Chapter 12: Human Microbiome Analysis
Figure 2
Ecological representations of microbial communities: collector's curves, alpha, and beta diversity.
These examples describe the A) sequence counts and B) relative abundances of six taxa (A, B, C, D, E, and F) detected in three samples. C) A collector's curve, typically generated using a richness estimator such as Chao1 [28] or ACE [29], approximates the relationship between the number of sequences drawn from each sample and the number of taxa expected to be present based on detected abundances. D) Alpha diversity captures both the organismal richness of a sample and the evenness of the organisms' abundance distribution. Here, alpha diversity is defined by the Shannon index [32], , where pi is the relative abundance of taxon i, although many other alpha diversity indices may be employed. E) Beta diversity represents the similarity (or difference) in organismal composition between samples. In this example, it can be simplistically defined by the equation
, where n1 and n2 are the number of taxa in samples 1 and 2, respectively, and c is the number of shared taxa, but again many metrics such as Bray-Curtis [34] or UniFrac [24] are commonly employed.