This chart replaces pie charts with something more useful – because it includes the taxonomic lineages.
We include in our reports a "Taxonomy Chart", which we find very useful. In fact, it's usually the first place that we look when reviewing data. However, the chart layout does require some explanation.
Bacteria are classified in a hierarchical taxonomy, from the broadest categories to the most specific: kingdom, phylum, class, order, family, genus, species, and in many cases, subspecies or strains. Some times, an MCA is unable to identify a population to the genus level, but the higher (more general) taxonomic levels can still provide some information: for example, the Firmicutes, which contain Bacillus and Clostridium, generally contain either facultative or obligate anaerobes. High levels of Firmicutes may suggest low dissolved oxygen in a system.
Our taxonomy chart is similar to stacking a bunch of bar charts side by side, showing the relative amounts of each taxon present at a taxonomic level, but with a twist. The first column covers the kingdom. In the example below, this kingdom is Bacteria, and it represents over 99% of the sequences. The next level shows the different phyla present in the sample, with Proteobacterium being the most-represented phylum. The chart repeats this all the way down to the genus level.
So, why a twist? Where taxa from two columns share a vertical edge, they are related. From the chart, the genus Thauera is a member of the family Rhodocyclaceae, which in turn is a member of the order Burkholderiales.
White space shows where sequence reads were classified at one level, but not classified at a lower taxonomic level. Or, the reads represented less than 0.3% of the total sequencing reads (or whatever the cutoff value may be, to make the chart easier to read).
