{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T01:02:16Z","timestamp":1774400536874,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Simple forms of mutualism between microorganisms are widespread in nature. Nevertheless, the role played by the environmental nutrient composition in mediating cross-feeding in microbial ecosystems is still poorly understood.<\/jats:p>\n               <jats:p>Results: Here, we use mixed-integer bilevel linear programming to investigate the cost of sharing metabolic resources in microbial communities. The algorithm infers an optimal combination of nutrients that can selectively sustain synergistic growth for a pair of species and guarantees minimum cost of cross-fed metabolites. To test model-based predictions, we selected a pair of Escherichia coli single gene knockouts auxotrophic, respectively, for arginine and leucine: \u0394argB and \u0394leuB and we experimentally verified that model-predicted medium composition significantly favors mutualism. Moreover, mass spectrometry profiling of exchanged metabolites confirmed the predicted cross-fed metabolites, supporting our constraint based modeling approach as a promising tool for engineering microbial consortia.<\/jats:p>\n               <jats:p>Availability and implementation: The software is freely available as a matlab script in the Supplementary materials.<\/jats:p>\n               <jats:p>Contact: \u00a0zampieri@imsb.biol.ethz.ch.<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw062","type":"journal-article","created":{"date-parts":[[2016,2,15]],"date-time":"2016-02-15T01:09:07Z","timestamp":1455498547000},"page":"1733-1739","source":"Crossref","is-referenced-by-count":12,"title":["Model-based media selection to minimize the cost of metabolic cooperation in microbial ecosystems"],"prefix":"10.1093","volume":"32","author":[{"given":"Mattia","family":"Zampieri","sequence":"first","affiliation":[{"name":"Department of Biology, Institute for Molecular Systems Biology, Zurich 8093, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Uwe","family":"Sauer","sequence":"additional","affiliation":[{"name":"Department of Biology, Institute for Molecular Systems Biology, Zurich 8093, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,2,1]]},"reference":[{"key":"2023020112291733500_btw062-B1","doi-asserted-by":"crossref","first-page":"2006.0008","DOI":"10.1038\/msb4100050","article-title":"Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection","volume":"2","author":"Baba","year":"2006","journal-title":"Mol. 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