ArticleNucleic acids research2013
Environmental shaping of codon usage and functional adaptation across microbial communities.
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 30 papers.
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Who cites it
30 citing papers in PubMed.
- Patterns and drivers of genome-wide codon usage bias in the fungal order Sordariales.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- The mitogenome of a swimming-behavior file shell reveals the phylogenetic relationships of Limida (Bivalvia: Pteriomorphia).Molecular biology reports · 2025Article
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- Codon usage bias in yeasts and its correlation with gene expression, growth temperature, and protein structure.Frontiers in microbiology · 2024Article
- Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis.NPJ biofilms and microbiomes · 2023Article
- Selection for Translational Efficiency in Genes Associated with Alphaproteobacterial Gene Transfer Agents.mSystems · 2022Article
- Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics.mSystems · 2022Article
- Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution.Molecular biology and evolution · 2022Article
- The Dynamic Codon Biaser: calculating prokaryotic codon usage biases.Microbial genomics · 2021Article
- Codon usage bias and environmental adaptation in microbial organisms.Molecular genetics and genomics : MGG · 2021Article
- Signatures of optimal codon usage in metabolic genes inform budding yeast ecology.PLoS biology · 2021Article
- Distinct Functions and Assembly Mechanisms of Soil Abundant and Rare Bacterial Taxa Under Increasing Pyrene Stresses.Frontiers in microbiology · 2021Article
- Building genomes to understand biology.Nature communications · 2020Review
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- Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code.Bioinformatics (Oxford, England) · 2018Article
- The evolutionary signal in metagenome phyletic profiles predicts many gene functions.Microbiome · 2018Article
- Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium.PloS one · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Microbial communities represent the largest portion of the Earth's biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the biosphere. Metagenome studies are generally based on (i) classifying and ranking functions of identified genes; and (ii) estimating the phyletic distribution of constituent microbial species. To understand microbial communities at the systems level, it is necessary to extend these studies beyond the species' boundaries and capture higher levels of metabolic complexity. We evaluated 11 metagenome samples and demonstrated that microbes inhabiting the same ecological niche share common preferences for synonymous codons, regardless of their phylogeny. By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifestyle-specific genes across the entire microbial community, effectively considering microbial communities as meta-genomes. These findings set up a 'functional metagenomics' platform for the identification of genes relevant for adaptations of entire microbial communities to environments. Our results provide valuable arguments in defining the concept of microbial species through the context of their interactions within the community.
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Registered trials
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