Design, analysis and application of synthetic microbial consortia

Purnick, 2009, The second wave of synthetic biology: from modules to systems, Nat Rev Mol Cell Biol, 10, 410, 10.1038/nrm2698

Brenner, 2008, Engineering microbial consortia: a new frontier in synthetic biology, Trends Biotechnol, 26, 483, 10.1016/j.tibtech.2008.05.004

Gerchman, 2004, Teaching bacteria a new language, Proc Natl Acad Sci USA, 101, 2221, 10.1073/pnas.0400473101

Shong, 2012, Towards synthetic microbial consortia for bioprocessing, Curr Opin Biotechnol, 23, 798, 10.1016/j.copbio.2012.02.001

Großkopf, 2014, Synthetic microbial communities, Curr Opin Microbiol, 18, 72, 10.1016/j.mib.2014.02.002

Woyke, 2006, Symbiosis insights through metagenomic analysis of a microbial consortium, Nature, 443, 950, 10.1038/nature05192

Li, 2010, Transcriptome shifts in response to furfural and acetic acid in Saccharomyces cerevisiae, Appl Microbiol Biotechnol, 86, 1915, 10.1007/s00253-010-2518-2

Ma, 2013, Quantitative proteomic profiling reveals photosynthesis responsible for inoculum size dependent variation in Chlorella sorokiniana, Biotechnol Bioeng, 110, 773, 10.1002/bit.24762

Wang, 2014, Comparative metabolic profiling revealed limitations in xylose-fermenting yeast during co-fermentation of glucose and xylose in the presence of inhibitors, Biotechnol Bioeng, 111, 152, 10.1002/bit.24992

Greenblum, 2012, Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease, Proc Natl Acad Sci USA, 109, 594, 10.1073/pnas.1116053109

Wang, 2014, Marine metaproteomics: current status and future directions, J Proteomics, 97, 27, 10.1016/j.jprot.2013.08.024

Du, 2012, Metabolomic profiling elucidates community dynamics of the Ketogulonicigenium vulgare-Bacillus megaterium consortium, Metabolomics, 8, 960, 10.1007/s11306-011-0392-2

Voigt, 2006, Genetic parts to program bacteria, Curr Opin Biotechnol, 17, 548, 10.1016/j.copbio.2006.09.001

Canton, 2008, Refinement and standardization of synthetic biological parts and devices, Nat Biotechnol, 26, 787, 10.1038/nbt1413

Slusarczyk, 2012, Foundations for the design and implementation of synthetic genetic circuits, Nat Rev Genet, 13, 406, 10.1038/nrg3227

Lim, 2010, Designing customized cell signalling circuits, Nat Rev Mol Cell Biol, 11, 393, 10.1038/nrm2904

Zuroff, 2013, Consortia-mediated bioprocessing of cellulose to ethanol with a symbiotic Clostridium phytofermentans/yeast co-culture, Biotechnol Biofuels, 6, 59, 10.1186/1754-6834-6-59

Rosenbaum, 2011, Shewanella oneidensis in a lactate-fed pure-culture and a glucose-fed co-culture with Lactococcus lactis with an electrode as electron acceptor, Bioresour Technol, 102, 2623, 10.1016/j.biortech.2010.10.033

Bobadilla Fazzini, 2010, Consortia modulation of the stress response: proteomic analysis of single strain versus mixed culture, Environ Microbiol, 12, 2436, 10.1111/j.1462-2920.2010.02217.x

Zhou, 2015, Distributing a metabolic pathway among a microbial consortium enhances production of natural products, Nat Biotechnol, 33, 377, 10.1038/nbt.3095

Brenner, 2007, Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium, Proc Natl Acad Sci USA, 104, 17300, 10.1073/pnas.0704256104

Basu, 2004, Spatiotemporal control of gene expression with pulse-generating networks, Proc Natl Acad Sci USA, 101, 6355, 10.1073/pnas.0307571101

Basu, 2005, A synthetic multicellular system for programmed pattern formation, Nature, 434, 1130, 10.1038/nature03461

Chen, 2005, Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana, Nat Biotechnol, 23, 1551, 10.1038/nbt1162

Chuang, 2009, Simpson's paradox in a synthetic microbial system, Science, 323, 272, 10.1126/science.1166739

Prindle, 2012, A sensing array of radically coupled genetic ‘biopixels‘, Nature, 481, 39, 10.1038/nature10722

Tabor, 2009, A synthetic genetic edge detection program, Cell, 137, 1272, 10.1016/j.cell.2009.04.048

Danino, 2010, A synchronized quorum of genetic clocks, Nature, 463, 326, 10.1038/nature08753

Song, 2009, Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem, Nat Chem Biol, 5, 929, 10.1038/nchembio.244

Liu, 2011, Sequential establishment of stripe patterns in an expanding cell population, Science, 334, 238, 10.1126/science.1209042

Hong, 2012, Synthetic quorum-sensing circuit to control consortial biofilm formation and dispersal in a microfluidic device, Nat Commun, 3, 613, 10.1038/ncomms1616

Smith, 2014, Programmed Allee effect in bacteria causes a tradeoff between population spread and survival, Proc Natl Acad Sci USA, 111, 1969, 10.1073/pnas.1315954111

Payne, 2013, Temporal control of self-organized pattern formation without morphogen gradients in bacteria, Mol Syst Biol, 9, 697, 10.1038/msb.2013.55

Hosoda, 2011, Cooperative adaptation to establishment of a synthetic bacterial mutualism, PLoS ONE, 6, e17105, 10.1371/journal.pone.0017105

Kerner, 2012, A programmable Escherichia coli consortium via tunable symbiosis, PLoS ONE, 7, e34032, 10.1371/journal.pone.0034032

Balagaddé, 2008, A synthetic Escherichia coli predator-prey ecosystem, Mol Syst Biol, 4, 187, 10.1038/msb.2008.24

Hu, 2010, An environment-sensitive synthetic microbial ecosystem, PLoS ONE, 5, 10619, 10.1371/journal.pone.0010619

Shou, 2007, Synthetic cooperation in engineered yeast populations, Proc Natl Acad Sci USA, 104, 1877, 10.1073/pnas.0610575104

Zhang, 2014, Adaptive evolution of synthetic cooperating communities improves growth performance, PLoS ONE, 9, e108297, 10.1371/journal.pone.0108297

Pande, 2014, Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria, ISME J, 8, 953, 10.1038/ismej.2013.211

Mee, 2014, Syntrophic exchange in synthetic microbial communities, Proc Natl Acad Sci USA, 111, E2149, 10.1073/pnas.1405641111

Kerr, 2002, Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors, Nature, 418, 171, 10.1038/nature00823

Reichenbach, 2007, Mobility promotes and jeopardizes biodiversity in rock-paper-scissors games, Nature, 448, 1046, 10.1038/nature06095

Gore, 2009, Snowdrift game dynamics and facultative cheating in yeast, Nature, 459, 253, 10.1038/nature07921

Waite, 2012, Adaptation to a new environment allows cooperators to purge cheaters stochastically, Proc Natl Acad Sci USA, 109, 19079, 10.1073/pnas.1210190109

Nadell, 2012, Mutually helping microbes can evolve by hitchhiking, Proc Natl Acad Sci USA, 109, 19037, 10.1073/pnas.1217199109

Eiteman, 2008, A co-fermentation strategy to consume sugar mixtures effectively, J Biol Eng, 2, 3, 10.1186/1754-1611-2-3

Shin, 2010, Escherichia coli binary culture engineered for direct fermentation of hemicellulose to a biofuel, Appl Environ Microbiol, 76, 8150, 10.1128/AEM.00908-10

Goyal, 2011, Simultaneous cell growth and ethanol production from cellulose by an engineered yeast consortium displaying a functional mini-cellulosome, Microb Cell Fact, 10, 89, 10.1186/1475-2859-10-89

Tsai, 2010, Surface display of a functional minicellulosome by intracellular complementation using a synthetic yeast consortium and its application to cellulose hydrolysis and ethanol production, Appl Environ Microbiol, 76, 7514, 10.1128/AEM.01777-10

Fan, 2013, In vitro assembly of minicellulosomes with two scaffoldins on the yeast cell surface for cellulose saccharification and bioethanol production, Process Biochem, 48, 430, 10.1016/j.procbio.2013.01.012

Fan, 2012, Self-surface assembly of cellulosomes with two miniscaffoldins on Saccharomyces cerevisiae for cellulosic ethanol production, Proc Natl Acad Sci USA, 109, 13260, 10.1073/pnas.1209856109

Zhang, 2015, Engineering Escherichia coli coculture systems for the production of biochemical products, Proc Natl Acad Sci USA, 112, 8266, 10.1073/pnas.1506781112

Marchand, 2013, Peptide-based communication system enables Escherichia coli to Bacillus megaterium interspecies signaling, Biotechnol Bioeng, 110, 3003, 10.1002/bit.24975

Kubo, 2013, Construction of bacteria-eukaryote synthetic mutualism, Biosystems, 113, 66, 10.1016/j.biosystems.2013.05.006

Santala, 2014, Rationally engineered synthetic coculture for improved biomass and product formation, PLoS ONE, 9, e113786, 10.1371/journal.pone.0113786

Meyer, 2013, Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth, J Bacteriol, 195, 990, 10.1128/JB.01959-12

Walker, 2009, The electron transfer system of syntrophically grown Desulfovibrio vulgaris, J Bacteriol, 191, 5793, 10.1128/JB.00356-09

Mallaá Shrestha, 2014, A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane, Energy Environ Sci, 7, 408, 10.1039/C3EE42189A

Dubey, 2011, Intercellular nanotubes mediate bacterial communication, Cell, 144, 590, 10.1016/j.cell.2011.01.015

Pande, 2015, Metabolic cross-feeding via intercellular nanotubes among bacteria, Nat Commun, 6, 1, 10.1038/ncomms7238

Zhou, 2011, Metabolome profiling reveals metabolic cooperation between Bacillus megaterium and Ketogulonicigenium vulgare during induced swarm motility, Appl Environ Microbiol, 77, 7023, 10.1128/AEM.05123-11

Ma, 2011, Integrated proteomic and metabolomic analysis of an artificial microbial community for two-step production of vitamin C, PLoS ONE, 6, e26108, 10.1371/journal.pone.0026108

Du, 2013, Combinational expression of sorbose/sorbosone dehydrogenases and cofactor pyrroloquinoline quinone increases 2-keto-l-gulonic acid production in Ketogulonigenium vulgare-Bacillus cereus consortium, Metab Eng, 19, 50, 10.1016/j.ymben.2013.05.006

Ashoor, 2015, Cell-recycle batch process of Scheffersomyces stipitis and Saccharomyces cerevisiae co-culture for second generation bioethanol production, Biotechnol Lett, 37, 2213, 10.1007/s10529-015-1919-9

Park, 2012, One-pot bioethanol production from cellulose by co-culture of Acremonium cellulolyticus and Saccharomyces cerevisiae, Biotechnol Biofuels, 5, 1, 10.1186/1754-6834-5-64

Costa, 2015, Prospective technology on bioethanol production from photofermentation, Bioresour Technol, 181, 330, 10.1016/j.biortech.2015.01.090

Minty, 2013, Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass, Proc Natl Acad Sci USA, 110, 14592, 10.1073/pnas.1218447110

Wang, 2015, Developing a mesophilic co-culture for direct conversion of cellulose to butanol in consolidated bioprocess, Biotechnol Biofuels, 8, 1, 10.1186/s13068-015-0266-3

Kiyoshi, 2015, Butanol production from alkali-pretreated rice straw by co-culture of Clostridium thermocellum and Clostridium saccharoperbutylacetonicum, Bioresour Technol, 186, 325, 10.1016/j.biortech.2015.03.061

Venkataraman, 2011, Metabolite-based mutualism between Pseudomonas aeruginosa PA14 and Enterobacter aerogenes enhances current generation in bioelectrochemical systems, Energy Environ Sci, 4, 4550, 10.1039/c1ee01377g

Wang, 2015, Metabolite-enabled mutualistic interaction between Shewanella oneidensis and Escherichia coli in a co-culture using an electrode as electron acceptor, Sci Rep, 5, 860

Qu, 2012, Use of a coculture to enable current production by Geobacter sulfurreducens, Appl Environ Microbiol, 78, 3484, 10.1128/AEM.00073-12

Bourdakos, 2014, A defined co-culture of Geobacter sulfurreducens and Escherichia coli in a membrane-less microbial fuel cell, Biotechnol Bioeng, 111, 709, 10.1002/bit.25137

Wu, 2015, Expanding the chemical space for natural products by Aspergillus-Streptomyces co-cultivation and biotransformation, Sci Rep, 5, 10868, 10.1038/srep10868

Wu, 2015, Metabolomics in the natural products field-a gateway to novel antibiotics, Drug Discov Today, 13, 11, 10.1016/j.ddtec.2015.01.004

Saeidi, 2011, Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen, Mol Syst Biol, 7, 521, 10.1038/msb.2011.55

Gupta, 2013, Genetically programmable pathogen sense and destroy, ACS Synth Biol, 2, 715, 10.1021/sb4000417

Hwang, 2013, Reprogramming microbes to be pathogen-seeking killers, ACS Synth Biol, 3, 228, 10.1021/sb400077j

Volzing, 2013, Antimicrobial peptides targeting gram-negative pathogens, produced and delivered by lactic acid bacteria, ACS Synth Biol, 2, 643, 10.1021/sb4000367

Claesen, 2014, Synthetic microbes as drug delivery systems, ACS Synth Biol, 4, 358, 10.1021/sb500258b

Ling, 2014, Lipid production by a mixed culture of oleaginous yeast and microalga from distillery and domestic mixed wastewater, Bioresour Technol, 173, 132, 10.1016/j.biortech.2014.09.047

Wrede, 2014, Co-cultivation of fungal and microalgal cells as an efficient system for harvesting microalgal cells, lipid production and wastewater treatment, PLoS ONE, 9, e113497, 10.1371/journal.pone.0113497

Ren, 2015, Hydrogen and lipid production from starch wastewater by co-culture of anaerobic sludge and oleaginous microalgae with simultaneous COD, nitrogen and phosphorus removal, Water Res, 85, 404, 10.1016/j.watres.2015.08.057

Gieg, 2014, Syntrophic biodegradation of hydrocarbon contaminants, Curr Opin Biotechnol, 27, 21, 10.1016/j.copbio.2013.09.002

Chen, 2014, Enhanced biodegradation of alkane hydrocarbons and crude oil by mixed strains and bacterial community analysis, Appl Biochem Biotechnol, 172, 3433, 10.1007/s12010-014-0777-6

Lee, 2015, Systems strategies for developing industrial microbial strains, Nat Biotechnol, 33, 1061, 10.1038/nbt.3365

Weber, 2007, Synthetic ecosystems based on airborne inter-and intrakingdom communication, Proc Natl Acad Sci USA, 104, 10435, 10.1073/pnas.0701382104

Kim, 2008, Defined spatial structure stabilizes a synthetic multispecies bacterial community, Proc Natl Acad Sci USA, 105, 18188, 10.1073/pnas.0807935105

Scholten, 2007, Development and assessment of whole-genome oligonucleotide microarrays to analyze an anaerobic microbial community and its responses to oxidative stress, Biochem Biophys Res Commun, 358, 571, 10.1016/j.bbrc.2007.04.160

Li, 2015, Anaerobic mineralization of 2, 4, 6-tribromophenol to CO2 by a synthetic microbial community comprising Clostridium, Dehalobacter, and Desulfatiglans, Bioresour Technol, 176, 225, 10.1016/j.biortech.2014.10.097

Hošková, 2015, Structural and physiochemical characterization of rhamnolipids produced by Acinetobacter calcoaceticus, Enterobacter asburiae and Pseudomonas aeruginosa in single strain and mixed cultures, J Biotechnol, 193, 45, 10.1016/j.jbiotec.2014.11.014

Brethauer, 2014, Consolidated bioprocessing of lignocellulose by a microbial consortium, Energy Environ Sci, 7, 1446, 10.1039/c3ee41753k

Song, 2014, Synthetic microbial consortia: from systematic analysis to construction and applications, Chem Soc Rev, 43, 6954, 10.1039/C4CS00114A

Jakiela, 2013, Bacterial growth and adaptation in microdroplet chemostats, Angew Chem Int Ed Engl, 52, 8908, 10.1002/anie.201301524

Gebreselassie, 2015, 13C-Metabolic flux analysis of co-cultures: a novel approach, Metab Eng, 31, 132, 10.1016/j.ymben.2015.07.005

Burmølle, 2014, Interactions in multispecies biofilms: do they actually matter?, Trends Microbiol, 22, 84, 10.1016/j.tim.2013.12.004

Ran, 2015, Cellulosic ethanol production by natural bacterial consortia is enhanced by Pseudoxanthomonas taiwanensis, Biotechnol Biofuels, 8, 1