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Alpha and beta diversity

Alpha diversity

Species richness (OTU count)  "How many?"
How many different species could be detected in a microbial ecosystem?
Species richness is the number of different species in a sample.
Practically, we count the number of distinguishable taxa:

Species diversity (Shannon index)  "How different?"
How are the microbes balanced to each other? Do we have species evenness (similar abundance level) or do some species dominate others?
Shannon index measures how evenly the microbes are distributed in a sample.

Beta diversity

How different is the microbial composition in one environment compared to another?
Beta diversity shows the different between microbial communities from different environments. Main focus is on the difference in taxonomic abundance profiles from different samples.

Bray–Curtis dissimilarity
- based on abundance or read count data
- differences in microbial abundances between two samples (e.g., at species level)
    values are from 0 to 1
    0 means both samples share the same species at exact the same abundances
    1 means both samples have complete different species abundances

Jaccard distance
- based on presence or absence of species (does not include abundance information)
- different in microbial composition between two samples
    0 means both samples share exact the same species
    1 means both samples have no species in common

- sequence distances (phylogenetic tree)
- based on the fraction of branch length that is shared between two samples or unique to one or the other sample
unweighted UniFrac: purely based on sequence distances (does not include abundance information)
weighted UniFrac: branch lengths are weighted by relative abundances (includes both sequence and abundance information)

Software tools

for calculating alpha and beta diversity