Table 1 Glossary of microbial analysis terms.

Phylogeny

The evolution of a group of organisms relative to a common ancestor based on genetics, represented as a tree diagram with nodes (points of genetic divergence or speciation), branches (descendants of a common ancestor), and tips (individual species)

Taxonomy

The classification of a group of organisms relative to other groups or individual organisms based on shared characteristics (e.g., target sequence similarity)

Richness

The total number of organisms in a sample measured as a count of unique sequences (e.g., number of distinct features)

Evenness

The relative distribution of organisms in a sample measured as a function of unique sequences and counts of each unique sequence (e.g., Pielou’s evenness index \(J\)’)

Alpha-diversity

Variance within a single sample described as a metric of either species richness, evenness, or both (diversity, e.g. Shannon’s diversity index \(H\)’)

Beta-diversity

Variance in communities between multiple samples represented as a matrix of scores that quantify each individual sample’s similarity or dissimilarity when compared to all other samples in a population of interest