Multifunctional Nanoculture Systems for Studying Microbial Dynamics

Microbes self-organize at various interfaces while transitioning to a sessile form within a protective biofilm matrix. While the biological implications of biofilms for the environment, health, and industry are widely appreciated, the earlier developmental stage of microbes as microcolonies has received scant attention. Here, we present a new approach to investigate microbial dynamics in spatially confined microsystems. Using microfluidics-enabled fabrication, a nanoliter-scale sessile culture system (the nanoculture) is designed to grow synthetic microbial communities. Each nanoculture begins as a several nanoliter droplets of suspended cells, encapsulated by a polydimethylsiloxane (PDMS) membrane. The physicochemical properties of the encapsulation materials allow the diffusion of functional molecules to interrogate cell physiology under chemical insults, allowing microbial interactions to be probed within or across the confining vessel. Alternatively, multiple species of microbes can be co-cultured within a nanoculture. Because chemical communication across the membrane occurs, this system can be used to decouple the effects of the physical and chemical interactions between cells, and investigate microbial pathophysiology or bacterial-fungal (inter-kingdom) dynamics that play a central role in early childhood dental caries and many infections. Such a culture system now provides unique opportunities to assess their therapeutic use for personalized medicine, or for high throughput screening of unculturable microbial species relevant to biotechnology and drug discovery.