Analysis of adaptive evolution using an automated culture system of E. coli

细菌适应性进化中表型与基因型的关系尚不清楚。在本研究中，我们利用细菌细胞的实验进化，量化了在适应各种胁迫条件下的进化过程中的表型变化和遗传变化。为此，我们首先开发了一个自动培养系统，通过它我们可以维持数百个独立培养系列的细菌细胞。然后，通过使用该自动化系统，我们进行了大肠杆菌在各种应激条件下的实验进化，包括酸、洗涤剂和抗生素应激，以获得对这些应激的耐受性菌株。通过微阵列实验和下一代测序分析耐药菌株的表达变化和基因突变。结果表明，部分适应性表型变化不能用固定的基因突变来解释，这表明一种未知的非遗传机制在适应性进化的动力学中起作用。

Phenotype-genotype relationship in bacterial adaptive evolution still remains unclear. In this study, by using experimental evolution of bacterial cells, we quantified phenotypic change and genetic change during adaptive evolution to various stress conditions. For this purpose, first we developed an automated culture system by which we can maintain hundreds of independent culture series of bacterial cells. Then, by using this automated system, we performed experimental evolution of E. coli under various stress conditions, including acid, detergent, and antibiotic stresses, to obtain tolerant strains for these stresses. Expression changes and genetic mutations in the tolerant strains were analyzed by microarray experiments and next-gen sequencers, respectively. The results demonstrated that a part of adaptive phenotypic changes cannot be explained by fixed genetic mutations, suggesting that an unknown non-genetic mechanism plays a role in the dynamics of adaptive evolution.