Alpha and beta diversity
Alpha diversity
Variation of microbes in a single sample
Species richness "How many microbes?"
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:
→ DADA2 (QIIME-2) amplicon sequence variant (ASV) count
→ QIIME-1 sequence clusters, OTU count
Species diversity "How are the microbes balanced to each other?"
Do we have species evenness (equal abundance) or do some species dominate others?
Species diversity tells us how evenly the microbes are distributed in a sample.
Shannon diversity index combines richness and diversity. It measures both the number of species and the inequality between species abundances. A large value is given by the presence of many species with well balanced abundances. Values can range from one (in case of a single dominant species) to the total number of all species (in case of all species having equal abundance).
Shannon evenness index (Shannon's equitability index) is a pure diversity index, independent of species richness. It measures how evenly the microbes are distributed in a sample without considering the number of species. Values can range from zero to one: from high dominance of a single species to perfectly equal abundances across all species.
Beta diversity
Variation of microbial communities 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)
Software tools
for calculating alpha and beta diversity
→ 16S sequencing: alpha & beta using QIIME
read more
http://www.tiem.utk.edu/~gross/bioed/bealsmodules/shannonDI.html
https://methodsblog.wordpress.com/2015/05/27/beta_diversity/
http://blog.metagenomics.anl.gov/less-frequently-asked-questions/
http://cnx.org/contents/t8i_eHU4@2/Alpha-Beta-and-Gamma-Diversity