235:genetics*; D010802:Phylogeny; D012984:Software
Highthroughput sequencing; Microbial community analyses; Microbial ecology; Microbiome; QIIME