Abstract
SignificanceMicrobes commonly reside within complex, multispecies communities in nature. Recent advances in high-throughput metagenomic sequencing have offered unprecedented systems-level insight into the diversity of microbial communities. However, the dissection of chemical and biological interactions is often limited by tools optimized for studying individual microbes or single compounds. Here, we report a modular and scalable microbial coculture platform designated the microbial community interaction (µCI) device for systematically measuring populations of a target strain when treated with three-member combinations of compounds or microbes. The µCI device is a simple platform that could become a routine tool in combinatorial screening of chemical and biological factors influencing microbial growth or gene expression.
Multispecies microbial communities drive most ecosystems on Earth. Chemical and biological interactions within these communities can affect the survival of individual members and the entire community. However, the prohibitively high number of possible interactions within a microbial community has made the characterization of factors that influence community development challenging. Here, we report a Microbial Community Interaction (µCI) device to advance the systematic study of chemical and biological interactions within a microbial community. The µCI creates a combinatorial landscape made up of an array of triangular wells interconnected with circular wells, which each contains either a different chemical or microbial strain, generating chemical gradients and revealing biological interactions. Bacillus cereus UW85 containing green fluorescent protein provided the “target” readout in the triangular wells, and antibiotics or microorganisms in adjacent circular wells are designated the “variables.” The µCI device revealed that gentamicin and vancomycin are antagonistic to each other in inhibiting the target B. cereus UW85, displaying weaker inhibitory activity when used in combination than alone. We identified three-member communities constructed with isolates from the plant rhizosphere that increased or decreased the growth of B. cereus. The µCI device enables both strain-level and community-level insight. The scalable geometric design of the µCI device enables experiments with high combinatorial efficiency, thereby providing a simple, scalable platform for systematic interrogation of three-factor interactions that influence microorganisms in solitary or community life.