Shen Zhi Yong, Koh Xiu Pei, Yu Yan Ping, Lau Stanley C K
Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
Division of Environment and Sustainability, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
Microorganisms. 2020 Oct 31;8(11):1713. doi: 10.3390/microorganisms8111713.
The evolution, habitat, and lifestyle of the cryptic clade II of , which were first recovered at low frequency from non-human hosts and later from external environments, were poorly understood. Here, the genomes of selected strains were analyzed for preliminary indications of ecological differentiation within their population. We adopted the delta bitscore metrics to detect functional divergence of their orthologous genes and trained a random forest classifier to differentiate the genomes according to habitats (gastrointestinal vs external environment). Model was built with inclusion of other genomes previously demonstrated to have exhibited genomic traits of adaptation to one of the habitats. Overall, gene degradation was more prominent in the gastrointestinal strains. The trained model correctly classified the genomes, identifying a set of predictor genes that were informative of habitat association. Functional divergence in many of these genes were reflective of ecological divergence. Accuracy of the trained model was confirmed by its correct prediction of the habitats of an independent set of strains with known habitat association. In summary, the cryptic clade II of Escherichia displayed genomic signatures that are consistent with divergent adaptation to gastrointestinal and external environments.
最初在非人类宿主中低频发现、后来又在外部环境中发现的隐秘进化枝II的进化、栖息地和生活方式鲜为人知。在此，对选定菌株的基因组进行了分析，以初步了解其种群内生态分化的迹象。我们采用delta比特分数指标来检测其直系同源基因的功能差异，并训练了一个随机森林分类器，根据栖息地（胃肠道与外部环境）对基因组进行区分。构建模型时纳入了先前已证明表现出适应其中一种栖息地基因组特征的其他基因组。总体而言，胃肠道菌株中的基因降解更为明显。经过训练的模型正确地对基因组进行了分类，识别出一组有助于判断栖息地关联的预测基因。其中许多基因的功能差异反映了生态差异。通过正确预测一组已知栖息地关联的独立菌株的栖息地，证实了经过训练的模型的准确性。总之，大肠杆菌的隐秘进化枝II显示出与胃肠道和外部环境的不同适应性相一致的基因组特征。
