Ultra-High Throughput Screening of Synthetic Microbial Communities in Agriculture and Human Health

To harness the power of beneficial microbial communities in biotechnology, agriculture, and medicine, a deeper understanding of the assembly rules governing microbial communities is needed. Empirical screening of synthetic microbial consortia can systematically explore interspecies interactions and environmental dependencies; however, assembling many combinations of microbes for such screening is logistically complex and difficult to achieve on a timescale commensurate with microbial growth. The kChip is a droplets-based platform that performs rapid, massively parallel, bottom-up construction and screening of synthetic microbial communities. Here, we present a screen of ~100,000 multispecies communities comprising up to 19 soil isolates in which we identified consortia that promote the growth of the model plant symbiont Herbaspirillum frisingense in a manner robust to carbon source variation and the presence of additional species. Furthermore, we explore the use of kChip for screening microbial consortia constructed from human microbiome isolates.