Research graph
References from Metabolic modelling approaches for describing and engineering microbial communities. Local targets link to admitted publications; unresolved targets remain external evidence.
Metabolic Engineering of Microorganisms for the Production of Natural Compounds
10.1002/adbi.201700190 · 2018 · External reference
10.1038/nrg2775
10.1038/nrg2775 · External reference
Recent developments in systems biology and metabolic engineering of plant-microbe interactions
10.3389/fpls.2016.01421 · 2016 · External reference
Microbial biotechnology for the synthesis of (pro)vitamins, biopigments and antioxidants: challenges and opportunities
10.1111/1751-7915.12379 · 2016 · External reference
10.1016/b978-0-12-407776-8.00001-3
10.1016/b978-0-12-407776-8.00001-3 · External reference
10.1016/j.biotechadv.2017.08.001
10.1016/j.biotechadv.2017.08.001 · External reference
Metabolic engineering of microbial cell factories for production of nutraceuticals
2019 · External reference
10.1039/c4cs00114a
10.1039/c4cs00114a · External reference
10.5936/csbj.201210017
10.5936/csbj.201210017 · External reference
10.1016/j.copbio.2019.09.004
10.1016/j.copbio.2019.09.004 · External reference
Synthetic microbial consortia for small molecule production
10.1016/j.copbio.2019.09.011 · 2020 · External reference
10.3390/life9010022
10.3390/life9010022 · External reference
10.1007/s10295-019-02211-4
10.1007/s10295-019-02211-4 · External reference
10.1016/j.biotechadv.2019.107500
10.1016/j.biotechadv.2019.107500 · External reference
10.1016/j.ymben.2016.05.007
10.1016/j.ymben.2016.05.007 · External reference
10.1016/j.copbio.2020.07.001
10.1016/j.copbio.2020.07.001 · External reference
Simultaneous cell growth and ethanol production from cellulose by an engineered yeast consortium displaying a functional mini-cellulosome
10.1186/1475-2859-10-89 · 2011 · External reference
Butanol production from alkali-pretreated rice straw by co-culture of Clostridium thermocellum and Clostridium saccharoperbutylacetonicum
10.1016/j.biortech.2015.03.061 · 2015 · External reference
10.1111/1751-7915.13544
10.1111/1751-7915.13544 · External reference
Construction and analysis of an artificial consortium based on the fast-growing cyanobacterium synechococcus elongatus UTEX 2973 to produce the platform chemical 3-hydroxypropionic acid from CO2
10.1186/s13068-020-01720-0 · 2020 · External reference
Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass
10.1073/pnas.1218447110 · 2013 · External reference
Escherichia coli binary culture engineered for direct fermentation of hemicellulose to a biofuel
10.1128/aem.00908-10 · 2010 · External reference
Synthetic escherichia coli-corynebacterium glutamicum consortia for l-lysine production from starch and sucrose
10.1016/j.biortech.2018.03.113 · 2018 · External reference
Imaging secondary metabolism of Streptomyces sp. Mg1 during cellular lysis and colony degradation of competing Bacillus subtilis
10.1007/s10482-012-9769-0 · 2012 · External reference
10.1038/ismej.2016.195
10.1038/ismej.2016.195 · External reference
10.1038/nbt.3095
10.1038/nbt.3095 · External reference
Heterologous biosynthesis of natural product naringenin by co-culture engineering
10.1016/j.synbio.2017.08.003 · 2017 · External reference
Escherichia coli modular coculture system for resveratrol glucosides production
10.1007/s11274-018-2458-z · 2018 · External reference
Engineering of a microbial coculture of Escherichia coli strains for the biosynthesis of resveratrol
10.1186/s12934-016-0562-z · 2016 · External reference
10.1016/j.ymben.2019.03.002
10.1016/j.ymben.2019.03.002 · External reference
Complete biosynthesis of anthocyanins using E. coli polycultures
10.1128/mbio.00621-17 · 2017 · External reference
10.1016/j.ymben.2018.03.016
10.1016/j.ymben.2018.03.016 · External reference
A diverse community to study communities: integration of experiments and mathematical models to study microbial consortia
10.1128/jb.00865-16 · 2017 · External reference
10.1016/j.copbio.2019.03.002
10.1016/j.copbio.2019.03.002 · External reference
10.1016/j.freeradbiomed.2016.12.017
10.1016/j.freeradbiomed.2016.12.017 · External reference
10.1042/bst20170265
10.1042/bst20170265 · External reference
10.3389/fmolb.2016.00003
10.3389/fmolb.2016.00003 · External reference
10.3389/fmicb.2014.00219
10.3389/fmicb.2014.00219 · External reference
10.1016/j.mib.2016.03.008
10.1016/j.mib.2016.03.008 · External reference
10.1016/j.physa.2010.02.047
10.1016/j.physa.2010.02.047 · External reference
Unresolved reference
External reference
10.1038/nrmicro1461
10.1038/nrmicro1461 · External reference
10.1371/journal.pcbi.1000716
10.1371/journal.pcbi.1000716 · External reference
10.1111/j.1420-9101.2006.01119.x
10.1111/j.1420-9101.2006.01119.x · External reference
Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities
10.1038/s41467-017-01407-5 · 2017 · External reference
10.1038/nrmicro2832
10.1038/nrmicro2832 · External reference
10.1017/cbo9781139173179
10.1017/cbo9781139173179 · External reference
10.2307/j.ctvs32rq4
10.2307/j.ctvs32rq4 · External reference
10.1128/aem.01338-07
10.1128/aem.01338-07 · External reference
10.1111/j.1574-6968.2007.00790.x
10.1111/j.1574-6968.2007.00790.x · External reference
Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota
10.1371/journal.pcbi.1003388 · 2013 · External reference
10.1126/science.aad2602
10.1126/science.aad2602 · External reference
Mapping the ecological networks of microbial communities
10.1038/s41467-017-02090-2 · 2017 · External reference
10.1016/0169-5347(94)90225-9
10.1016/0169-5347(94)90225-9 · External reference
10.1038/nrmicro.2016.62
10.1038/nrmicro.2016.62 · External reference
NuFeb: a massively parallel simulator for individual-based modelling of microbial communities
2019 · External reference
From genes to ecosystems in microbiology: modeling approaches and the importance of individuality
10.3389/fmicb.2017.02299 · 2017 · External reference
Current status and applications of genome-scale metabolic models
2019 · External reference
10.1093/bioinformatics/bty561
10.1093/bioinformatics/bty561 · External reference
10.1016/j.cell.2015.05.019
10.1016/j.cell.2015.05.019 · External reference
13C metabolic flux analysis
2001 · External reference
Subpopulation-specific metabolic pathway usage in mixed cultures as revealed by reporter protein-based 13C analysis
2011 · External reference
Metabolism in dense microbial colonies: 13 C metabolic flux analysis of E. coli grown on agar identifies two distinct cell populations with acetate cross-feeding
10.1016/j.ymben.2018.08.013 · 2018 · External reference
Integrating Cellular Metabolism into a Multiscale Whole-Body Model
10.1371/journal.pcbi.1002750 · 2012 · External reference
Multiscale metabolic modeling: dynamic flux balance analysis on a whole-plant scale
10.1104/pp.113.224006 · 2013 · External reference
10.1098/rsif.2016.0627
10.1098/rsif.2016.0627 · External reference
In Silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study
10.1186/1752-0509-3-114 · 2009 · External reference
10.3389/fmicb.2016.00673
10.3389/fmicb.2016.00673 · External reference
Perspectives and challenges in microbial communities metabolic modeling
10.3389/fgene.2017.00088 · 2017 · External reference
10.1038/s41564-019-0491-9
10.1038/s41564-019-0491-9 · External reference
10.1073/pnas.0806162105
10.1073/pnas.0806162105 · External reference
Microbial community metabolic modeling: a community data-driven network reconstruction
10.1002/jcp.25428 · 2016 · External reference
10.1038/nbt.4163
10.1038/nbt.4163 · External reference
A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems
10.1371/journal.pone.0171744 · 2017 · External reference
Metabolic modeling of a mutualistic microbial community
10.1038/msb4100131 · 2007 · External reference
Competitive and cooperative metabolic interactions in bacterial communities
10.1038/ncomms1597 · 2011 · External reference
Environments that induce synthetic microbial ecosystems
10.1371/journal.pcbi.1001002 · 2010 · External reference
Community flux balance analysis for microbial consortia at balanced growth
10.1371/journal.pone.0064567 · 2013 · External reference
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology
10.1186/1752-0509-5-180 · 2011 · External reference
10.1371/journal.pcbi.1002363
10.1371/journal.pcbi.1002363 · External reference
10.1021/sb4001307
10.1021/sb4001307 · External reference
MMinte: an application for predicting metabolic interactions among the microbial species in a community
10.1186/s12859-016-1230-3 · 2016 · External reference
10.1371/journal.pcbi.1005539
10.1371/journal.pcbi.1005539 · External reference
10.1093/nar/gky537
10.1093/nar/gky537 · External reference
The microbiome modeling toolbox: from microbial interactions to personalized microbial communities
10.1093/bioinformatics/bty941 · 2019 · External reference
10.1128/msystems.00606-19
10.1128/msystems.00606-19 · External reference
10.1016/s0006-3495(02)73903-9
10.1016/s0006-3495(02)73903-9 · External reference
10.1038/ismej.2010.117
10.1038/ismej.2010.117 · External reference
10.1016/j.celrep.2014.03.070
10.1016/j.celrep.2014.03.070 · External reference
10.1371/journal.pcbi.1004875
10.1371/journal.pcbi.1004875 · External reference
10.7554/elife.08208
10.7554/elife.08208 · External reference
10.1111/1462-2920.13743
10.1111/1462-2920.13743 · External reference
10.1016/j.ecolmodel.2016.05.011
10.1016/j.ecolmodel.2016.05.011 · External reference
10.1371/journal.pcbi.1005544
10.1371/journal.pcbi.1005544 · External reference
Emergent subpopulation behavior uncovered with a community dynamic metabolic model of escherichia coli diauxic growth
10.1128/msystems.00230-18 · 2019 · External reference
Dynamic simulations of microbial communities under perturbations: opportunities for microbiome engineering
2020 · External reference
10.1042/bst20170268
10.1042/bst20170268 · External reference
10.1002/wsbm.1393
10.1002/wsbm.1393 · External reference
10.1016/j.margen.2017.06.003
10.1016/j.margen.2017.06.003 · External reference
Understanding the interactions between bacteria in the human gut through metabolic modeling
10.1038/srep02532 · 2013 · External reference
10.1016/j.cmet.2015.07.001
10.1016/j.cmet.2015.07.001 · External reference
10.1038/nbt.3703
10.1038/nbt.3703 · External reference
10.1128/aem.00101-15
10.1128/aem.00101-15 · External reference
From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn’s disease
10.1038/s41540-018-0063-2 · 2018 · External reference
Host-microbe-drug-nutrient screen identifies bacterial effectors of metformin therapy
10.1016/j.cell.2019.08.003 · 2019 · External reference
Personalized whole-body models integrate metabolism, physiology, and the gut microbiome
10.15252/msb.20198982 · 2020 · External reference
Computational approaches for integrative analysis of the metabolome and microbiome
10.3390/metabo7040062 · 2017 · External reference
10.1038/s41564-018-0124-8
10.1038/s41564-018-0124-8 · External reference
Defining and evaluating microbial contributions to metabolite variation in microbiome-metabolome association studies
10.1128/msystems.00579-19 · 2019 · External reference
Optimization of multi-omic genome-scale models: Methodologies, hands-on tutorial, and perspectives
10.1007/978-1-4939-7528-0_18 · 2018 · External reference
Integrating -omics data into genome-scale metabolic network models: principles and challenges
2018 · External reference
Analysis of omics data with genome-scale models of metabolism
2013 · External reference
Co-evolution of strain design methods based on flux balance and elementary mode analysis
10.1016/j.meteno.2015.04.001 · 2015 · External reference
10.1002/bit.10803
10.1002/bit.10803 · External reference
10.1101/gr.2872004
10.1101/gr.2872004 · External reference
Evolutionary programming as a platform for in silico metabolic engineering
10.1186/1471-2105-6-308 · 2005 · External reference
Large-scale identification of genetic design strategies using local search
2009 · External reference
10.1049/iet-syb.2013.0021
10.1049/iet-syb.2013.0021 · External reference
Experimental and computational optimization of an Escherichia coli co-culture for the efficient production of flavonoids
10.1016/j.ymben.2016.01.006 · 2016 · External reference
Stability of cross-feeding polymorphisms in microbial communities
10.1371/journal.pcbi.1005269 · 2016 · External reference
10.1093/bioinformatics/btw107
10.1093/bioinformatics/btw107 · External reference
10.1109/cdc.2016.7799357
10.1109/cdc.2016.7799357 · External reference
10.1007/s00239-005-0027-1
10.1007/s00239-005-0027-1 · External reference
A combinatorial algorithm for microbial consortia synthetic design
10.1038/srep29182 · 2016 · External reference
Designing metabolic division of labor in microbial communities
10.1128/msystems.00263-18 · 2019 · External reference
Distributed flux balance analysis simulations of serial biomass fermentation by two organisms
10.1371/journal.pone.0227363 · 2020 · External reference
10.1093/bioinformatics/btw062
10.1093/bioinformatics/btw062 · External reference
Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)
10.1371/journal.pcbi.1007127 · 2019 · External reference
Metabolic modeling of a chronic wound biofilm consortium predicts spatial partitioning of bacterial species
10.1186/s12918-016-0334-8 · 2016 · External reference
Synthetic microbial ecology: engineering habitats for modular consortia
10.3389/fmicb.2017.01125 · 2017 · External reference
Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process
10.1186/s13068-016-0429-x · 2016 · External reference
Recent advances on constraint-based models by integrating machine learning
2020 · External reference
Machine and deep learning meet genome-scale metabolic modeling
10.1371/journal.pcbi.1007084 · 2019 · External reference
Machine learning applications in systems metabolic engineering
2020 · External reference
Conflict, and the Evolution of Eusociality
10.1371/journal.pbio.1002098 · 2015 · External reference
Common principles and best practices for engineering microbiomes
2019 · External reference
Application of the dynamic gastrointestinal simulator (simgi®) to assess the impact of probiotic supplementation in the metabolism of grape polyphenols
10.1016/j.foodres.2019.108790 · 2020 · External reference
EcoFABs: advancing microbiome science through standardized fabricated ecosystems
10.1038/s41592-019-0465-0 · 2019 · External reference
Synthetic klebsiella pneumoniae-shewanella oneidensis consortium enables glycerol-fed high-performance microbial fuel cells
10.1002/biot.201700491 · 2018 · External reference
Engineering of artificial microbial consortia of Ralstonia eutropha and Bacillus subtilis for poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer production from sugarcane sugar without precursor feeding
10.1016/j.biortech.2018.02.056 · 2018 · External reference
Co-culture-based biological carbon monoxide conversion by Citrobacter amalonaticus Y19 and Sporomusa ovata via a reducing-equivalent transfer mediator
10.1016/j.biortech.2018.02.129 · 2018 · External reference
Production of cellulosic organic acids via synthetic fungal consortia
10.1002/bit.26509 · 2018 · External reference
10.1371/journal.pone.0113786
10.1371/journal.pone.0113786 · External reference
Batch and fed-batch carotenoid production by rhodotorula glutinis-debaryomyces castellii co-cultures in corn syrup
10.1046/j.1365-2672.2001.01319.x · 2001 · External reference
Microbial interactions for enhancement of alpha-amylase production by Bacillus amyloliquefaciens 04BBA15 and Lactobacillus fermentum 04BBA19
10.1016/j.btre.2014.09.004 · 2014 · External reference
Engineering a predatory bacterium as a proficient killer agent for intracellular bio-products recovery: The case of the polyhydroxyalkanoates
2016 · External reference
Metabolite-based mutualism between Pseudomonas aeruginosaPA14 and Enterobacter aerogenes enhances current generation in bioelectrochemical systems
10.1039/c1ee01377g · 2011 · External reference
10.1038/s41467-020-14371-4
10.1038/s41467-020-14371-4 · External reference
Engineering a microbial consortium based whole-cell system for efficient production of glutarate from L-lysine
10.3389/fmicb.2019.00341 · 2019 · External reference
Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture
10.1038/s41598-017-18630-1 · 2018 · External reference
10.1073/pnas.1506781112
10.1073/pnas.1506781112 · External reference
Metabolic exchange with non-alkane-consuming pseudomonas stutzeri SLG510A3-8 improves n-alkane biodegradation by the alkane degrader Dietzia sp. strain DQ12-45-1b
2020 · External reference
A novel process for cadaverine bio-production using a consortium of two engineered Escherichia coli
10.3389/fmicb.2018.01312 · 2018 · External reference
10.1039/c6ee03705d
10.1039/c6ee03705d · External reference
Metabolite-enabled mutualistic interaction between shewanella oneidensis and escherichia coli in a co-culture using an electrode as electron acceptor
10.1038/srep11222 · 2015 · External reference
10.1371/journal.pone.0108297
10.1371/journal.pone.0108297 · External reference
10.1002/bit.20765
10.1002/bit.20765 · External reference
The Crc/CrcZ-CrcY global regulatory system helps the integration of gluconeogenic and glycolytic metabolism in Pseudomonas putida
10.1111/1462-2920.12812 · 2015 · External reference
10.1073/pnas.1300926110
10.1073/pnas.1300926110 · External reference
Metabolic-network-driven analysis of bacterial ecological strategies
10.1186/gb-2009-10-6-r61 · 2009 · External reference
Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments
10.1186/1471-2180-10-149 · 2010 · External reference
Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation
10.1038/ismej.2012.82 · 2013 · External reference
Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data
10.1093/bioinformatics/btv036 · 2015 · External reference
10.1073/pnas.1421834112
10.1073/pnas.1421834112 · External reference
Metabolic potential of microbial mats and microbialites: Autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources
10.1142/s0219720016500207 · 2016 · External reference
Metabolic modelling of syntrophic-like growth of a 1,3-propanediol producer, Clostridium butyricum, and a methanogenic archeon, Methanosarcina mazei, under anaerobic conditions
10.1007/s00449-009-0359-0 · 2010 · External reference
10.3389/fpls.2015.00004
10.3389/fpls.2015.00004 · External reference
10.1186/1752-0509-4-120
10.1186/1752-0509-4-120 · External reference
Emergent cooperation in microbial metabolism
10.1038/msb.2010.66 · 2010 · External reference
10.1093/genetics/137.4.903
10.1093/genetics/137.4.903 · External reference
Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association
10.1038/ncomms3809 · 2013 · External reference
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2–32 and Faecalibacterium prausnitzii A2–165 and their interaction
2014 · External reference
Metabolic model reconstruction and analysis of an artificial microbial ecosystem for vitamin C production
10.1016/j.jbiotec.2014.04.027 · 2014 · External reference
10.1002/btpr.2028
10.1002/btpr.2028 · External reference
10.1002/bit.25880
10.1002/bit.25880 · External reference
Metabolic niche of a prominent sulfate-reducing human gut bacterium
2013 · External reference
Recon3D enables a three-dimensional view of gene variation in human metabolism
10.1038/nbt.4072 · 2018 · External reference
A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities
10.1186/1752-0509-5-167 · 2011 · External reference
Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing
10.1002/biot.201000159 · 2010 · External reference
The design of long-term effective uranium bioremediation strategy using a community metabolic model
10.1002/bit.24528 · 2012 · External reference
10.1101/gad.1985210
10.1101/gad.1985210 · External reference
Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment
10.1186/s12862-016-0733-x · 2016 · External reference
10.1186/s12918-017-0430-4
10.1186/s12918-017-0430-4 · External reference
10.1128/msystems.00170-17
10.1128/msystems.00170-17 · External reference
Dynamic metabolic modeling of a microaerobic yeast co-culture: Predicting and optimizing ethanol production from glucose/xylose mixtures
10.1186/1754-6834-6-44 · 2013 · External reference
Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures
10.1002/bit.22954 · 2011 · External reference
Methanogenesis from ethanol by defined mixed continuous cultures
1989 · External reference
Ex uno plures: clonal reinforcement drives evolution of a simple microbial community
10.1371/journal.pgen.1004430 · 2014 · External reference
Emergent biosynthetic capacity in simple microbial communities
2014 · External reference
Model-based quantification of metabolic interactions from dynamic microbial-community data
10.1371/journal.pone.0173183 · 2017 · External reference
Novel cooperation experimentally evolved between species
2010 · External reference
