Using natural bacterial interactions to control microbial communities
Molecular Genetics & Microbiology
Precisely manipulating microbial communities in humans (the human microbiota) remains challenging. In particular, we lack techniques for modulating the growth of a single bacterial species while leaving an overall microbial community intact. Such tools are crucial for basic research on host-microbiota interactions and could enable new therapies targeting the human microbiota. One approach for controlling species levels is to exploit existing ecological interactions, by introducing into communities bacteria that naturally promote or inhibit the growth of a target species. However, comprehensive discovery of bacteria with useful ecological properties is presently unfeasible for complex microbial communities. Here, I present microfluidic approaches for efficiently identifying bacteria that thrive in humans and interact with a target microbial species. These approaches promise co-culture and evaluation millions of distinct bacterial interactions in a week. Ultimately, the bacteria isolated from these devices should permit new causal studies in human microbiota research, by enabling us to manipulate these complex bacterial ecosystems in vivo.