Operational taxonomic unit

An operational taxonomic unit (OTU) is an operational definition used to classify groups of closely related individuals. The term was originally introduced by Robert R. Sokal & Peter H. A. Sneath in the context of Numerical taxonomy, where an "Operational Taxonomic Unit" is simply the group of organisms currently being studied. In this sense, an OTU is a pragmatic definition to group individuals by similarity, equivalent to but necessarily in line with classical Linnaean taxonomy or modern Evolutionary taxonomy.

Nowadays, however, the term "OTU" is generally used in a different context and refers to clusters of (uncultivated or unknown) microorganisms, grouped by DNA sequence similarity of a specific taxonomic marker gene. In other words, OTUs are pragmatic proxies for microbial "species" at different taxonomic levels, in the absence of traditional systems of biological classification as are available for macroscopic organisms. For several years, OTUs have been the most commonly used units of microbial diversity, especially when analysing small subunit 16S or 18S rRNA marker gene sequence datasets.

Sequences can be clustered according to their similarity to one another, and operational taxonomic units are defined based on the similarity threshold (usually 97% similarity) set by the researcher. Typically, OTU's are based on similar 16S rDNA sequences. It remains debatable how well this commonly-used method recapitulates true microbial species phylogeny or ecology. Although OTUs can be calculated differently when using different algorithms or thresholds, recent research by Schmidt et al. demonstrated that microbial OTUs were generally ecologically consistent across habitats and several OTU clustering approaches.