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Corbata: CORe microBiome Analysis Tools

Ubiquity-Abundance Plot

The core members of a microbiome can be visualized with the Ubiquity-Abundance (Ub-Ab) plot.  Because of the continuous and nonlinear relationship between abundance and ubiquity, seeing how this relationship changes between different taxon, can provide a richer glimpse into the structure of the microbiomes across a single cohort of interest.

Each taxon's curve of the Ub-Ab plot is essentially a cumulative distribution function (CDF), except with the x-axis in reverse. In a traditional CDF plot, the curve starts on the bottom left where y=0, and increases monotonically towards the right until y=1. As you increase the abundance cutoff of a taxa (which has been logarithm-base-10 transformed in the figure), you would expect to find that taxon at that abundance level to be at a smaller proportion of that cohort (ubiquity). In other words, you would not expect to find any samples with 100% abundance of a particular taxon (the bottom right), and every taxa within every sample with an abundance of greater than or equal to 0 (the top left).

Together, the abundance and ubiquity can be used to isolate taxonomic segments of the cohort's microbiome. Two key Ub-Ab plots can be generated with the Corbata scripts. The first is the major core. These are the more commonly reported core, when an analyst picks a single relatively large abundance and ubiquity cutoff. The second identifiable core is the minor core.  These are taxa that are ubiquitous, but at a very low abundance.

Major Core Analysis

The major core refers to the members of the microbiome that are present in a significant proportion of the population and with a significant abundance.  The Ub-Ab plot displayed below indicate the taxa that would be considered members of the major core if the cutoffs for ubiquity and abundance were set to 80% and 1%, i.e. -2=log(0.01), respectively.  This specific point is demarcated with the red bull's eye.  Taxa with curves above the red bull's eye are considered members of the core at those cutoffs.

Minor Core Analysis

The minor core refers to the members of the microbiome that are present in a majority of the cohort, but at a very low abundances. These are potentially interesting because they are ubiquitous in spite of their lower proportions in each sample. Although their contribution to the environment and why they may be successful at these low levels is still a matter of speculation, what is important at this point is the ability to detect them.

To identify the minor core, a slightly looser cutoff for ubiquity is used. In this case, the ubiquity range for the minor core is set between 50-100% of the cohort. This is demarcated by the solid blue bar on the top left of the Ub-Ab plot. Because we are interested in the low abundance taxa, the abundance cutoff is set to be less than 1%, or -2=log(0.01). The solid blue bar on the bottom left of the Ub-Ab plot represents the range of abundances constraining the minor core. To detect the minor, you can think of any taxa lines that originate from the vertical blue bar, and terminate in the horizontal blue bar, to be considered the minor core. 

 
 
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