Engineering the Mammalian Gut Microbiome in Situ

Engineering microbial populations in open environments, such as the mammalian gastrointestinal tract, is an outstanding challenge. Current approaches require laboratory cultivation and tedious optimizations to develop genetic tools for each new non-model microbe. Here, we describe an enabling platform, Gene Transfer In Situ (GeTIS), to identify and engineer genetically tractable yet undomesticated microbes from complex microbial communities. Using engineered horizontal gene transfer and transposon systems, we identified and isolated bacteria from the mammalian gut microbiome that were amenable to genetic manipulation and then redeployed them back into the mammalian host as host-optimized engineerable probiotics. Furthermore, we demonstrated in situ gene transfer in a live animal to deliver new traits directly into its established gut microbiota. This in situ genome engineering approach enables the accelerated development of new microbial chasses for synthetic biology and the introduction of novel capabilities into established microbial communities with minimal disruption to their native milieu.