Commensal or pathogenic, is everything written in the genome ?

In a single species,Escherichia coli represents an extraordinary diversity of clones that have evolved towards commensal or pathogenic specialization (pathovars) under the effect of selective pressures that are poorly understood, apart from the evidence of an increase in the mutator phenotype when exposed to stress. However, this specialization is not only linked to the occurrence of mutations, but also to the horizontal acquisition of genes encoding specific functions, particularly in pathogenicity. As a result, E. coli has a huge pangenome, which increases as new genomes are sequenced. It is therefore exciting to attempt to retrace the evolutionary path of this specialization and identify the factors that facilitated it. It is equally important to try and decipher, by combining genome analysis and in vivo experiments, what the factors really are that determine the cost of adaptation to certain niches.