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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.^[1] It is the most commonly used microbial diversity unit, especially when analyzing the small subunit 16S or 18S rRNA marker gene microbial datasets. ^[2]

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.^[3]

OTU classification approaches

hierarchical clustering algorithms (HCA): uclust^[4] & cd-hit^[5] & ESPRIT^[6]

"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:^[7]

The number of OTUs defined may be inflated due to errors in DNA sequencing.^[8]

References

^ Blaxter, M.; Mann, J.; Chapman, T.; Thomas, F.; Whitton, C.; Floyd, R.; Abebe, E. (Oct 2005). "Defining operational taxonomic units using DNA barcode data". Philos Trans R Soc Lond B Biol Sci. 360 (1462): 1935–43. doi:10.1098/rstb.2005.1725. PMC 1609233. PMID 16214751.
^ "Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units". March 2013. {{cite journal}}: Cite journal requires |journal= (help)
^ Schmidt, Thomas S. B.; Rodrigues, João F. Matias; Mering, Christian von (24 April 2014). "Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale". PLOS Comput Biol. 10 (4): e1003594. doi:10.1371/journal.pcbi.1003594. ISSN 1553-7358.{{cite journal}}: CS1 maint: unflagged free DOI (link)
^ Edgar, Robert C. (1 October 2010). "Search and clustering orders of magnitude faster than BLAST". Bioinformatics. 26 (19): 2460–2461. doi:10.1093/bioinformatics/btq461. ISSN 1367-4803.
^ Fu, Limin; Niu, Beifang; Zhu, Zhengwei; Wu, Sitao; Li, Weizhong (1 December 2012). "CD-HIT: accelerated for clustering the next-generation sequencing data". Bioinformatics. 28 (23): 3150–3152. doi:10.1093/bioinformatics/bts565. ISSN 1367-4803.
^ Fu, Limin; Niu, Beifang; Zhu, Zhengwei; Wu, Sitao; Li, Weizhong (1 December 2012). "CD-HIT: accelerated for clustering the next-generation sequencing data". Bioinformatics. 28 (23): 3150–3152. doi:10.1093/bioinformatics/bts565. ISSN 1367-4803.
^ Wooley, John C. "A Primer on Metagenomics". PLOS Computational Biology. Retrieved 14 November 2012.
^ Kunin, V.; Engelbrektson, A.; Ochman, H.; Hugenholtz, P. (Jan 2010). "Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates". Environ Microbiol. 12 (1): 118–23. doi:10.1111/j.1462-2920.2009.02051.x. PMID 19725865.

Category:Genomics

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[Blaxter-2005-1] Blaxter, M.; Mann, J.; Chapman, T.; Thomas, F.; Whitton, C.; Floyd, R.; Abebe, E. (Oct 2005). "Defining operational taxonomic units using DNA barcode data". Philos Trans R Soc Lond B Biol Sci. 360 (1462): 1935–43. doi:10.1098/rstb.2005.1725. PMC 1609233. PMID 16214751.

[2] "Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units". March 2013. {{cite journal}}: Cite journal requires |journal= (help)

[3] Schmidt, Thomas S. B.; Rodrigues, João F. Matias; Mering, Christian von (24 April 2014). "Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale". PLOS Comput Biol. 10 (4): e1003594. doi:10.1371/journal.pcbi.1003594. ISSN 1553-7358.{{cite journal}}: CS1 maint: unflagged free DOI (link)

[4] Edgar, Robert C. (1 October 2010). "Search and clustering orders of magnitude faster than BLAST". Bioinformatics. 26 (19): 2460–2461. doi:10.1093/bioinformatics/btq461. ISSN 1367-4803.

[5] Fu, Limin; Niu, Beifang; Zhu, Zhengwei; Wu, Sitao; Li, Weizhong (1 December 2012). "CD-HIT: accelerated for clustering the next-generation sequencing data". Bioinformatics. 28 (23): 3150–3152. doi:10.1093/bioinformatics/bts565. ISSN 1367-4803.

[6] Fu, Limin; Niu, Beifang; Zhu, Zhengwei; Wu, Sitao; Li, Weizhong (1 December 2012). "CD-HIT: accelerated for clustering the next-generation sequencing data". Bioinformatics. 28 (23): 3150–3152. doi:10.1093/bioinformatics/bts565. ISSN 1367-4803.

[7] Wooley, John C. "A Primer on Metagenomics". PLOS Computational Biology. Retrieved 14 November 2012.

[Kunin-2010-8] Kunin, V.; Engelbrektson, A.; Ochman, H.; Hugenholtz, P. (Jan 2010). "Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates". Environ Microbiol. 12 (1): 118–23. doi:10.1111/j.1462-2920.2009.02051.x. PMID 19725865.

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OTU classification approaches

See also

References