ArticlePLoS computational biology2014
Ecological consistency of SSU rRNA-based operational taxonomic units at a global scale.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 2 of them syntheses that pooled it.
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Who cites it
38 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Microbiome of the paranasal sinuses: Update and literature review.American journal of rhinology & allergyPooled it
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- The coral microbiome in sickness, in health and in a changing world.Nature reviews. Microbiology · 2024Review
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- Nuclear Magnetic Resonance Metabolomics of Symbioses between Bacterial Vaginosis-Associated Bacteria.mSphere · 2022Article
- The Intestinal Microbiota May Be a Potential Theranostic Tool for Personalized Medicine.Journal of personalized medicine · 2022Review
- Improving Taxonomic Delimitation of Fungal Species in the Age of Genomics and Phenomics.Frontiers in microbiology · 2022Review
- Microbiome Preprocessing Machine Learning Pipeline.Frontiers in immunology · 2021Article
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- Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota.Microorganisms · 2020Article
- Assessment of bacterial diversity of Rhipicephalus microplus ticks from two livestock agroecosystems in Antioquia, Colombia.PloS one · 2020Article
- The concept of operational taxonomic units revisited: genomes of bacteria that are regarded as closely related are often highly dissimilar.Folia microbiologica · 2019Article
- Application of Machine Learning in Microbiology.Frontiers in microbiology · 2019Review
- Current insights into fungal species diversity and perspective on naming the environmental DNA sequences of fungi.Mycology · 2019Review
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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