LTREB: The long-term evolution experiment with Escherichia coli

细菌在许多环境过程、人类健康和疾病以及生物技术中发挥着关键作用。因此，重要的是要了解细菌随时间变化的过程，并测量它们的基因和生态功能的变化率。密歇根州立大学的研究人员将研究大肠杆菌复制实验种群的进化变化，因为它们在受控的实验室环境中进化了数千代细菌。为了衡量适应情况，研究人员将后代的细菌与祖先的菌株进行竞争，祖先的菌株被冷冻保存并为这些实验复活。为了量化遗传进化，研究人员将对多个时间点的细菌基因组进行排序，并将它们与祖先的DNA序列进行比较。这些分析将提供有关细菌进化的速度、机制、影响和可预测性的独特信息。所获得的知识将使科学和社会受益，因为细菌是环境、健康和技术的关键参与者。这个实验通过产生来自12个重复种群的超长时间序列的样本，提供了一种独特的细菌进化研究，这些样本都是从相同的大肠杆菌菌株建立的，并在相同的环境中保持。研究小组将通过每天将它们转移到新鲜的介质中来繁殖种群；每500代，样本被冷冻储存，在那里它们仍然活着。在接下来的十年里，这项实验将超过8.5万代。冰冻样本将用于分析自然选择的适应动态，表型和遗传进化的耦合，以及进化变化的重复性。有待解决的研究问题包括：进化中的细菌相对于其祖先的适合度是否会继续无限期地增加？相对适合度和基因组进化的轨迹是相似的曲线，还是不协调的？在复制种群中，适合度的提高和基因组变化的可重复性如何？该项目中产生的生物样本和数据集将与科学界共享。

Bacteria play critical roles in many environmental processes, in human health and disease, and in biotechnology. It is important, therefore, to understand the processes by which bacteria change over time, and to measure the rates of change in their genes and ecological functions. Reseachers at Michigan State University will study evolutionary changes in replicate experimental populations of the bacteria species Escherichia coli, as they evolve in a controlled laboratory environment for thousands of bacterial generations. To measure adaptation, the researchers place the bacteria from later generations in competition with the ancestral strain, which is stored frozen and revived for these experiments. To quantify genetic evolution, the researchers will sequence the genomes of bacteria from many time points and compare them to the ancestor's DNA sequence. These analyses will provide unique information about the rates, mechanisms, effects, and predictability of bacterial evolution. The knowledge gained will benefit both science and society because bacteria are key players in the environment, health, and technology. This experiment provides a unique study of bacterial evolution by generating exceptionally long time-series of samples from 12 replicate populations, all founded from the same strain of E. coli and maintained in identical environments. The research team will propagate the populations by transferring them every day into fresh medium; every 500 generations, samples are stored frozen, where they remain viable. Over the next decade, the experiment will surpass 85,000 generations. The frozen samples will be used to analyze the dynamics of adaptation by natural selection, the coupling of phenotypic and genetic evolution, and the repeatability of evolutionary changes. Research questions to be addressed include: Will the fitness of the evolving bacteria relative to their ancestor continue to increase indefinitely? Do the trajectories for relative fitness and genomic evolution have similar curvatures, or are they discordant? How repeatable are fitness gains and genomic changes across replicate populations? The biological samples and datasets generated in this project will be shared with the scientific community.