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An operational taxonomic unit (OTU) is an operational definition used to classify groups of closely related individuals. This unit is especially useful when only DNA sequence data is available. It is the most commonly used microbial diversity unit, especially when analyzing the small subunit 16S or 18S rRNA marker gene microbial 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. 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.

OTU classification approaches

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

"Taxonomic level of sampling selected by the user to be used in a study, such as individuals, populations, species, genera, or bacterial strains."

Another definition:

The number of OTUs defined may be inflated due to errors in DNA sequencing.