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Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale
Operational Taxonomic Units (OTUs), usually defined as clusters of similar 16S/18S rRNA sequences, are the most widely used basic diversity units in large-scale characterizations of microbial communities. However, it remains unclear how well the various proposed OTU clustering algorithms approximate...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998914/ https://www.ncbi.nlm.nih.gov/pubmed/24763141 http://dx.doi.org/10.1371/journal.pcbi.1003594 |
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author | Schmidt, Thomas S. B. Matias Rodrigues, João F. von Mering, Christian |
author_facet | Schmidt, Thomas S. B. Matias Rodrigues, João F. von Mering, Christian |
author_sort | Schmidt, Thomas S. B. |
collection | PubMed |
description | Operational Taxonomic Units (OTUs), usually defined as clusters of similar 16S/18S rRNA sequences, are the most widely used basic diversity units in large-scale characterizations of microbial communities. However, it remains unclear how well the various proposed OTU clustering algorithms approximate ‘true’ microbial taxa. Here, we explore the ecological consistency of OTUs – based on the assumption that, like true microbial taxa, they should show measurable habitat preferences (niche conservatism). In a global and comprehensive survey of available microbial sequence data, we systematically parse sequence annotations to obtain broad ecological descriptions of sampling sites. Based on these, we observe that sequence-based microbial OTUs generally show high levels of ecological consistency. However, different OTU clustering methods result in marked differences in the strength of this signal. Assuming that ecological consistency can serve as an objective external benchmark for cluster quality, we conclude that hierarchical complete linkage clustering, which provided the most ecologically consistent partitions, should be the default choice for OTU clustering. To our knowledge, this is the first approach to assess cluster quality using an external, biologically meaningful parameter as a benchmark, on a global scale. |
format | Online Article Text |
id | pubmed-3998914 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-39989142014-04-29 Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale Schmidt, Thomas S. B. Matias Rodrigues, João F. von Mering, Christian PLoS Comput Biol Research Article Operational Taxonomic Units (OTUs), usually defined as clusters of similar 16S/18S rRNA sequences, are the most widely used basic diversity units in large-scale characterizations of microbial communities. However, it remains unclear how well the various proposed OTU clustering algorithms approximate ‘true’ microbial taxa. Here, we explore the ecological consistency of OTUs – based on the assumption that, like true microbial taxa, they should show measurable habitat preferences (niche conservatism). In a global and comprehensive survey of available microbial sequence data, we systematically parse sequence annotations to obtain broad ecological descriptions of sampling sites. Based on these, we observe that sequence-based microbial OTUs generally show high levels of ecological consistency. However, different OTU clustering methods result in marked differences in the strength of this signal. Assuming that ecological consistency can serve as an objective external benchmark for cluster quality, we conclude that hierarchical complete linkage clustering, which provided the most ecologically consistent partitions, should be the default choice for OTU clustering. To our knowledge, this is the first approach to assess cluster quality using an external, biologically meaningful parameter as a benchmark, on a global scale. Public Library of Science 2014-04-24 /pmc/articles/PMC3998914/ /pubmed/24763141 http://dx.doi.org/10.1371/journal.pcbi.1003594 Text en © 2014 Schmidt et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Schmidt, Thomas S. B. Matias Rodrigues, João F. von Mering, Christian Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale |
title | Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale |
title_full | Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale |
title_fullStr | Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale |
title_full_unstemmed | Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale |
title_short | Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale |
title_sort | ecological consistency of ssu rrna-based operational taxonomic units at a global scale |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998914/ https://www.ncbi.nlm.nih.gov/pubmed/24763141 http://dx.doi.org/10.1371/journal.pcbi.1003594 |
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