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. 2011 Dec:Chapter 10:10.7.1-10.7.20.
doi: 10.1002/0471250953.bi1007s36.

Using QIIME to analyze 16S rRNA gene sequences from microbial communities

Justin Kuczynski  1 , Jesse Stombaugh  2 , William Anton Walters  1 , Antonio González  3 , J Gregory Caporaso  4 , Rob Knight  2
Affiliations

Using QIIME to analyze 16S rRNA gene sequences from microbial communities

Justin Kuczynski et al. Curr Protoc Bioinformatics. 2011 Dec.

Abstract

QIIME (canonically pronounced "chime") is a software application that performs microbial community analysis. It is an acronym for Quantitative Insights Into Microbial Ecology, and has been used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities. The following protocols describe how to install QIIME on a single computer and use it to analyze microbial 16S sequence data from nine distinct microbial communities.

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Figures

Figure 1
Figure 1
A screenshot of the QIIME Virtualbox, with the terminal icon indicated, and a terminal window open.
Figure 2
Figure 2
Contents of the mapping file (Fasting_Map.txt). Note that the SampleIDs contain only letters, numbers, and period characters.
Figure 3
Figure 3
The first few lines of the taxonomy assignment file, showing on each line the OTU identifier, the representative sequence identifier, the taxonomy assigned to that sequence, and the confidence in that assignment.
Figure 4
Figure 4
A visualization of the phylogenetic tree using FigTree. The tips are unlabeled here, but can be inspected interactively.
Figure 5
Figure 5
An OTU table heatmap, showing the relative abundance of each OTU within each microbial community.
Figure 6
Figure 6
Magic-Table visualization of the OTU table heatmap.
Figure 7
Figure 7
An OTU table heatmap showing taxonomy assignment for each OTU.
Figure 8
Figure 8
An area chart showing the relative abundance of each phylum within each microbial community.
Figure 9
Figure 9
A bar chart of phylum level abundance within communities, similar to figure 8.
Figure 10
Figure 10
A web browser window displaying rarefaction plots. The vertical axis displays the diversity of the community, while the horizontal axis displays the number of sequences considered in the diversity calculation. Each line on the figure represents the average of all microbial belonging to a group within a category: here the green line represents all fasted mouse communities, and the blue line represents the control communities.
Figure 11
Figure 11
A visualization of bootstrap-supported hierarchical clustering of the 9 microbial communities under investigation. Note that the fasted mouse communities (PC.6xx) cluster together, and the result is supported by jackknife tests (red implies > 75% support).
Figure 12
Figure 12
A Principal Coordinates plot of the 9 communities, showing jackknife-supported confidence ellipsoids. The first two principal axes are shown.
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