Infants are born germ-free and ready for microbial colonization. The first consortium of microbial colonizers can shape the growth, development, and health of the host during infancy and well into later life. As newborns mature, their diet, immune system and microbiome composition change rapidly, creating shifting selective pressures on members of the gut microbial community. These changes are expected to drive enhanced evolutionary dynamics, giving rise to new microbial traits and co-existing strains, which may, in turn, further influence the host in the years ahead.

We study the evolution and ecology of the gut microbiome at high resolution, with a particular focus on the infant gut as a model system. Our work combines basic research with the development of computational tools – both to advance our own research aims and to provide valuable resources for the broader scientific community.