QIIME (Quantitative Insights Into Microbial Ecology) ( Caporaso, Kuczynski, Stombaugh, Bittinger, Bushman, Costello et al., 2010b) is an open-source pipeline designed to provide self-contained microbial community analyses, from interacting with raw sequence data through publication-quality statistical analyses and visualizations. The rapidly increasing data volumes typical of recent studies drives a need for more efficient and scalable tools to study the human microbiome ( Gonzalez & Knight, 2012a). Illumina's MiSeq and HiSeq DNA sequencing instruments respectively sequence tens of millions, or billions, of DNA fragments in a single sequencing run ( Kuczynski, Lauber, Walters, Parfrey, Clemente, Gevers et al., 2012). More recently, evidence from transplants into germ-free mice suggests that some of these associations may be causal, because certain phenotypes can be transmitted by transmitting the microbiota ( Carvalho, Koren, Goodrich, Johansson, Nalbantoglu, Aitken et al., 2012 McLean, Bergonzelli, Collins, & Bercik, 2012 Turnbaugh et al., 2009), even including transmission of human phenotypes into mice ( Diaz Heijtz, Wang, Anuar, Qian, Bjorkholm, Samuelsson et al., 2011 Koren, Goodrich, Cullender, Spor, Laitinen, Backhed et al., 2012 Smith, Yatsunenko, Manary, Trehan, Mkakosya, Cheng et al., 2013). These microbial communities contribute to healthy human physiology ( De Filippo, Cavalieri, Di Paola, Ramazzotti, Poullet, Massart et al., 2010 Dethlefsen & Relman, 2011 Spencer, Hamp, Reid, Fischer, Zeisel, & Fodor, 2011) and development ( Dominguez-Bello, Costello, Contreras, Magris, Hidalgo, Fierer et al., 2010 Koenig, Spor, Scalfone, Fricker, Stombaugh, Knight et al., 2011), and dysbiosis (or imbalance in these communities) is now known to be associated with disease, including obesity ( Turnbaugh, Hamady, Yatsunenko, Cantarel, Duncan, Ley et al., 2009) and Crohn's disease ( Eckburg & Relman, 2007).
The human microbiota, the collection of microbes living in or on the human body, is of considerable interest: microbial cells outnumber human cells in our bodies by a ratio of up to 10 to 1 ( Savage, 1977).
#Rarify qiime software
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.Īdvances in DNA sequencing technologies, together with the availability of culture-independent sequencing methods and software for analyzing the massive quantities of data resulting from these technologies, have vastly improved our ability to characterize microbial communities in many diverse environments.
We present our recommended pipeline for performing microbial community analysis, and provide guidelines for making critical choices in the process. In this paper, 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. 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. High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding of the human microbiome.
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