Terminology
Descriptive Terms
OTU: An “Operational Taxonomic Unit” is a collection of related sequences that represent an organism or group of organisms. In other words, the sequences define an OTU, the latter of which we believe to map onto a phylogenetically coherent group of organisms. Explicet views numerical OTUs as interchangeable with classification OTUs.
Metadata: Information about a collection of data (e.g., sample type, GPS coordinate, pH, patient, disease status, age, weight, etc.).
Library: A set of OTUs derived from a discrete sample/specimen.
Ecological Terms
Biodiversity: The degree of variation of life forms within a given ecosystem or biome. Biodiversity often is measured by the following indices:
Alpha Diversity: The biodiversity within a particular sample; usually expressed as OTU richness, complexity, and evenness:
Richness: The number of different OTUs in a given environment. Q: How diverse is the sample?
Complexity: Diversity indices like Shannon H and Simpson D are attempts to quantify the number of types of organisms present while simultaneously measuring how all of the organisms in a sample are distributed among the types (the evenness of the sample).
Evenness: Quantifies how equally distributed are the OTUs in a library. Q: Is there one dominant OTU, or are all OTUs present at the same relative abundance?
Rarefaction: Process that randomly resamples all libraries to the sampling depth of the smallest library (called the rarefaction point), thus allowing the alpha diversity metrics measured for a set of libraries to be compared directly.
Beta Diversity: The degree of overlap in biodiversity between two environments, or samples; involves comparing the number and/or abundance of taxa that are shared by two libraries.