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.

在每个基因组中，同义密码子的使用频率不同；这种普遍现象被称为密码子使用偏差。此前人们已经认识到密码子使用偏差可能会影响细胞的适应性，并且可能与微生物有机体的生态有关。在这项探索性研究中，我们调查了密码子使用偏差、生活方式（嗜热菌与嗜温菌；致病性与非致病性；嗜盐与非嗜盐；需氧与厌氧和兼性）和栖息地（水生、陆生、宿主）之间的关系。 - 615 种微生物（544 种细菌和 71 种古生菌）的相关、专门、多重）。主成分分析表明，具有给定表型性状并生活在相似环境条件下的物种具有相似的密码子偏好（以相对同义密码子使用（RSCU）指数表示），以及相似的 tRNA 可用性谱（以 tRNA 基因拷贝数衡量）（ tGCN）。此外，通过测量每个基因组的平均 tRNA 适应指数（tAI）（该指数与翻译效率相关），我们观察到能够生活在多种栖息地的生物体，包括兼性生物体、嗜温菌和病原菌，其特征是翻译效率降低，这与他们适应不同环境的需要一致。我们的结果表明，同义密码子的选择可能受到强翻译选择的影响，这会根据生物体的生活方式需求调节密码子的选择，以不同方式匹配 tRNA 的可用性。据我们所知，这是第一项大规模研究，探讨密码子偏倚和翻译效率在微生物适应其生存环境中的作用。