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，并测量其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的重复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。为了测量适应性，研究人员将后代的细菌与祖先的菌株进行竞争，这些菌株被冷冻储存并复活用于这些实验。为了量化遗传进化，研究人员将对许多时间点的细菌基因组进行测序，并将其与祖先的DNA序列进行比较。这些分析将提供有关细菌进化的速率、机制、影响和可预测性的独特信息。所获得的知识将有利于科学和社会，因为细菌是环境，健康和技术的关键参与者。该实验提供了一个独特的细菌进化研究，通过从12个重复群体中产生非常长的时间序列的样品，所有这些样品都来自同一株大肠杆菌。大肠杆菌并保持在相同的环境中。研究小组将通过每天将它们转移到新鲜培养基中来繁殖种群;每500代，样品被冷冻储存，在那里它们保持活力。在接下来的十年里，这个实验将超过85,000代。冷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可重复性。需要解决的研究问题包括：进化中的细菌相对于其祖先的适应性是否会无限期地继续增加？相对适应度和基因组进化的轨迹是否具有相似的曲率，或者它们是不一致的？复制种群之间的适应度增益和基因组变化的可重复性如何？该项目产生的生物样本和数据集将与科学界分享。

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.