ArticleMolecular genetics and genomics : MGG2021
Codon usage bias and environmental adaptation in microbial organisms.
Article in Molecular genetics and genomics : MGG, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
44 citing papers in PubMed, 76 citations in OpenAlex.
- Plastome Evolution and Codon Usage Dynamics inEcology and evolution · 2026Article
- From nature to clinic: tracking genetic and environmental drivers of Stenotrophomonas maltophilia pathogenicity.Archives of microbiology · 2026Review
- Genome comparison of the bacteria in Mycobacterium avium complex (MAC) reveals the role of translational selection in shaping codon usage patterns.Molecular genetics and genomics : MGG · 2026Article
- Screen for signatures of positive selection in the core genome ofMicrobial genomics · 2026Article
- Natural Selection Drives AT-Biased Codon Usage in Mitochondrial Genomes of Early-DivergingJournal of fungi (Basel, Switzerland) · 2026Article
- Comparative analysis of complete mitogenomes of two ornamental plants Chimonanthus salicifolius and Chimonanthus praecox in the family Calycanthaceae.BMC plant biology · 2026Article
- Codon bias variation in Staphylococcus aureus.PloS one · 2026Article
- Codon usage bias and molecular evolution ofFrontiers in genetics · 2026Article
- Plastomes provide new insights into phylogeny and evolution in Chlorellaceae (Chlorophyta, Trebouxiophyceae).BMC plant biology · 2025Article
- Article
- Integrating multi-omic data to identify key genes and pathways involved in rice bacterial leaf streak disease.Scientific reports · 2025Article
- GBRAP: A Comprehensive Database and Tool for Exploring Genomic Diversity Across All Domains of Life.Molecular biology and evolution · 2025Article
- Comparative mitogenomics analysis ofFrontiers in microbiology · 2025Article
- Glacier influence shapes the genomic architecture of the downstream aquatic microbiome.ISME communications · 2025Article
- Article
- Genomic personalities ofISME communications · 2025Article
- Unravelling Prokaryotic Codon Usage: Insights from Phylogeny, Influencing Factors and Pathogenicity.Current genomics · 2025Review
- Comparative mitogenomic analysis reveals variations and evolution of ectomycorrhizal fungalIMA fungus · 2025Article
- Examining the Effects of Temperature on the Evolution of Bacterial tRNA Pools.Genome biology and evolution · 2024Article
- Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains.BMC genomics · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In each genome, synonymous codons are used with different frequencies; this general phenomenon is known as codon usage bias. It has been previously recognised that codon usage bias could affect the cellular fitness and might be associated with the ecology of microbial organisms. In this exploratory study, we investigated the relationship between codon usage bias, lifestyles (thermophiles vs. mesophiles; pathogenic vs. non-pathogenic; halophilic vs. non-halophilic; aerobic vs. anaerobic and facultative) and habitats (aquatic, terrestrial, host-associated, specialised, multiple) of 615 microbial organisms (544 bacteria and 71 archaea). Principal component analysis revealed that species with given phenotypic traits and living in similar environmental conditions have similar codon preferences, as represented by the relative synonymous codon usage (RSCU) index, and similar spectra of tRNA availability, as gauged by the tRNA gene copy number (tGCN). Moreover, by measuring the average tRNA adaptation index (tAI) for each genome, an index that can be associated with translational efficiency, we observed that organisms able to live in multiple habitats, including facultative organisms, mesophiles and pathogenic bacteria, are characterised by a reduced translational efficiency, consistently with their need to adapt to different environments. Our results show that synonymous codon choices might be under strong translational selection, which modulates the choice of the codons to differently match tRNA availability, depending on the organism's lifestyle needs. To our knowledge, this is the first large-scale study that examines the role of codon bias and translational efficiency in the adaptation of microbial organisms to the environment in which they live.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.