Escherichia coli is mostly a commensal of birds and mammals, including humans, where it can act as an opportunistic pathogen. It is also found in water and sediments. We investigated the phylogeny, genetic diversification, and habitat-association of 1,294 isolates representative of the phylogenetic diversity of more than 5,000 isolates from the Australian continent. Since many previous studies focused on clinical isolates, we investigated mostly other isolates originating from humans, poultry, wild animals and water. These strains represent the species genetic diversity and reveal widespread associations between phylogroups and isolation sources. The analysis of strains from the same sequence types revealed very rapid change of gene repertoires in the very early stages of divergence, driven by the acquisition of many different types of mobile genetic elements. These elements also lead to rapid variations in genome size, even if few of their genes rise to high frequency in the species. Variations in genome size are associated with phylogroup and isolation sources, but the latter determine the number of MGEs, a marker of recent transfer, suggesting that gene flow reinforces the association of certain genetic backgrounds with specific habitats. After a while, the divergence of gene repertoires becomes linear with phylogenetic distance, presumably reflecting the continuous turnover of mobile element and the occasional acquisition of adaptive genes. Surprisingly, the phylogroups with smallest genomes have the highest rates of gene repertoire diversification and fewer but more diverse mobile genetic elements. This suggests that smaller genomes are associated with higher, not lower, turnover of genetic information. Many of these genomes are from freshwater isolates and have peculiar traits, including a specific capsule, suggesting adaptation to this environment. Altogether, these data contribute to explain why epidemiological clones tend to emerge from specific phylogenetic groups in the presence of pervasive horizontal gene transfer across the species.

大肠杆菌它主要是鸟类和哺乳动物（包括人类）的代名词，在这里它可以作为机会病原体。它也存在于水和沉积物中。我们调查了1,294个分离株的系统发育，遗传多样性和栖息地关联，这些分离株代表了来自澳大利亚大陆的5,000多个分离株的系统发育多样性。由于先前的许多研究都集中在临床分离株上，因此我们主要调查了其他源自人类，家禽，野生动物和水的分离株。这些菌株代表物种的遗传多样性，并揭示出种群与隔离源之间的广泛关联。对来自相同序列类型的菌株的分析显示，在趋异的非常早期，由于获得了许多不同类型的移动遗传元件，基因库的变化非常快。这些元素也导致基因组大小的快速变化，即使它们中的极少数基因在物种中升高为高频。基因组大小的变化与种系和隔离源有关，但后者决定了MGE的数量，MGE是最近转移的标志，表明基因流加强了某些遗传背景与特定栖息地的联系。一段时间后，基因组成的差异随系统发生距离的变化而线性变化，大概反映了移动元件的持续更新和偶尔获得适应性基因。出乎意料的是，基因组最小的植物群具有最高的基因组多样化率，而流动遗传要素却较少，但更为多样化。这表明较小的基因组与较高而不是较低的 遗传信息的周转率。这些基因组中的许多基因都来自淡水分离株，并具有特殊的性状，包括特定的荚膜，表明对这种环境的适应性。总之，这些数据有助于解释为什么在整个物种中普遍存在水平基因转移的情况下，流行病学克隆往往会从特定的系统发育群体中出现。