Multi-Species Co-Culture Platform to Enable Spatial Analysis of Microbial Communication

Microbes naturally interact with neighboring organisms and environments in a "social network" of shared molecules. The collective consortia of organisms can often perform tasks more complex than isolated monocultures. Understanding community interaction will enable synthetic biologists to engineer designer communities that solve problems in the natural world. Typical co-culture studies rely on agar plate diffusion assays, or diffusion between two liquid chambers separated by a porous membranes. Herein, we demonstrate a multi-well porous hydrogel platform that enables bacterial multispecies co-culture. The hydrogel physically isolates individual cultures while allowing media and small molecule exchange. Recovery of liquid culture wells after growth can be fed into existing bio-analysis pipelines such as cytometry, mass spectroscopy, and sequencing to obtain spatially resolved information. Herein, we demonstrate the detection of biologically relevant molecule gradients through the device, including pH, small molecule inducers, and antibiotic gradients originating from a single seeded well. We also demonstrate the long-term co-culture of bacterial and algal cells within the device, and assess population changes in bacterial cultures with and without algae present.
These data suggest the use of a nanoporous growth chamber to study community-level interactions between microbes and their neighbors.