Do the total number of microbes differ between samples?
How many different species are present in a microbial ecosystem?
Species richness is the number of different species in a sample.
Instead counting observed taxa (OTU or ASV counts), we better use methods to estimate the true richness (adjusted for species below detection limit).
Chao1 estimates true species richness based on the observed least abundant taxa.
Do we have many species of nearly equal abundance? Or do some species dominate others?
Species diversity tells us not only total numbers, but also how equally the microbes are distributed in a sample.
Shannon diversity index combines richness and evenness. It measures both the number of species and the inequality between species abundances. A large value is given by the presence of many species that show well balanced abundances.
Do the proportions of individual species differ between samples?
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
UniFrac
- 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)
for calculating alpha and beta diversity
https://methodsblog.wordpress.com/2015/05/27/beta_diversity/
Entropy, information theory (Shannon diversity index)
https://towardsdatascience.com/understanding-entropy-2ee52b387f8c