Toward merging bottom–up and top–down model-based designing of synthetic microbial communities

ElsevierVolume 69, October 2022, 102169Current Opinion in MicrobiologyHighlights•

Analysis and designing of microbiomes have become a new paradigm in microbiology.

Understanding and rational engineering of microbiomes require model-based frameworks.

Computational bottom-up and top-down designing lead to superior synthetic microbiomes.

New middle-out approaches will provide synthetic communities with high performance.

The increasing interest of microbial communities as promising biocatalyst is leading an intense effort into the development of computational frameworks assisting the analysis and rational engineering of such complex ecosystems. Here, we critically review the recent computational and model-guided advances in the system-level engineering of microbiome, including both the rational bottom-up and the evolutionary top-down approaches. Furthermore, we highlight modeling and computational methods supporting both engineering paradigms. Finally, we discuss the advantages of combining both strategies into a hybrid top-down/bottom-up (middle-out) strategy to engineer synthetic microbial communities with improved performance and scope.

© 2022 The Author(s). Published by Elsevier Ltd.

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