Evolution of a dominant natural isolate of Escherichia coli in the human gut over the course of 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（in vitro）与体内（in vivo）进化实验，已揭示出若干细菌适应性的核心规律。然而，目前文献中鲜有关于大肠杆菌在自然环境中生存行为的相关数据。本研究通过纵向基因组研究，旨在分析一株隶属于B2系统群（B2 phylogroup）的共生优势大肠杆菌克隆ED1a在人体肠道内的进化历程。我们对一名健康个体在近一年时间内、三个不同时间点采集的24株细菌分离株进行了全基因组测序。经测算，健康人体肠道内的大肠杆菌ED1a，其染色体每年每碱基的突变率为6.90×10^-7。本研究观察到极低的基因组多样性，且未检测到任何选择作用的证据——这与相近时长实验进化中观察到的现象相悖。据此我们推测，由于ED1a已高度适应健康人体肠道环境，其进化主要以中性模式进行，且有效种群大小（effective population size, Ne）约为500至1700。