Each of 3,323 metabolic innovations in the evolution of E. coli arose through the horizontal transfer of a single DNA segment

Significance Bacteria often evolve by copying genes from other strains, a process termed horizontal gene transfer. As a consequence, different strains of the bacterial species Escherichia coli differ substantially in the sets of genes they possess. Here, we use the inferred gene sets of all recent ancestors of 53 E. coli strains to reconstruct the ancestors’ abilities to grow in different nutritional environments. This allows us to infer over 3,000 metabolic innovations in E. coli ’s evolutionary history. All innovations arose through the copying (transfer) of only one small piece of DNA from another strain, demonstrating an amazing capacity of E. coli to quickly adapt to new environments.