ArticleNucleic acids research2013
Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers, 1 of them a synthesis that pooled it.
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Who cites it
56 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units.Scientific reports · 2018Pooled it
- Pruning the Tree: Comparing OTUs and ASVs in High-Throughput Sequencing of 5S-IGS Nuclear Ribosomal DNA in Phylogenetic Studies.Ecology and evolution · 2025Article
- Maximizing Identification Precision of Hymenoptera and Brachycera (Diptera) With a Non-Destructive DNA Metabarcoding Approach.Ecology and evolution · 2025Article
- Microdiversity and fine-scale niche differentiation support persistence and coexistence of acidophiles in acid mine drainage.Frontiers in microbiology · 2025Article
- Accurately clustering biological sequences in linear time by relatedness sorting.Nature communications · 2024Article
- Microdiversity sustains the distribution of rhizosphere-associated bacterial species from the root surface to the bulk soil region in maize crop fields.Frontiers in plant science · 2023Article
- Probiotic and postbiotic analytical methods: a perspective of available enumeration techniques.Frontiers in microbiology · 2023Review
- Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method.mSphere · 2022Article
- Taxonomy Informed Clustering, an Optimized Method for Purer and More Informative Clusters in Diversity Analysis and Microbiome Profiling.Frontiers in bioinformatics · 2022Article
- Bacterioplankton Zonation Does Exist in High Elevation, Polymictic Lakes.Frontiers in microbiology · 2022Article
- RESCRIPt: Reproducible sequence taxonomy reference database management.PLoS computational biology · 2021Article
- Genome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild Drosophila Gut Microbiome.Genome biology and evolution · 2021Article
- Diversity and Ecology of Chlorophyta (Viridiplantae) Assemblages in Protected and Non-protected Sites in Deception Island (Antarctica, South Shetland Islands) Assessed Using an NGS Approach.Microbial ecology · 2021Article
- Abundance-Occupancy Relationships Along Taxonomic Ranks Reveal a Consistency of Niche Differentiation in Marine Bacterioplankton With Distinct Lifestyles.Frontiers in microbiology · 2021Article
- Application of Deep Learning in Plant-Microbiota Association Analysis.Frontiers in genetics · 2021Review
- Microbial Community Field Surveys Reveal AbundantFrontiers in microbiology · 2021Article
- How can microbial population genomics inform community ecology?Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Review
- Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions.The ISME journal · 2019Article
- The Role of Pseudomonas in Heterotrophic Nitrification: A Case Study on Shrimp Ponds (Microorganisms · 2019Article
- Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The lack of a consensus bacterial species concept greatly hampers our ability to understand and organize bacterial diversity. Operational taxonomic units (OTUs), which are clustered on the basis of DNA sequence identity alone, are the most commonly used microbial diversity unit. Although it is understood that OTUs can be phylogenetically incoherent, the degree and the extent of the phylogenetic inconsistency have not been explicitly studied. Here, we tested the phylogenetic signal of OTUs in a broad range of bacterial genera from various phyla. Strikingly, we found that very few OTUs were monophyletic, and many showed evidence of multiple independent origins. Using previously established bacterial habitats as benchmarks, we showed that OTUs frequently spanned multiple ecological habitats. We demonstrated that ecological heterogeneity within OTUs is caused by their phylogenetic inconsistency, and not merely due to 'lumping' of taxa resulting from using relaxed identity cut-offs. We argue that ecotypes, as described by the Stable Ecotype Model, are phylogenetically and ecologically more consistent than OTUs and therefore could serve as an alternative unit for bacterial diversity studies. In addition, we introduce QuickES, a new wrapper program for the Ecotype Simulation algorithm, which is capable of demarcating ecotypes in data sets with tens of thousands of sequences.
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Registered trials
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