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

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)12804-12809
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume116
Issue number26
DOIs
StatePublished - Jan 1 2019

Keywords

  • Community assembly
  • Droplet microfluidics
  • High-throughput screening
  • Microbial interactions
  • Synthetic ecology

ASJC Scopus subject areas

  • General

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  • Cite this

    Kehe, J., Kulesa, A., Ortiz, A., Ackerman, C. M., Thakku, S. G., Sellers, D., Kuehn, S., Gore, J., Friedman, J., & Blainey, P. C. (2019). Massively parallel screening of synthetic microbial communities. Proceedings of the National Academy of Sciences of the United States of America, 116(26), 12804-12809. https://doi.org/10.1073/pnas.1900102116