ArticleThe ISME journal2016
Predicting microbial traits with phylogenies.
Article in The ISME journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
67 citing papers in PubMed.
- High phylogenetic turnover magnifies evolutionary relatedness along bacterial primary succession.Ecology · 2026Article
- Life strategies of bacterial taxa in rearing water microbiomes of whiteleg shrimp (Litopenaeus vannamei) larviculture.World journal of microbiology & biotechnology · 2026Article
- Article
- Community conservatism is widespread across microbial phyla and environments.Nature ecology & evolution · 2026Article
- Constructing a "periodic table" of bacteria to map diversity in trait space.The ISME journal · 2026Article
- Distribution patterns and community assembly processes of generalists and specialists in river affected by wastewater discharge from distilleries in typical Chinese spirits production area in China.Frontiers in microbiology · 2026Article
- Relative abundances of bacterial phyla are strong indicators of community-scale microbial growth rates in soil.Environmental microbiome · 2025Article
- Improved maximum growth rate prediction from microbial genomes by integrating phylogenetic information.Nature communications · 2025Article
- Trait-Based Life History Strategies Shape Bacterial Niche Breadth.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Tiny but mighty? Overview of a decade of research on nectar bacteria.The New phytologist · 2025Review
- The Role of Phenotypic Plasticity and Within-Environment Trait Variability in the Assembly of the Nectar Microbiome and Plant-Microbe-Animal Interactions.Ecology and evolution · 2025Review
- Coupling between bacterial phylogenetic diversity and heterotrophic productivity in a coastal ecosystem affected by estuarine plumes.ISME communications · 2025Article
- Predicting gene distribution in ammonia-oxidizing archaea using phylogenetic signals.ISME communications · 2025Article
- Fusion/fission protein family identification in Archaea.mSystems · 2024Article
- Planktonic eukaryotes in the Chesapeake Bay: contrasting responses of abundant and rare taxa to estuarine gradients.Microbiology spectrum · 2024Article
- Article
- A bacterial sensor taxonomy across earth ecosystems for machine learning applications.mSystems · 2024Article
- Leveraging genomic information to predict environmental preferences of bacteria.The ISME journal · 2024Review
- Neglected role of microelements in determining soil microbial communities and fruit micronutrients in loquat orchards.Frontiers in microbiology · 2024Article
- Predictability of the community-function landscape in wine yeast ecosystems.Molecular systems biology · 2023Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phylogeny reflects genetic and phenotypic traits in Bacteria and Archaea. The phylogenetic conservatism of microbial traits has prompted the application of phylogeny-based algorithms to predict unknown trait values of extant taxa based on the traits of their evolutionary relatives to estimate, for instance, rRNA gene copy numbers, gene contents or tolerance to abiotic conditions. Unlike the 'macrobial' world, microbial ecologists face scenarios potentially compromising the accuracy of trait reconstruction methods, as, for example, extremely large phylogenies and limited information on the traits of interest. We review 990 bacterial and archaeal traits from the literature and support that phylogenetic trait conservatism is widespread through the tree of life, while revealing that it is generally weak for ecologically relevant phenotypic traits and high for genetically complex traits. We then perform a simulation exercise to assess the accuracy of phylogeny-based trait predictions in common scenarios faced by microbial ecologists. Our simulations show that ca. 60% of the variation in phylogeny-based trait predictions depends on the magnitude of the trait conservatism, the number of species in the tree, the proportion of species with unknown trait values and the mean distance in the tree to the nearest neighbour with a known trait value. Results are similar for both binary and continuous traits. We discuss these results under the light of the reviewed traits and provide recommendations for the use of phylogeny-based trait predictions for microbial ecologists.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.