Environments that Induce Synthetic Microbial Ecosystems

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dc.contributor.author Klitgord, Niels en_US
dc.contributor.author Segrè, Daniel en_US
dc.date.accessioned 2012-01-11T00:41:23Z
dc.date.available 2012-01-11T00:41:23Z
dc.date.issued 2010-11-18 en_US
dc.identifier.citation Klitgord, Niels, Daniel Segrè. "Environments that Induce Synthetic Microbial Ecosystems" PLoS cComputational Biology 6(11): e1001002. (2010) en_US
dc.identifier.issn 1553-7358 en_US
dc.identifier.uri http://hdl.handle.net/2144/3044
dc.description.abstract Interactions between microbial species are sometimes mediated by the exchange of small molecules, secreted by one species and metabolized by another. Both one-way (commensal) and two-way (mutualistic) interactions may contribute to complex networks of interdependencies. Understanding these interactions constitutes an open challenge in microbial ecology, with applications ranging from the human microbiome to environmental sustainability. In parallel to natural communities, it is possible to explore interactions in artificial microbial ecosystems, e.g. pairs of genetically engineered mutualistic strains. Here we computationally generate artificial microbial ecosystems without re-engineering the microbes themselves, but rather by predicting their growth on appropriately designed media. We use genome-scale stoichiometric models of metabolism to identify media that can sustain growth for a pair of species, but fail to do so for one or both individual species, thereby inducing putative symbiotic interactions. We first tested our approach on two previously studied mutualistic pairs, and on a pair of highly curated model organisms, showing that our algorithms successfully recapitulate known interactions, robustly predict new ones, and provide novel insight on exchanged molecules. We then applied our method to all possible pairs of seven microbial species, and found that it is always possible to identify putative media that induce commensalism or mutualism. Our analysis also suggests that symbiotic interactions may arise more readily through environmental fluctuations than genetic modifications. We envision that our approach will help generate microbe-microbe interaction maps useful for understanding microbial consortia dynamics and evolution, and for exploring the full potential of natural metabolic pathways for metabolic engineering applications. Author Summary Microbial metabolism affects biogeochemical cycles and human health. In most natural environments, multiple microbial species interact with each other, forming complex ecosystems whose properties are poorly understood. In an effort to understand inter-microbial interactions, and to explore new metabolic engineering avenues, researchers have started building artificial microbial ecosystems, e.g. pairs of genetically engineered strains that require each other for survival. Here we computationally explore the possibility of creating artificial microbial ecosystems without re-engineering the microbes themselves, but rather by manipulating the environment in which they grow. Specifically, using the framework of flux balance analysis, we predict environments in which either one or both microbes in a pair would not be able to grow without the other, inducing commensal (one-way) or mutualistic (two-way) interactions, respectively. Our algorithms can successfully recapitulate known inter-microbial interactions, and predict millions of new ones across any pair amongst different microbial species. Surprisingly, we find that it is always possible to identify conditions that induce mutualistic or commensal interactions between any two species. Hence, our method should help in mapping naturally occurring microbe-microbe interactions, and in engineering new ones through a novel, environment-driven branch of synthetic ecology. en_US
dc.description.sponsorship Office of Science; U.S. Department of Energy (DE-FG02-07ER64388, DE-FG02-07ER64483, DESC0004962); NASA (NNA08CN84A) en_US
dc.language.iso en en_US
dc.publisher Public Library of Science en_US
dc.rights Klitgord, Segrè. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. en_US
dc.title Environments that Induce Synthetic Microbial Ecosystems en_US
dc.type article en_US
dc.identifier.doi 10.1371/journal.pcbi.1001002 en_US
dc.identifier.pubmedid 21124952 en_US
dc.identifier.pmcid 2987903 en_US

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