An Operational Taxonomic Unit (OTU) is an operational definition used to classify groups of closely related individuals. The term was originally introduced in 1963 by Robert R. Sokal and

Peter H. A. Sneath Peter Henry Andrews Sneath FRS, MD (17 November 1923 – September 9, 2011) was a microbiologist who co-founded the field of numerical taxonomy, together with Robert R. Sokal Robert Reuven Sokal (January 13, 1926 in Vienna, Austria – Ap ...

in the context of

numerical taxonomy Numerical taxonomy is a classification system in biological systematics which deals with the grouping by numerical methods of taxonomic units based on their character states. It aims to create a taxonomy using numeric algorithms like cluster ...

, 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 not necessarily in line with classical

Linnaean taxonomy Linnaean taxonomy can mean either of two related concepts: # The particular form of biological classification (taxonomy) set up by Carl Linnaeus, as set forth in his ''Systema Naturae'' (1735) and subsequent works. In the taxonomy of Linnaeus t ...

or modern

evolutionary taxonomy Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship (shared descent), progenitor-descendant relat ...

. Nowadays, however, the term "OTU" is commonly used in a different context and refers to clusters of (uncultivated or unknown) organisms, grouped by DNA sequence similarity of a specific taxonomic marker gene (originally coined as mOTU; molecular OTU). In other words, OTUs are pragmatic proxies for "

species In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriat ...

" (microbial or metazoan) at different taxonomic levels, in the absence of traditional systems of

biological classification In biology, taxonomy () is the scientific study of naming, defining ( circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa (singular: taxon) and these groups are give ...

as are available for macroscopic organisms. For several years, OTUs have been the most commonly used units of diversity, especially when analysing small subunit 16S (for prokaryotes) or 18S rRNA (for eukaryotes) 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; however also 100% similarity is common, also known as single variants) set by the researcher. 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. (2014) demonstrated that microbial OTUs were generally ecologically consistent across habitats and several OTU clustering approaches. The number of OTUs defined may be inflated due to errors in DNA sequencing.

OTU classification approaches

Hierarchical clustering In data mining and statistics, hierarchical clustering (also called hierarchical cluster analysis or HCA) is a method of cluster analysis that seeks to build a hierarchy of clusters. Strategies for hierarchical clustering generally fall into t ...

algorithms (HCA): uclust & cd-hit & ESPRIT * Bayesian clustering: CROP

OTU classification approaches

See also

References

Further reading