Dissecting the genetic components of adaptation of E. coli to the mouse gut

New insights into the evolutionary mechanisms that facilitate the remarkably fast adaptation of intestinal bacteria within their natural environment are provided in the January issue of PLoS Genetics by researchers from INSERM and INRA at University Paris Descartes.

Using germ-free mice – a simplified but ecologically relevant system – the authors analyzed the intestinal adaptation of a model bacterial strain, Escherichia coli MG1655. E. coli is naturally resident within the adult mammalian gut and one of the first bacteria to colonize the human intestine at birth. The mammalian intestine is therefore a privileged site to study how co-evolution between hosts and the trillions of bacteria that form the commensal flora has shaped the genome of each partner and promoted the development of mutualistic interactions.

Commensal bacteria settle on all surfaces exposed to the outside but most prominently in our intestine where they develop a high degree of interdependency with their host. Recent work has shown how these bacteria may impact on our health by modulating our metabolic functions and immune defences. Much less is known on how commensal bacteria adapt to the open and constantly changing ecosystem represented by our intestine.

Intestinal colonization of germ-free mice by E. coli was followed by the very rapid selection of bacteria carrying mutations in a master regulator that controls and coordinates the expression of over 100 target genes. The important selective advantage conferred by the mutations was related with their additive and independent effects on genes regulating bacterial motility and permeability.

These results suggest that global regulators may have evolved to coordinate physiological activities necessary for adaptation to complex environments and that mutations offer a complementary genetic mechanism to adjust the scale of the physiological regulation controlled by these regulators in distinct environments.

While this study yields an interesting model to analyze how intestinal bacteria can adapt to their host, the authors stress that it represents a simplified ecological system compared with the complexity prevailing within the human intestine. Future work will be necessary to assess how commensal bacteria can adapt to their host while simultaneously competing with hundreds of other bacterial species present in the intestinal microecological system.