Microbial model communities: To understand complexity, harness the power of simplicity
暂无分享,去创建一个
[1] Mary E. Miller,et al. Budding Yeast for Budding Geneticists: A Primer on the Saccharomyces cerevisiae Model System , 2014, Genetics.
[2] C. Fuqua,et al. Bacterial competition: surviving and thriving in the microbial jungle , 2010, Nature Reviews Microbiology.
[3] S. Sørensen,et al. Low‐abundant species facilitates specific spatial organization that promotes multispecies biofilm formation , 2017, Environmental microbiology.
[4] L. Öhman,et al. Gut Microbiota as Potential Orchestrators of Irritable Bowel Syndrome , 2015, Gut and liver.
[5] N. Gutierrez,et al. Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes , 2019, mSystems.
[6] F. Hildebrand,et al. From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes , 2020, Computational and structural biotechnology journal.
[7] Sigal Ben-Yehuda,et al. Intercellular Nanotubes Mediate Bacterial Communication , 2011, Cell.
[8] James Q. Boedicker,et al. The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community , 2016, PLoS Comput. Biol..
[9] S. Sørensen,et al. High-Throughput Screening of Multispecies Biofilm Formation and Quantitative PCR-Based Assessment of Individual Species Proportions, Useful for Exploring Interspecific Bacterial Interactions , 2013, Microbial Ecology.
[10] M. Antoniewicz. A guide to deciphering microbial interactions and metabolic fluxes in microbiome communities. , 2020, Current opinion in biotechnology.
[11] S. Sørensen,et al. Priority of Early Colonizers but No Effect on Cohabitants in a Synergistic Biofilm Community , 2019, Front. Microbiol..
[12] K. Zengler,et al. The social network of microorganisms — how auxotrophies shape complex communities , 2018, Nature Reviews Microbiology.
[13] Matthew F. Traxler,et al. In Search of Model Ecological Systems for Understanding Specialized Metabolism , 2018, mSystems.
[14] C. Ubeda,et al. Manipulation of the quorum sensing signal AI-2 affects the antibiotic-treated gut microbiota. , 2015, Cell reports.
[15] Alex H. Lang,et al. Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. , 2014, Cell reports.
[16] L. Engstrand,et al. No distinct microbiome signature of irritable bowel syndrome found in a Swedish random population , 2019, Gut.
[17] James J Collins,et al. Designing microbial consortia with defined social interactions , 2018, Nature Chemical Biology.
[18] Erin Wilson,et al. Quantitative and Qualitative Assessment Methods for Biofilm Growth: A Mini-review. , 2017, Research & reviews. Journal of engineering and technology.
[19] Trevor R. Zuroff,et al. Consortia-mediated bioprocessing of cellulose to ethanol with a symbiotic Clostridium phytofermentans/yeast co-culture , 2013, Biotechnology for Biofuels.
[20] Robert Marsland,et al. The Community Simulator: A Python package for microbial ecology , 2019, bioRxiv.
[21] S. Rice,et al. Interspecific diversity reduces and functionally substitutes for intraspecific variation in biofilm communities , 2015, The ISME Journal.
[22] K. Foster,et al. Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species , 2012, Current Biology.
[23] E. Papoutsakis,et al. Direct cell-to-cell exchange of matter in a synthetic Clostridium syntrophy enables CO2 fixation, superior metabolite yields, and an expanded metabolic space. , 2019, Metabolic engineering.
[24] Daniel St Johnston,et al. The art and design of genetic screens: Drosophila melanogaster , 2002, Nature Reviews Genetics.
[25] S. Sørensen,et al. A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community , 2017, Scientific Reports.
[26] M. Keller,et al. Self-establishing communities enable cooperative metabolite exchange in a eukaryote , 2015, eLife.
[27] J. Choi,et al. Defined spatial structure stabilizes a synthetic multispecies bacterial community , 2008, Proceedings of the National Academy of Sciences.
[28] Z. D. Blount,et al. The unexhausted potential of E. coli , 2015, eLife.
[29] Rachel J. Dutton,et al. Cheese Rind Communities Provide Tractable Systems for In Situ and In Vitro Studies of Microbial Diversity , 2014, Cell.
[30] S. Sørensen,et al. Bacterial social interactions and the emergence of community-intrinsic properties. , 2018, Current opinion in microbiology.
[31] Allan Konopka,et al. What is microbial community ecology? , 2009, The ISME Journal.
[32] Kiran Raosaheb Patil,et al. Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow , 2017, Cell systems.
[33] Orkun S. Soyer,et al. Synthetic microbial communities , 2014, Current opinion in microbiology.
[34] S. Rice,et al. Pseudomonas aeruginosa PAO1 exopolysaccharides are important for mixed species biofilm community development and stress tolerance , 2015, Front. Microbiol..
[35] V. Cooper,et al. Character displacement and the evolution of niche complementarity in a model biofilm community , 2015, Evolution; international journal of organic evolution.
[36] B. Kerr,et al. Big questions, small worlds: microbial model systems in ecology. , 2004, Trends in ecology & evolution.
[37] Orkun S. Soyer,et al. Cooperation in microbial communities and their biotechnological applications , 2017, Environmental microbiology.
[38] E. Casamayor,et al. The microbial contribution to macroecology , 2014, Front. Microbiol..
[39] P. Silver,et al. Emergent cooperation in microbial metabolism , 2010, Molecular systems biology.
[40] Gabriel L. Lozano,et al. Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior , 2018, mBio.
[41] H. Vlamakis,et al. Microbial genes and pathways in inflammatory bowel disease , 2019, Nature Reviews Microbiology.
[42] B. Wolfe,et al. Fungal volatiles mediate cheese rind microbiome assembly. , 2020, Environmental microbiology.
[43] B. Glick,et al. Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms. , 2018, Microbiological research.
[44] J. Bengtsson-Palme. Strategies for Taxonomic and Functional Annotation of Metagenomes , 2018 .
[45] Trent R Northen,et al. Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism. , 2016, ACS synthetic biology.
[46] Kiran Raosaheb Patil,et al. Model microbial communities for ecosystems biology , 2017 .
[47] S. Sørensen,et al. Community-intrinsic properties enhance keratin degradation from bacterial consortia , 2020, PloS one.
[48] R. Amann,et al. Use of green fluorescent protein as a marker for ecological studies of activated sludge communities , 1997 .
[49] Mat E. Barnet,et al. A synthetic Escherichia coli predator–prey ecosystem , 2008, Molecular systems biology.
[50] K. Rumbaugh,et al. Synergistic Interactions of Pseudomonas aeruginosa and Staphylococcus aureus in an In Vitro Wound Model , 2014, Infection and Immunity.
[51] Yan Sun,et al. In vitro multispecies Lubbock chronic wound biofilm model , 2008, Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society.
[52] H. Blanck,et al. Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms. , 2016, The Science of the total environment.
[53] Aaron Clauset,et al. Using null models to infer microbial co-occurrence networks , 2016, bioRxiv.
[54] M. Chevrette,et al. Experimental Microbiomes: Models Not to Scale , 2019, mSystems.
[55] S. Rice,et al. Biofilm development and enhanced stress resistance of a model, mixed-species community biofilm , 2013, The ISME Journal.
[56] F. Abram. Systems-based approaches to unravel multi-species microbial community functioning , 2014, Computational and structural biotechnology journal.
[57] R. Rosenzweig,et al. Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli. , 1994, Genetics.
[58] Maciek R Antoniewicz,et al. (13)C-metabolic flux analysis of co-cultures: A novel approach. , 2015, Metabolic engineering.
[59] S. Sørensen,et al. Deciphering links between bacterial interactions and spatial organization in multispecies biofilms , 2019, The ISME Journal.
[60] Bonnie L. Bassler,et al. Interference with AI-2-mediated bacterial cell–cell communication , 2005, Nature.
[61] Aidong Yang,et al. Analysis of productivity and stability of synthetic microbial communities , 2019, Journal of the Royal Society Interface.
[62] S. Sørensen,et al. Synergistic Interactions within a Multispecies Biofilm Enhance Individual Species Protection against Grazing by a Pelagic Protozoan , 2018, Front. Microbiol..
[63] Peer Bork,et al. children with inflammatory bowel disease and healthy siblings in taxonomic and functional composition : a metagenomic analysis , 2018 .
[64] A. Maurelli,et al. Shigella flexneri LuxS Quorum-Sensing System Modulates virB Expression but Is Not Essential for Virulence , 2001, Infection and Immunity.
[65] Mikhail Tikhonov,et al. Emergent simplicity in microbial community assembly , 2017, Science.
[66] William R. Harcombe,et al. Cross-feeding modulates antibiotic tolerance in bacterial communities , 2018, The ISME Journal.
[67] J. H. Burns,et al. More closely related species are more ecologically similar in an experimental test , 2011, Proceedings of the National Academy of Sciences.
[68] J. Snape,et al. The ‘SELection End points in Communities of bacTeria’ (SELECT) Method: A Novel Experimental Assay to Facilitate Risk Assessment of Selection for Antimicrobial Resistance in the Environment , 2020, Environmental health perspectives.
[69] N. Sanders,et al. Macroecology to Unite All Life, Large and Small. , 2018, Trends in ecology & evolution.
[70] A. Goulsbra,et al. Green fluorescent protein as a novel species-specific marker in enteric dual-species biofilms. , 1998, Microbiology.
[71] Courtney R. Armour,et al. A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome , 2018, mSystems.
[72] M. Blaser,et al. The human microbiome: at the interface of health and disease , 2012, Nature Reviews Genetics.
[73] Søren Molin,et al. Metabolic Commensalism and Competition in a Two-Species Microbial Consortium , 2002, Applied and Environmental Microbiology.
[74] S. Rice,et al. Influence of interspecies interactions on the spatial organization of dual species bacterial communities , 2020, Biofilm.
[75] Federica Villa,et al. Development of a Laboratory Model of a Phototroph-Heterotroph Mixed-Species Biofilm at the Stone/Air Interface , 2015, Front. Microbiol..
[76] Jingyuan Fu,et al. Structural variation in the gut microbiome associates with host health , 2019, Nature.
[77] L. Lynd,et al. Coculture of Staphylococcus aureus with Pseudomonas aeruginosa Drives S. aureus towards Fermentative Metabolism and Reduced Viability in a Cystic Fibrosis Model , 2015, Journal of bacteriology.
[78] Christopher P. Long,et al. Metabolism in dense microbial colonies: 13C metabolic flux analysis of E. coli grown on agar identifies two distinct cell populations with acetate cross-feeding. , 2018, Metabolic engineering.
[79] Jennifer L. Reed,et al. Adaptive Evolution of Synthetic Cooperating Communities Improves Growth Performance , 2014, PloS one.
[80] Jizhong Zhou,et al. A general framework for quantitatively assessing ecological stochasticity , 2019, Proceedings of the National Academy of Sciences.
[81] James J Collins,et al. Syntrophic exchange in synthetic microbial communities , 2014, Proceedings of the National Academy of Sciences.
[82] Ophelia S. Venturelli,et al. Deciphering microbial interactions in synthetic human gut microbiome communities , 2017, bioRxiv.
[83] Karsten Zengler,et al. Modelling approaches for studying the microbiome , 2019, Nature Microbiology.
[84] Gabriel L. Lozano,et al. Bacterial Analogs of Plant Tetrahydropyridine Alkaloids Mediate Microbial Interactions in a Rhizosphere Model System , 2019, Applied and Environmental Microbiology.
[85] Souichiro Kato,et al. Stable Coexistence of Five Bacterial Strains as a Cellulose-Degrading Community , 2005, Applied and Environmental Microbiology.
[86] William R. Harcombe,et al. Cross-feeding modulates the rate and mechanism of antibiotic resistance evolution in a model microbial community of Escherichia coli and Salmonella enterica , 2019, bioRxiv.
[87] S. Schnitzer,et al. Soil microbes regulate ecosystem productivity and maintain species diversity , 2011, Plant signaling & behavior.
[88] R. Britton,et al. Identification of Simplified Microbial Communities That Inhibit Clostridioides difficile Infection through Dilution/Extinction , 2020, mSphere.
[89] Michel Loreau,et al. Microbial diversity, producer–decomposer interactions and ecosystem processes: a theoretical model , 2001, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[90] E. Kristiansson,et al. The structure and diversity of human, animal and environmental resistomes , 2016, Microbiome.
[91] Sixing Huang,et al. Dilution-to-Stimulation/Extinction Method: a Combination Enrichment Strategy To Develop a Minimal and Versatile Lignocellulolytic Bacterial Consortium , 2020, Applied and Environmental Microbiology.
[92] Andrew Gonzalez,et al. Are natural microcosms useful model systems for ecology? , 2004, Trends in ecology & evolution.
[93] K. Foster,et al. The ecology of the microbiome: Networks, competition, and stability , 2015, Science.
[94] Aravinthan D. T. Samuel,et al. Caenorhabditis elegans: a model system for systems neuroscience , 2009, Current Opinion in Neurobiology.
[95] M. Feldman,et al. Local dispersal promotes biodiversity in a real-life game of rock–paper–scissors , 2002, Nature.
[96] Michaeline B. N. Albright,et al. Function and functional redundancy in microbial systems , 2018, Nature Ecology & Evolution.