Czajka J, Wang Q, Wang Y, Tang YJ. Synthetic biology for manufacturing chemicals: constraints drive the use of non-conventional microbial platforms. Appl Microbiol Biotechnol. 2017;101:7427–34.
Article
CAS
PubMed
Google Scholar
Glick BR. Metabolic load and heterologous gene expression. Biotechnol Adv. 1995;13:247–61.
Article
CAS
PubMed
Google Scholar
Poust S, Hagen A, Katz L, Keasling JD. Narrowing the gap between the promise and reality of polyketide synthases as a synthetic biology platform. Curr Opin Biotechnol. 2014;30:32–9.
Article
CAS
PubMed
Google Scholar
Wu SG, He L, Wang Q, Tang YJ. An ancient Chinese wisdom for metabolic engineering: Yin-Yang. Microb Cell Fact. 2015;14:39.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bhan N, Xu P, Koffas MAG. Pathway and protein engineering approaches to produce novel and commodity small molecules. Curr Opin Biotechnol. 2013;24:1137–43.
Article
CAS
PubMed
Google Scholar
Hoehler TM, Jorgensen BB. Microbial life under extreme energy limitation. Nat Rev Microbiol. 2013;11:83–94.
Article
CAS
PubMed
Google Scholar
He L, Xiu Y, Jones JA, Baidoo EEK, Keasling JD, Tang YJ, Koffas MAG. Deciphering flux adjustments of engineered E. coli cells during fermentation with changing growth conditions. Metabo Eng. 2017;39:247–56.
Article
CAS
Google Scholar
Dong P, Maddali MV, Srimani JK, Thelot F, Nevins JR, Mathey-Prevot B, You L. Division of labour between Myc and G1 cyclins in cell cycle commitment and pace control. Nat Commun. 2014;5:4750.
Article
CAS
PubMed
Google Scholar
Saleski T, Tan JY, Lin XN. Dissecting the ecology of microbes using a systems toolbox. Cell Syst. 2017;5:442–4.
Article
CAS
PubMed
Google Scholar
Jones JA, Toparlak ÖD, Koffas MAG. Metabolic pathway balancing and its role in the production of biofuels and chemicals. Curr Opin Biotechnol. 2015;33:52–9.
Article
CAS
PubMed
Google Scholar
de Lima Brossi MJ, Jiménez DJ, Cortes-Tolalpa L, van Elsas JD. Soil-derived microbial consortia enriched with different plant biomass reveal distinct players acting in lignocellulose degradation. Microb Ecol. 2016;71:616–27.
Article
PubMed
CAS
Google Scholar
Hanly TJ, Henson MA. Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures. Biotechnol Bioeng. 2011;108:376–85.
Article
CAS
PubMed
Google Scholar
Biliouris K, Babson D, Schmidt-Dannert C, Kaznessis YN. Stochastic simulations of a synthetic bacteria-yeast ecosystem. BMC Syst Biol. 2012;6:58.
Article
PubMed
PubMed Central
Google Scholar
Zhang H, Pereira B, Li Z, Stephanopoulos G. Engineering Escherichia coli coculture systems for the production of biochemical products. Proc Natl Acad Sci USA. 2015;112:8266–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou K, Qiao K, Edgar S, Stephanopoulos G. Distributing a metabolic pathway among a microbial consortium enhances production of natural products. Nat Biotechnol. 2015;33:377–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jones JA, Vernacchio VR, Sinkoe AL, Collins SM, Ibrahim MHA, Lachance DM, Hahn J, Koffas MAG. Experimental and computational optimization of an Escherichia coli co-culture for the efficient production of flavonoids. Metab Eng. 2016;35:55–63.
Article
CAS
PubMed
Google Scholar
Fang Z, Jones JA, Zhou J, Koffas MAG. Engineering Escherichia coli co-cultures for production of curcuminoids from glucose. Biotechnol J. 2017;13:e1700576.
Article
PubMed
CAS
Google Scholar
Jones JA, Vernacchio VR, Collins SM, Shirke AN, Xiu Y, Englaender JA, Cress BF, McCutcheon CC, Linhardt RJ, Gross RA, Koffas MAG. Complete biosynthesis of anthocyanins using E. coli polycultures. MBio. 2017;8:e00621–17.
Article
PubMed
PubMed Central
Google Scholar
Stolyar S, Van Dien S, Hillesland KL, Pinel N, Lie TJ, Leigh JA, Stahl DA. Metabolic modeling of a mutualistic microbial community. Mol Syst Biol. 2007;3:92.
Article
PubMed
PubMed Central
CAS
Google Scholar
Shuler ML, Kargi F, DeLisa M. Bioprocess engineering: basic concepts. 3rd ed. NJ: Prentice Hall Englewood Cliffs; 2017.
Google Scholar
Zhang H, Wang X. Modular co-culture engineering, a new approach for metabolic engineering. Metab Eng. 2016;37:114–21.
Article
PubMed
CAS
Google Scholar
Carbonell X, Corchero JL, Cubarsí R, Vila P, Villaverde A. Control of Escherichia coli growth rate through cell density. Microbiol Res. 2002;157:257–65.
Article
PubMed
Google Scholar
Fu N, Peiris P, Markham J, Bavor J. A novel co-culture process with Zymomonas mobilis and Pichia stipitis for efficient ethanol production on glucose/xylose mixtures. Enzyme Microb Technol. 2009;45:210–7.
Article
CAS
Google Scholar
Harcombe WR, Riehl WJ, Dukovski I, Granger BR, Betts A, Lang AH, Bonilla G, Kar A, Leiby N, Mehta P, Marx CJ, Segrè D. Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell Rep. 2014;7:1104–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Harcombe WR, Chacón JM, Adamowicz EM, Chubiz LM, Marx CJ. Evolution of bidirectional costly mutualism from byproduct consumption. Proc Natl Acad Sci. 2018;115:12000.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cortes-Tolalpa L, Salles JF, van Elsas JD. Bacterial synergism in lignocellulose biomass degradation—complementary roles of degraders as influenced by complexity of the carbon source. Front Microbiol. 2017;8:1628.
Article
PubMed
PubMed Central
Google Scholar
Wen F, Sun J, Zhao H. Yeast surface display of trifunctional minicellulosomes for simultaneous saccharification and fermentation of cellulose to ethanol. Appl Environ Microbiol. 2010;76:1251–60.
Article
CAS
PubMed
Google Scholar
Weimer PJ, Zeikus JG. Fermentation of cellulose and cellobiose by Clostridium thermocellum in the absence of Methanobacterium thermoautotrophicum. Appl Environ Microbiol. 1977;33:289–97.
CAS
PubMed
PubMed Central
Google Scholar
He Q, Hemme CL, Jiang H, He Z, Zhou J. Mechanisms of enhanced cellulosic bioethanol fermentation by co-cultivation of Clostridium and Thermoanaerobacter spp. Bioresour Technol. 2011;102:9586–92.
Article
CAS
PubMed
Google Scholar
Wang Z, Cao G, Zheng J, Fu D, Song J, Zhang J, Zhao L, Yang Q. Developing a mesophilic co-culture for direct conversion of cellulose to butanol in consolidated bioprocess. Biotechnol Biofuels. 2015;8:84.
Article
PubMed
PubMed Central
CAS
Google Scholar
Minty JJ, Singer ME, Scholz SA, Bae CH, Ahn JH, Foster CE, Liao JC, Lin XN. Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proc Natl Acad Sci USA. 2013;110:14592–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Scholz SA, Graves I, Minty JJ, Lin XN. Production of cellulosic organic acids via synthetic fungal consortia. Biotechnol Bioeng. 2018;115:1096–100.
Article
CAS
PubMed
Google Scholar
Chen L, Du JL, Zhan YJ, Li JA, Zuo RR, Tian S. Consolidated bioprocessing for cellulosic ethanol conversion by cellulase–xylanase cell-surfaced yeast consortium. Prep Biochem Biotechnol. 2018;48:653–61.
Article
CAS
PubMed
Google Scholar
Verhoeven MD, de Valk SC, Daran J-MG, van Maris AJA, Pronk JT. Fermentation of glucose–xylose–arabinose mixtures by a synthetic consortium of single-sugar-fermenting Saccharomyces cerevisiae strains. FEMS Yeast Res. 2018;18:foy075.
Google Scholar
Lee CR, Kim C, Song YE, Im H, Oh YK, Park S, Kim JR. Co-culture-based biological carbon monoxide conversion by Citrobacter amalonaticus Y19 and Sporomusa ovata via a reducing-equivalent transfer mediator. Bioresour Technol. 2018;259:128–35.
Article
CAS
PubMed
Google Scholar
Boetius A, Ravenschlag K, Schubert CJ, Rickert D, Widdel F, Gieseke A, Amann R, Jørgensen BB, Witte U, Pfannkuche O. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature. 2000;407:623–6.
Article
CAS
PubMed
Google Scholar
Jones PR. Genetic instability in cyanobacteria—an elephant in the room? Front Bioeng Biotechnol. 2014;2:12.
Article
PubMed
PubMed Central
Google Scholar
Ducat DC, Avelar-Rivas JA, Way JC, Silver PA. Rerouting carbon flux to enhance photosynthetic productivity. Appl Environ Microbiol. 2012;78:2660–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Smith MJ, Francis MB. A designed A. vinelandii–S. elongatus coculture for chemical photoproduction from air, water, phosphate, and trace metals. ACS Synth Biol. 2016;5:955–61.
Article
CAS
PubMed
Google Scholar
Hays SG, Yan LLW, Silver PA, Ducat DC. Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction. J Biol Eng. 2017;11:4.
Article
PubMed
PubMed Central
CAS
Google Scholar
Weiss TL, Young EJ, Ducat DC. A synthetic, light-driven consortium of cyanobacteria and heterotrophic bacteria enables stable polyhydroxybutyrate production. Metab Eng. 2017;44:236–45.
Article
CAS
PubMed
Google Scholar
Li T, Li CT, Butler K, Hays SG, Guarnieri MT, Oyler GA, Betenbaugh MJ. Mimicking lichens: incorporation of yeast strains together with sucrose-secreting cyanobacteria improves survival, growth, ROS removal, and lipid production in a stable mutualistic co-culture production platform. Biotechnol Biofuels. 2017;10:55.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bohutskyi P, Kucek LA, Hill E, Pinchuk GE, Mundree SG, Beliaev AS. Conversion of stranded waste-stream carbon and nutrients into value-added products via metabolically coupled binary heterotroph–photoautotroph system. Bioresour Technol. 2018;260:68–75.
Article
CAS
PubMed
Google Scholar
Higgins BT, Labavitch JM, VanderGheynst JS. Co-culturing Chlorella minutissima with Escherichia coli can increase neutral lipid production and improve biodiesel quality. Biotechnol Bioeng. 2015;112:1801–9.
Article
CAS
PubMed
Google Scholar
Zhuang WQ, Yi S, Bill M, Brisson VL, Feng X, Men Y, Conrad ME, Tang YJ, Alvarez-Cohen L. Incomplete Wood–Ljungdahl pathway facilitates one-carbon metabolism in organohalide-respiring Dehalococcoides mccartyi. Proc Natl Acad Sci USA. 2014;111:6419–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang WXH. Industrial fermentation of vitamin C. In: Vandamme ERJ, editor. Industrial biotechnology of vitamins, biopigments, and antioxidants. Weinheim: Wiley; 2016.
Google Scholar
Song H, Ding MZ, Jia XQ, Ma Q, Yuan YJ. Synthetic microbial consortia: from systematic analysis to construction and applications. Chem Soc Rev. 2014;43:6954–81.
Article
CAS
PubMed
Google Scholar
Chang MCY, Eachus RA, Trieu W, Ro DK, Keasling JD. Engineering Escherichia coli for production of functionalized terpenoids using plant P450s. Nat Chem Biol. 2007;3:274–7.
Article
CAS
PubMed
Google Scholar
Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO biotechnology: tools to design, construct, evaluate, and optimize the metabolic pathway for biosynthesis of chemicals. Chem Rev. 2018;118:4–72.
Article
CAS
PubMed
Google Scholar
Shou W, Ram S, Vilar JMG. Synthetic cooperation in engineered yeast populations. Proc Natl Acad Sci. 2007;104:1877–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou K, Zou R, Stephanopoulos G, Too HP. Metabolite profiling identified methylerythritol cyclodiphosphate efflux as a limiting step in microbial isoprenoid production. PLoS ONE. 2012;7:e47513.
Article
CAS
PubMed
PubMed Central
Google Scholar
Abernathy MH, He L, Tang YJ. Channeling in native microbial pathways: implications and challenges for metabolic engineering. Biotechnol Adv. 2017;35:805–14.
Article
CAS
PubMed
Google Scholar
Wolfsberg E, Long CP, Antoniewicz MR. Metabolism in dense microbial colonies: 13C metabolic flux analysis of E. coli grown on agar identifies two distinct cell populations with acetate cross-feeding. Metab Eng. 2018;49:242–7.
Article
CAS
PubMed
Google Scholar
Bruce JB, Cooper GA, Chabas H, West SA, Griffin AS. Cheating and resistance to cheating in natural populations of the bacterium Pseudomonas fluorescens. Evolution. 2017;71:2484–95.
Article
CAS
PubMed
Google Scholar
Xiao Y, Bowen CH, Liu D, Zhang F. Exploiting nongenetic cell-to-cell variation for enhanced biosynthesis. Nat Chem Biol. 2016;12:339–44.
Article
CAS
PubMed
Google Scholar
Xiu Y, Jang S, Jones JA, Zill NA, Linhardt RJ, Yuan Q, Jung GY, Koffas MAG. Naringenin-responsive riboswitch-based fluorescent biosensor module for Escherichia coli co-cultures. Biotechnol Bioeng. 2017;114:2235–44.
Article
CAS
PubMed
Google Scholar
Li H, Opgenorth PH, Wernick DG, Rogers S, Wu TY, Higashide W, Malati P, Huo YX, Cho KM, Liao JC. Integrated electromicrobial conversion of CO2 to higher alcohols. Science. 2012;335:1596.
Article
CAS
PubMed
Google Scholar
Morrison CS, Armiger WB, Dodds DR, Dordick JS, Koffas MAG. Improved strategies for electrochemical 1,4-NAD(P)H2 regeneration: a new era of bioreactors for industrial biocatalysis. Biotechnol Adv. 2018;36:120–31.
Article
CAS
PubMed
Google Scholar
Kornienko N, Sakimoto KK, Herlihy DM, Nguyen SC, Alivisatos AP, Harris CB, Schwartzberg A, Yang P. Spectroscopic elucidation of energy transfer in hybrid inorganic-biological organisms for solar-to-chemical production. Proc Natl Acad Sci USA. 2016;113:11750–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sakimoto KK, Wong AB, Yang P. Self-photosensitization of nonphotosynthetic bacteria for solar-to-chemical production. Science. 2016;351:74–7.
Article
CAS
PubMed
Google Scholar
LaSarre B, McCully AL, Lennon JT, McKinlay JB. Microbial mutualism dynamics governed by dose-dependent toxicity of cross-fed nutrients. ISME J. 2017;11:337–48.
Article
CAS
PubMed
Google Scholar
McCully AL, LaSarre B, McKinlay JB. Growth-independent cross-feeding modifies boundaries for coexistence in a bacterial mutualism. Environ Microbiol. 2017;19:3538–50.
Article
CAS
PubMed
Google Scholar
Tang J. Microbial metabolomics. Curr Genomics. 2011;12:391–403.
Article
CAS
PubMed
PubMed Central
Google Scholar
Boghigian BA, Seth G, Kiss R, Pfeifer BA. Metabolic flux analysis for pharmaceutical production. Metab Eng. 2010;12:81–95.
Article
CAS
PubMed
Google Scholar
Schuetz R, Kuepfer L, Sauer U. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol. 2007;3:119.
Article
PubMed
PubMed Central
CAS
Google Scholar
Burgard AP, Pharkya P, Maranas CD. Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng. 2003;84:647–57.
Article
CAS
PubMed
Google Scholar
Xu P, Ranganathan S, Fowler ZL, Maranas CD, Koffas MAG. Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. Metab Eng. 2011;13:578–87.
Article
CAS
PubMed
Google Scholar
Chemler JA, Fowler ZL, McHugh KP, Koffas MAG. Improving NADPH availability for natural product biosynthesis in Escherichia coli by metabolic engineering. Metab Eng. 2010;12:96–104.
Article
CAS
PubMed
Google Scholar
Koch S, Benndorf D, Fronk K, Reichl U, Klamt S. Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process. Biotechnol Biofuels. 2016;9:17.
Article
PubMed
PubMed Central
CAS
Google Scholar
Milne CB, Kim PJ, Eddy JA, Price ND. Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology. Biotechnol J. 2009;4:1653–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Miller IJ, Vanee N, Fong SS, Lim-Fong GE, Kwan JC. Lack of overt genome reduction in the bryostatin-producing bryozoan symbiont “Candidatus Endobugula sertula”. Appl Environ Microbiol. 2016;82:6573–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Salimi F, Zhuang K, Mahadevan R. Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing. Biotechnol J. 2010;5:726–38.
Article
CAS
PubMed
Google Scholar
Gomez JA, Höffner K, Barton PI. From sugars to biodiesel using microalgae and yeast. Green Chem. 2016;18:461–75.
Article
CAS
Google Scholar
Eng A, Borenstein E. An algorithm for designing minimal microbial communities with desired metabolic capacities. Bioinformatics. 2016;32:2008–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Julien-Laferrière A, Bulteau L, Parrot D, Marchetti-Spaccamela A, Stougie L, Vinga S, Mary A, Sagot MF. A combinatorial algorithm for microbial consortia synthetic design. Sci Rep. 2016;6:29182.
Article
PubMed
PubMed Central
CAS
Google Scholar
Magnúsdóttir S, Heinken A, Kutt L, Ravcheev DA, Bauer E, Noronha A, Greenhalgh K, Jäger C, Baginska J, Wilmes P, Fleming RMT, Thiele I. Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nat Biotechnol. 2016;35:81–9.
Article
PubMed
CAS
Google Scholar
Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI, Covert MW. A whole-cell computational model predicts phenotype from genotype. Cell. 2012;150:389–401.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thiele I, Fleming RMT, Que R, Bordbar A, Diep D, Palsson BO. Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. PLoS ONE. 2012;7:e45635.
Article
CAS
PubMed
PubMed Central
Google Scholar
You L, Liu H, Blankenship RE, Tang YJ. Using photosystem I as a reporter protein for 13C analysis in a coculture containing cyanobacterium and a heterotrophic bacterium. Anal Biochem. 2015;477:86–8.
Article
CAS
PubMed
Google Scholar
Shaikh AS, Tang YJ, Mukhopadhyay A, Keasling JD. Isotopomer distributions in amino acids from a highly expressed protein as a proxy for those from total protein. Anal Chem. 2008;80:886–90.
Article
CAS
PubMed
Google Scholar
Rühl M, Hardt WD, Sauer U. Subpopulation-specific metabolic pathway usage in mixed cultures as revealed by reporter protein-based 13C analysis. Appl Environ Microbiol. 2011;77:1816–21.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ghosh A, Nilmeier J, Weaver D, Adams PD, Keasling JD, Mukhopadhyay A, Petzold CJ, Martin HG. A peptide-based method for 13C metabolic flux analysis in microbial communities. PLoS Comput Biol. 2014;10:e1003827.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gebreselassie NA, Antoniewicz MR. (13)C-metabolic flux analysis of co-cultures: a novel approach. Metab Eng. 2015;31:132–9.
Article
CAS
PubMed
PubMed Central
Google Scholar