Microdroplet-Enabled Co-Cultivation and Characterization of Natural Microbial Communities

Microdroplet-enabled co-cultivation and characterization of natural microbial communities

Sida "Steven" Wang¹, Mark A. Burns^1,2, Xiaoxia "Nina" Lin^1,2

¹Department of Chemical Engineering, 3074 H.H. Dow, 2300 Hayward Street, Ann Arbor, MI 48109-2136

²Department of Biomedical Engineering, 1107 Carl A. Gerstacker Building, 2200 Bonisteel Blvd., Ann Arbor, MI 48109-2099

The majority of existing microbial species, in particular bacteria living in synergistic communities, have not been cultured and characterized in the laboratory. One important reason behind this "unculturability" is that conventional laboratory cultivation is aimed at pure cultures of individual species. This eliminates any potential interactions between different microbial species within a community necessary for growth of certain species.  Another challenge comes from the sheer size and complexity of many microbial communities that require high-throughput cultivation, which conventional laboratory techniques cannot accomplish.  We have developed a microfluidic platform utilizing aqueous-in-oil microdroplets for high throughput parallel co-cultivation of symbiotic microbial communities. We previously demonstrated the effectiveness of this cultivation platform using genetically engineered auxotrophic E. coli strains as our model system. In this work, we report new progresses in employing this conceptual and technological framework to isolate previously uncultured bacteria from natural microbial communities such as host-associated microbiomes.

Keywords: Droplet Microfluidics, Microbial Communities, Co-Cultivation, Unculturable Bacteria