title: Microdroplet-enabled highly parallel co-cultivation of microbial communities.
abstract: Microbial interactions in natural microbiota are, in many cases, crucial for the sustenance of the communities, but the precise nature of these interactions remain largely unknown because of the inherent complexity and difficulties in laboratory cultivation. Conventional pure culture-oriented cultivation does not account for these interactions mediated by small molecules, which severely limits its utility in cultivating and studying "unculturable" microorganisms from synergistic communities. In this study, we developed a simple microfluidic device for highly parallel co-cultivation of symbiotic microbial communities and demonstrated its effectiveness in discovering synergistic interactions among microbes. Using aqueous micro-droplets dispersed in a continuous oil phase, the device could readily encapsulate and co-cultivate subsets of a community. A large number of droplets, up to ∼1,400 in a 10 mm × 5 mm chamber, were generated with a frequency of 500 droplets/sec. A synthetic model system consisting of cross-feeding E. coli mutants was used to mimic compositions of symbionts and other microbes in natural microbial communities. Our device was able to detect a pair-wise symbiotic relationship when one partner accounted for as low as 1% of the total population or each symbiont was about 3% of the artificial community.
authors.affiliation: Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America.
authors.forename: Jihyang
authors.initials: J
authors.lastname: Park
authors.forename: Alissa
authors.initials: A
authors.lastname: Kerner
authors.forename: Mark A
authors.initials: MA
authors.lastname: Burns
authors.forename: Xiaoxia Nina
authors.initials: XN
authors.lastname: Lin
mesh_terms: D058448:Biota; D018920:Coculture Techniques / Q000379:methods; D003470:Culture Media / Q000737:chemistry; D004339:Drug Compounding / Q000379:methods; D004926:Escherichia coli / Q000235:genetics / Q000254:growth & development / Q000502:physiology; D059013:Microbial Consortia / Q000502:physiology; D056265:Microbial Interactions / Q000502:physiology; D008828:Microbiological Techniques / Q000379:methods*; D046210:Microfluidic Analytical Techniques; D008904:Miniaturization; D008954:Models, Biological; D030781:Organisms, Genetically Modified; D013559:Symbiosis / Q000502:physiology
chemical_list: D003470:Culture Media