Massively parallel screening of synthetic microbial communities

Jared Kehe, Anthony Kulesa, Anthony Ortiz, Cheri M. Ackerman, Sri Gowtham Thakku, Daniel Sellers, Seppe Kuehn, Jeff Gore, Jonathan Friedman, Paul C. Blainey

פרסום מחקרי: פרסום בכתב עתמאמרביקורת עמיתים

תקציר

Microbial communities have numerous potential applications in biotechnology, agriculture, and medicine. Nevertheless, the limited accuracy with which we can predict interspecies interactions and environmental dependencies hinders efforts to rationally engineer beneficial consortia. Empirical screening is a complementary approach wherein synthetic communities are combinatorially constructed and assayed in high throughput. However, assembling many combinations of microbes is logistically complex and difficult to achieve on a timescale commensurate with microbial growth. Here, we introduce the kChip, a droplets-based platform that performs rapid, massively parallel, bottom-up construction and screening of synthetic microbial communities. We first show that the kChip enables phenotypic characterization of microbes across environmental conditions. Next, in a screen of ∼100,000 multispecies communities comprising up to 19 soil isolates, we identified sets 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. Broadly, kChip screening can identify multispecies consortia possessing any optically assayable function, including facilitation of biocontrol agents, suppression of pathogens, degradation of recalcitrant substrates, and robustness of these functions to perturbation, with many applications across basic and applied microbial ecology.

שפה מקוריתאנגלית אמריקאית
עמודים (מ-עד)12804-12809
מספר עמודים6
כתב עתProceedings of the National Academy of Sciences of the United States of America
כרך116
מספר גיליון26
מזהי עצם דיגיטלי (DOIs)
סטטוס פרסוםפורסם - 2019

ASJC Scopus subject areas

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