According to this paper, among 61 strains of E. coli they studied only 6% of the genes are common in all. Which means that the overwhelming majority of the genes are not shared.
And wikipedia defines E. coli like this:
... is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms (endotherms).
Which is a phenotypic definition. My question is: what defines E. coli as a species: its genotype or its phenotype?