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Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods

Noto Guillen, Mariana
Rosener, Brittany
Sayin, Serkan
Mitchell, Amir
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Abstract

Metabolic cross-feeding frequently underlies mutualistic relationships in natural microbial communities and is often exploited to assemble synthetic microbial consortia. We systematically identified all single-gene knockouts suitable for imposing cross-feeding in Escherichia coli and used this information to assemble syntrophic communities. Most strains benefiting from shared goods were dysfunctional in biosynthesis of amino acids, nucleotides, and vitamins or mutants in central carbon metabolism. We tested cross-feeding potency in 1,444 strain pairs and mapped the interaction network between all functional groups of mutants. This network revealed that auxotrophs for vitamins are optimal cooperators. Lastly, we monitored how assemblies composed of dozens of auxotrophs change over time and observed that they rapidly and repeatedly coalesced to seven strain consortia composed primarily from vitamin auxotrophs. The composition of emerging consortia suggests that they were stabilized by multiple cross-feeding interactions. We conclude that vitamins are ideal shared goods since they optimize consortium growth while still imposing member co-dependence.

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Noto Guillen M, Rosener B, Sayin S, Mitchell A. Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods. Cell Syst. 2021 Nov 17;12(11):1064-1078.e7. doi: 10.1016/j.cels.2021.08.002. Epub 2021 Aug 31. PMID: 34469744; PMCID: PMC8602757.

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10.1016/j.cels.2021.08.002
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34469744
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Copyright © 2021 Elsevier Inc. All rights reserved.
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