linguistic:translation, structural:expansion, information:highlighting, structural:summarization
Phylogeny of E. coli strains

Many strains belonging to this species have been isolated and characterised. In addition to serotype (vide supra), they can be classified according to their phylogeny, i.e. the inferred evolutionary history, as shown below where the species is divided into six groups as of 2014. Particularly the use of whole genome sequences yields highly supported phylogenies. The phylogroup structure remains robust to newer methods and sequences, which sometimes adds newer groups, giving 8 or 14 as of 2023.

The link between phylogenetic distance ("relatedness") and pathology is small, e.g. the O157:H7 serotype strains, which form a clade ("an exclusive group")—group E below—are all enterohaemorragic strains (EHEC), but not all EHEC strains are closely related. In fact, four different species of Shigella are nested among E. coli strains (vide supra), while E. albertii and E. fergusonii are outside this group. Indeed, all Shigella species were placed within a single subspecies of E. coli in a phylogenomic study that included the type strain. All commonly used research strains of E. coli belong to group A and are derived mainly from Clifton's K-12 strain (λ F; O16) and to a lesser degree from d'Herelle 's " Bacillus coli " strain (B strain; O7).

There have been multiple proposals to revise the taxonomy to match phylogeny. However, all these proposals need to face the fact that Shigella remains a widely used name in medicine and find ways to reduce any confusion that can stem from renaming.