Data from: Evolution of a dominant natural isolate of Escherichia coli in the human gut over a year suggests a neutral evolution with reduced effective population size

In vitro and in vivo evolution experiments on Escherichia coli revealed several principles of bacterial adaptation. However, few data are available in the literature describing the behavior of E. coli in its natural environment. We attempted here to study the evolution in the human gut of a commensal dominant E. coli clone ED1a belonging to B2 phylogroup, through a longitudinal genomic study. We sequenced 24 isolates sampled at three different time points within a healthy individual over almost a year. We computed amutation rate of 6.90x10-7 per base per year of the chromosome for E. coli ED1a in healthy human gut. We observed a very limited genomic diversity, and could not detect any evidence of selection contrary to what is observed in experimental evolution over similar length of time. We therefore suggest that ED1a being well adapted to the healthy human gut evolves mostly neutrally with a low effective population size (Ne ≈ 500 – 1700).

针对大肠杆菌（Escherichia coli）开展的体外与体内进化实验，已揭示出多项细菌适应性演化的核心规律。然而，现有学术文献中鲜有关于大肠杆菌在其自然生境中行为特征的相关研究数据。本研究借助纵向基因组学分析策略，对一株隶属于B2系统发育群的共生优势大肠杆菌克隆株ED1a在人体肠道内的演化过程展开探究。我们对一名健康个体在近一年内的三个不同时间点采集的24株菌株分离物完成了全基因组测序。经计算，健康人体肠道内的大肠杆菌ED1a，其染色体的年碱基突变率为6.90×10^-7每碱基每年。本研究观测到该菌株的基因组多样性极低，且未检测到任何选择作用的相关证据——这与相近时长的实验进化研究中观测到的结果完全相悖。据此我们推测，由于ED1a已高度适配健康人体肠道环境，其演化过程主要以中性演化模式为主，且有效种群大小（effective population size, Ne ≈ 500~1700）较低。