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Curr Opin Biotechnol. 2019 Apr 2;58:117-128. doi: 10.1016/j.copbio.2019.03.002. [Epub ahead of print]

Microbial community design: methods, applications, and opportunities.

Author information

1
Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
2
Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA; Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Santa Fe Institute, Santa Fe, NM 87501, USA. Electronic address: elbo@uw.edu.

Abstract

Microbial communities can perform a variety of behaviors that are useful in both therapeutic and industrial settings. Engineered communities that differ in composition from naturally occurring communities offer a unique opportunity for improving upon existing community functions and expanding the range of microbial community applications. This has prompted recent advances in various community design approaches including artificial selection procedures, reduction from existing communities, combinatorial evaluation of potential microbial combinations, and model-based in silico community optimization. Computational methods in particular offer a likely avenue toward improved synthetic community development going forward. This review introduces each class of design approach and surveys their recent applications and notable innovations, closing with a discussion of existing design challenges and potential opportunities for advancement.

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