To identify forces shaping the Escherichia coli intraspecies ecological structure, we have characterized in terms of phylogenetic group (A, B1, D and B2) belonging, presence/absence of extraintestinal virulence genes (pap, sfa, hly and aer) and intra-host phylotype diversity a collection of 1898 commensal isolates originating from 387 animals (birds and mammals) sampled in the 1980s and the 2000s. These data have been compared with 760 human commensal isolates, sampled from 152 healthy subjects in the 2000s, and analysed with the same approach. The prevalence of the E. coli phylogenetic groups in birds, non-human mammals and humans is clearly different with a predominance of D/B1, A/B1 and A/B2 strains respectively. A major force shaping the ecological structure is the environment with a strong effect of domestication and the year of sampling followed by the climate. Host characteristics, as the diet and body mass, also influence the ecological structure. Human microbiota are characterized by a higher prevalence of virulence genes and a lower intra-host diversity than the non-human mammal ones. This work identifies for the first time a group of strains specific to the animals, the B1 phylogenetic group strains exhibiting the hly gene. In conclusion, a complex network of factors seems to shape the ecological structure of commensal E. coli, with anthropogenic factors playing a major role and perturbing natural niche equilibrium.