To illustrate the effectiveness of SitePainter, we show the results of a study in which different regions from a subject's hand were sampled for microbes. The subject's hand was outlined, and each region divided into smaller areas that were then sampled using cotton swabs dipped in saline solution. Using SitePainter, we were able to rapidly deduce which bacteria were in different regions of the hand, along with a graphical representation of microbial abundances by processing the sequence data with QIIME (Caporaso et al., 2010
) and mapping the abundance of each taxon onto the hand image (B). Using this display, we can immediately see that Gammaproteobacteria
is present in the palm, Bacilli
are more visible toward the fingertips and Actinomycetales
is present in only one area of the hand. This feature thus allows the user to easily visualize the distribution and abundance of microbes across sites.
Going beyond the abundances of individual microbial taxa, SitePainter also allows the user to view similarities and differences at the whole-community level by loading the PCoA axis of the microbial data to reveal patterns that are not obvious in the PCoA plot but are immediately obvious when displayed in the context of the site itself (C: compare left panel to the right two panels. In this case, we can see a clear gradient from the thumb and index fingers to the left-bottom corner of the hand; additionally we can see that the distal phalanges are similar, maybe due to constant contact).
In addition to analyses of microbial taxa, as shown here, SitePainter can also be used to interpret the abundance of genes or pathways across sites for metabolic studies. Several further examples can be found in the Human Microbiome Project web site: http://hmpdacc.org/sp/
. These examples analyze the entire Human Microbiome Project (Peterson et al., 2009
; Turnbaugh et al., 2007
) dataset at several taxonomic levels, and at several different levels of functional classification for shotgun metagenomic reads. We expect that this will be a useful community resource for those trying to interpret the complexities of the human microbiome.