OptCom A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities 英文参考文献.docVIP

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OptCom A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities 英文参考文献.doc

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OptCom A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities 英文参考文献

OptCom:AMulti-LevelOptimizationFrameworkforthe MetabolicModelingandAnalysisofMicrobial Communities AliR.Zomorrodi,CostasD.Maranas* DepartmentofChemicalEngineering,ThePennsylvaniaStateUniversity,UniversityPark,Pennsylvania,UnitedStatesofAmerica Abstract Microorganisms rarely live isolated in their natural environments but rather function in consolidated and socializing communities.Despitethegrowingavailabilityofhigh-throughputsequencingandmetagenomicdata,westillknowvery little about the metabolic contributions of individual microbial players within an ecological niche and the extent and directionalityofinteractionsamongthem.Thiscallsfordevelopmentofefficientmodelingframeworkstoshedlightonless understoodaspectsofmetabolisminmicrobialcommunities.Here,weintroduceOptCom,acomprehensivefluxbalance analysisframeworkformicrobialcommunities,whichreliesonamulti-levelandmulti-objectiveoptimizationformulationto munitylevelfitnesscriteria.Incontrasttoearlierapproachesthat relyonasingleobjectivefunction,here,weconsiderspecies-levelfitnesscriteriafortheinnerproblemswhilerelyingon community-level objective maximization for the outer problem. OptCom is general enough to capture any type of interactions(positive,negativeorcombinationsthereof)andiscapableofaccommodatinganynumberofmicrobialspecies (or guilds) involved. We applied OptCom to quantify the syntrophic association in a well-characterized two-species microbial system, assess the level of sub-optimal growth in phototrophic microbial mats, and elucidate the extent and direction of inter-species metabolite and electron transfer in a model microbial community. We also used OptCom to examine addition of a new member to an existing community. Our study demonstrates the importance of trade-offs between species- and community-level fitness driving forces and lays the foundation for metabolic-driven analysis of varioustypesofinteractionsinmulti-speciesmicrobialsystemsusinggenome-scalemetabolicmodels. Citation: Zomorrodi AR, Maranas CD