Metagenomic engineering of the mammalian gut microbiome in situ

Engineering of microbial communities in open environments remains challenging. Here we describe a platform used to identify and modify genetically tractable mammalian microbiota by engineering community-wide horizontal gene transfer events in situ. With this approach, we demonstrate that diverse taxa in the mouse gut microbiome can be modified directly with a desired genetic payload. In situ microbiome engineering in living animals allows novel capabilities to be introduced into established communities in their native milieu. MAGIC introduces conjugative plasmids into complex microbial communities in situ, enabling genetic modifications in gut microbiota.