A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

Dukovski, Ilija; Bajić, Djordje; Chacón, Jeremy M.; Quintin, Michael; Vila, Jean C. C.; Sulheim, Snorre; Pacheco, Alan R.; Bernstein, David B.; Riehl, William J.; Korolev, Kirill S.; Sanchez, Alvaro; Harcombe, William R.; Segrè, Daniel

doi:10.1038/s41596-021-00593-3

Title: A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

Journal Article · Mon Oct 11 00:00:00 EDT 2021 · Nature Protocols

DOI:https://doi.org/10.1038/s41596-021-00593-3· OSTI ID:1825266

^[1]; Bajić, Djordje ^[2]; Chacón, Jeremy M. ^[3]; Quintin, Michael ^[1]; Vila, Jean C. C. ^[2];

^[4];

^[1];

^[5]; Riehl, William J. ^[6]; Korolev, Kirill S. ^[1]; Sanchez, Alvaro ^[2];

^[3];

^[1]

Boston Univ., MA (United States); Boston Univ., MA (United States). Biological Design Center
Yale Univ., New Haven, CT (United States); Yale Univ., New Haven, CT (United States). Microbial Sciences Inst.
Univ. of Minnesota, St. Paul, MN (United States); Univ. of Minnesota, St. Paul, MN (United States). BioTechnology Inst.
Boston Univ., MA (United States); Norwegian Univ. of Science and Technology, Trondheim (Norway); SINTEF Energy Research, Trondheim (Norway)
Boston Univ., MA (United States). Biological Design Center
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. Overall, this protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Science Foundation (NSF); Human Frontiers Science Program; Research Council of Norway; Simons Foundation

Grant/Contract Number:: AC02-05CH11231; SC0004962; T32GM100842; 5R01DE024468; R01GM121950; 1457695; BSF 1635070; RGP0020/2016; 248885; RO1GM121498; 1R35 GM133467-01; 409704

OSTI ID:: 1825266

Journal Information:: Nature Protocols, Vol. 16; ISSN 1754-2189

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (103)

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems Pacheco, Alan R.; Moel, Mauricio; Segrè, Daniel Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-018-07946-9	journal	January 2019
Photoacclimation of Prochlorococcus sp. (Prochlorophyta) Strains Isolated from the North Atlantic and the Mediterranean Sea Partensky, F.; Hoepffner, N.; Li, Wkw. Plant Physiology, Vol. 101, Issue 1 https://doi.org/10.1104/pp.101.1.285	journal	January 1993
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities Machado, Daniel; Andrejev, Sergej; Tramontano, Melanie Nucleic Acids Research, Vol. 46, Issue 15 https://doi.org/10.1093/nar/gky537	journal	June 2018
Metabolomics of recombinant yeast: Gene expression, flux analysis and a mathematical model for gene regulation of metabolism Asenjo, J. A.; Diaz, H.; Cintolesi, A. Journal of Biotechnology, Vol. 136 https://doi.org/10.1016/j.jbiotec.2008.07.030	journal	October 2008
Fundamentals of Microbial Community Resistance and Resilience Shade, Ashley; Peter, Hannes; Allison, Steven D. Frontiers in Microbiology, Vol. 3 https://doi.org/10.3389/fmicb.2012.00417	journal	January 2012
A shared limiting resource leads to competitive exclusion in a cross-feeding system: Role of environment for cross-feeder coexistence Hammarlund, Sarah P.; Chacón, Jeremy M.; Harcombe, William R. Environmental Microbiology, Vol. 21, Issue 2 https://doi.org/10.1111/1462-2920.14493	journal	January 2019
Metabolic modeling of a mutualistic microbial community Stolyar, Sergey; Van Dien, Steve; Hillesland, Kristina Linnea Molecular Systems Biology, Vol. 3, Issue 1 https://doi.org/10.1038/msb4100131	journal	January 2007
Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics Harcombe, William R.; Riehl, William J.; Dukovski, Ilija Cell Reports, Vol. 7, Issue 4 https://doi.org/10.1016/j.celrep.2014.03.070	journal	May 2014
Current status and applications of genome-scale metabolic models Gu, Changdai; Kim, Gi Bae; Kim, Won Jun Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1730-3	journal	June 2019
The spatial and metabolic basis of colony size variation Chacón, Jeremy M.; Möbius, Wolfram; Harcombe, William R. The ISME Journal, Vol. 12, Issue 3 https://doi.org/10.1038/s41396-017-0038-0	journal	January 2018
Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide Orth, Jeffrey D.; Palsson, Bernhard Ø.; Fleming, R. M. T. EcoSal Plus, Vol. 4, Issue 1 https://doi.org/10.1128/ecosalplus.10.2.1	journal	September 2010
Constrained Allocation Flux Balance Analysis Mori, Matteo; Hwa, Terence; Martin, Olivier C. PLOS Computational Biology, Vol. 12, Issue 6 https://doi.org/10.1371/journal.pcbi.1004913	journal	June 2016
The BioCyc collection of microbial genomes and metabolic pathways Karp, Peter D.; Billington, Richard; Caspi, Ron Briefings in Bioinformatics, Vol. 20, Issue 4 https://doi.org/10.1093/bib/bbx085	journal	August 2017
Interface growth and pattern formation in bacterial colonies Matsushita, M.; Wakita, J.; Itoh, H. Physica A: Statistical Mechanics and its Applications, Vol. 249, Issue 1-4 https://doi.org/10.1016/S0378-4371(97)00511-6	journal	January 1998
Tools and strategies of systems metabolic engineering for the development of microbial cell factories for chemical production Ko, Yoo-Sung; Kim, Je Woong; Lee, Jong An Chemical Society Reviews, Vol. 49, Issue 14 https://doi.org/10.1039/D0CS00155D	journal	January 2020
A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities Tzamali, Eleftheria; Poirazi, Panayiota; Tollis, Ioannis G. BMC Systems Biology, Vol. 5, Issue 1 https://doi.org/10.1186/1752-0509-5-167	journal	January 2011
Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities Germerodt, Sebastian; Bohl, Katrin; Lück, Anja PLOS Computational Biology, Vol. 12, Issue 6 https://doi.org/10.1371/journal.pcbi.1004986	journal	June 2016
MEMOTE for standardized genome-scale metabolic model testing Lieven, Christian; Beber, Moritz E.; Olivier, Brett G. Nature Biotechnology, Vol. 38, Issue 3 https://doi.org/10.1038/s41587-020-0446-y	journal	March 2020
Morphological instability and dynamics of fronts in bacterial growth models with nonlinear diffusion Müller, Judith; van Saarloos, Wim Physical Review E, Vol. 65, Issue 6 https://doi.org/10.1103/PhysRevE.65.061111	journal	June 2002
Establishing Causality: Opportunities of Synthetic Communities for Plant Microbiome Research Vorholt, Julia A.; Vogel, Christine; Carlström, Charlotte I. Cell Host & Microbe, Vol. 22, Issue 2 https://doi.org/10.1016/j.chom.2017.07.004	journal	August 2017
Cell design in bacteria as a convex optimization problem Goelzer, Anne; Fromion, Vincent; Scorletti, Gérard Automatica, Vol. 47, Issue 6 https://doi.org/10.1016/j.automatica.2011.02.038	journal	June 2011
Diversity, stability and resilience of the human gut microbiota Lozupone, Catherine A.; Stombaugh, Jesse I.; Gordon, Jeffrey I. Nature, Vol. 489, Issue 7415 https://doi.org/10.1038/nature11550	journal	September 2012
Diffusion-Limited Growth of Microbial Colonies Tronnolone, Hayden; Tam, Alexander; Szenczi, Zoltán Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-23649-z	journal	April 2018
Constraint-based models predict metabolic and associated cellular functions Bordbar, Aarash; Monk, Jonathan M.; King, Zachary A. Nature Reviews Genetics, Vol. 15, Issue 2 https://doi.org/10.1038/nrg3643	journal	January 2014
Spatiotemporal modeling of microbial metabolism Chen, Jin; Gomez, Jose A.; Höffner, Kai BMC Systems Biology, Vol. 10, Issue 1 https://doi.org/10.1186/s12918-016-0259-2	journal	March 2016
An evolutionary algorithm for designing microbial communities via environmental modification Pacheco, Alan R.; Segrè, Daniel Journal of The Royal Society Interface, Vol. 18, Issue 179 https://doi.org/10.1098/rsif.2021.0348	journal	June 2021
Bridging substrate intake kinetics and bacterial growth phenotypes with flux balance analysis incorporating proteome allocation Zeng, Hong; Yang, Aidong Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-61174-0	journal	March 2020
A communal catalogue reveals Earth’s multiscale microbial diversity Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel Nature, Vol. 551, Issue 7681 https://doi.org/10.1038/nature24621	journal	November 2017
Prochlorococcus and Synechococcus: A comparative study of their optical properties in relation to their size and pigmentation Morel, André; Ahn, Yu-Hwan; Partensky, Frédéric Journal of Marine Research, Vol. 51, Issue 3 https://doi.org/10.1357/0022240933223963	journal	August 1993
The biomass objective function Feist, Adam M.; Palsson, Bernhard O. Current Opinion in Microbiology, Vol. 13, Issue 3 https://doi.org/10.1016/j.mib.2010.03.003	journal	June 2010
On the growth of non-motile bacteria colonies: an agent-based model for pattern formation Vassallo, Lautaro; Hansmann, David; Braunstein, Lidia A. The European Physical Journal B, Vol. 92, Issue 9 https://doi.org/10.1140/epjb/e2019-100265-0	journal	September 2019
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities Bauer, Eugen; Zimmermann, Johannes; Baldini, Federico PLOS Computational Biology, Vol. 13, Issue 5 https://doi.org/10.1371/journal.pcbi.1005544	journal	May 2017
Rhizosphere interactions: root exudates, microbes, and microbial communities Huang, Xing-Feng; Chaparro, Jacqueline M.; Reardon, Kenneth F. Botany, Vol. 92, Issue 4 https://doi.org/10.1139/cjb-2013-0225	journal	April 2014
Spatially-resolved metabolic cooperativity within dense bacterial colonies Cole, John A.; Kohler, Lars; Hedhli, Jamila BMC Systems Biology, Vol. 9, Issue 1 https://doi.org/10.1186/s12918-015-0155-1	journal	March 2015
Using Genome-scale Models to Predict Biological Capabilities O’Brien, Edward J.; Monk, Jonathan M.; Palsson, Bernhard O. Cell, Vol. 161, Issue 5 https://doi.org/10.1016/j.cell.2015.05.019	journal	May 2015
Branching instability in expanding bacterial colonies Giverso, Chiara; Verani, Marco; Ciarletta, Pasquale Journal of The Royal Society Interface, Vol. 12, Issue 104 https://doi.org/10.1098/rsif.2014.1290	journal	March 2015
Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures Hanly, Timothy J.; Henson, Michael A. Biotechnology and Bioengineering, Vol. 108, Issue 2 https://doi.org/10.1002/bit.22954	journal	October 2010
The evolution of cooperation within the gut microbiota Rakoff-Nahoum, Seth; Foster, Kevin R.; Comstock, Laurie E. Nature, Vol. 533, Issue 7602 https://doi.org/10.1038/nature17626	journal	April 2016
Integration of Langevin Equations with Multiplicative Noise and the Viability of Field Theories for Absorbing Phase Transitions Dornic, Ivan; Chaté, Hugues; Muñoz, Miguel A. Physical Review Letters, Vol. 94, Issue 10 https://doi.org/10.1103/PhysRevLett.94.100601	journal	March 2005
Principles for designing synthetic microbial communities Johns, Nathan I.; Blazejewski, Tomasz; Gomes, Antonio LC Current Opinion in Microbiology, Vol. 31 https://doi.org/10.1016/j.mib.2016.03.010	journal	June 2016
The global ocean microbiome Moran, M. A. Science, Vol. 350, Issue 6266 https://doi.org/10.1126/science.aac8455	journal	December 2015
Emergent simplicity in microbial community assembly Goldford, Joshua E.; Lu, Nanxi; Bajić, Djordje Science, Vol. 361, Issue 6401 https://doi.org/10.1126/science.aat1168	journal	August 2018
Constraints-based models: Regulation of Gene Expression Reduces the Steady-state Solution Space Covert, Markus W.; Palsson, Bernhard O. Journal of Theoretical Biology, Vol. 221, Issue 3 https://doi.org/10.1006/jtbi.2003.3071	journal	April 2003
Evolution of bidirectional costly mutualism from byproduct consumption Harcombe, William R.; Chacón, Jeremy M.; Adamowicz, Elizabeth M. Proceedings of the National Academy of Sciences, Vol. 115, Issue 47 https://doi.org/10.1073/pnas.1810949115	journal	October 2018
Absorption spectrum (380–700 nm) of pure water II Integrating cavity measurements Pope, Robin M.; Fry, Edward S. Applied Optics, Vol. 36, Issue 33 https://doi.org/10.1364/AO.36.008710	journal	January 1997
Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli Mahadevan, Radhakrishnan; Edwards, Jeremy S.; Doyle, Francis J. Biophysical Journal, Vol. 83, Issue 3 https://doi.org/10.1016/S0006-3495(02)73903-9	journal	September 2002
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments Zhuang, Kai; Izallalen, Mounir; Mouser, Paula The ISME Journal, Vol. 5, Issue 2 https://doi.org/10.1038/ismej.2010.117	journal	July 2010
A Model of Extracellular Enzymes in Free-Living Microbes: Which Strategy Pays Off? Traving, Sachia J.; Thygesen, Uffe H.; Riemann, Lasse Applied and Environmental Microbiology, Vol. 81, Issue 21 https://doi.org/10.1128/AEM.02070-15	journal	August 2015
Context-Specific Metabolic Networks Are Consistent with Experiments Becker, Scott A.; Palsson, Bernhard O. PLoS Computational Biology, Vol. 4, Issue 5 https://doi.org/10.1371/journal.pcbi.1000082	journal	May 2008
Manufacturing Molecules Through Metabolic Engineering Keasling, Jay D. Science, Vol. 330, Issue 6009, p. 1355-1358 https://doi.org/10.1126/science.1193990	journal	December 2010
A New Improved and Extended Version of the Multicell Bacterial Simulator `gro` Gutiérrez, Martín; Gregorio-Godoy, Paula; Pérez del Pulgar, Guillermo ACS Synthetic Biology, Vol. 6, Issue 8 https://doi.org/10.1021/acssynbio.7b00003	journal	May 2017
A reliable simulator for dynamic flux balance analysis Höffner, K.; Harwood, S. M.; Barton, P. I. Biotechnology and Bioengineering, Vol. 110, Issue 3 https://doi.org/10.1002/bit.24748	journal	October 2012
Massively parallel screening of synthetic microbial communities Kehe, Jared; Kulesa, Anthony; Ortiz, Anthony Proceedings of the National Academy of Sciences, Vol. 116, Issue 26 https://doi.org/10.1073/pnas.1900102116	journal	June 2019
Metabolic dependencies drive species co-occurrence in diverse microbial communities Zelezniak, Aleksej; Andrejev, Sergej; Ponomarova, Olga Proceedings of the National Academy of Sciences, Vol. 112, Issue 20 https://doi.org/10.1073/pnas.1421834112	journal	May 2015
Deciphering microbial interactions in synthetic human gut microbiome communities Venturelli, Ophelia S.; Carr, Alex V.; Fisher, Garth Molecular Systems Biology, Vol. 14, Issue 6 https://doi.org/10.15252/msb.20178157	journal	June 2018
Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks DiMucci, Demetrius; Kon, Mark; Segrè, Daniel mSystems, Vol. 3, Issue 5 https://doi.org/10.1128/mSystems.00181-18	journal	October 2018
The evolution of the host microbiome as an ecosystem on a leash Foster, Kevin R.; Schluter, Jonas; Coyte, Katharine Z. Nature, Vol. 548, Issue 7665 https://doi.org/10.1038/nature23292	journal	August 2017
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models King, Zachary A.; Lu, Justin; Dräger, Andreas Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1049	journal	October 2015
Spatial structure, cooperation and competition in biofilms Nadell, Carey D.; Drescher, Knut; Foster, Kevin R. Nature Reviews Microbiology, Vol. 14, Issue 9 https://doi.org/10.1038/nrmicro.2016.84	journal	July 2016
Dynamic flux balance analysis for synthetic microbial communities Henson, Michael A.; Hanly, Timothy J. IET Systems Biology, Vol. 8, Issue 5 https://doi.org/10.1049/iet-syb.2013.0021	journal	October 2014
Ecological systems biology: The dynamics of interacting populations Friedman, Jonathan; Gore, Jeff Current Opinion in Systems Biology, Vol. 1 https://doi.org/10.1016/j.coisb.2016.12.001	journal	February 2017
OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities Zomorrodi, Ali R.; Maranas, Costas D. PLoS Computational Biology, Vol. 8, Issue 2 https://doi.org/10.1371/journal.pcbi.1002363	journal	February 2012
Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in a Revised Genome-Scale Model of Prochlorococcus Ofaim, Shany; Sulheim, Snorre; Almaas, Eivind Frontiers in Genetics, Vol. 12 https://doi.org/10.3389/fgene.2021.586293	journal	February 2021
Resistance, resilience, and redundancy in microbial communities Allison, S. D.; Martiny, J. B. H. Proceedings of the National Academy of Sciences, Vol. 105, Issue Supplement 1 https://doi.org/10.1073/pnas.0801925105	journal	August 2008
Finite Difference Methods for Ordinary and Partial Differential Equations LeVeque, Randall J. https://doi.org/10.1137/1.9780898717839	book	January 2007
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0 Heirendt, Laurent; Arreckx, Sylvain; Pfau, Thomas Nature Protocols, Vol. 14, Issue 3 https://doi.org/10.1038/s41596-018-0098-2	journal	February 2019
Genetic demixing and evolution in linear stepping stone models Korolev, K. S.; Avlund, Mikkel; Hallatschek, Oskar Reviews of Modern Physics, Vol. 82, Issue 2 https://doi.org/10.1103/RevModPhys.82.1691	journal	May 2010
Regulation of Gene Expression in Flux Balance Models of Metabolism Covert, Markus W.; Schilling, Christophe H.; Palsson, Bernhard Journal of Theoretical Biology, Vol. 213, Issue 1 https://doi.org/10.1006/jtbi.2001.2405	journal	November 2001
Microbial carbon use efficiency predicted from genome-scale metabolic models Saifuddin, Mustafa; Bhatnagar, Jennifer M.; Segrè, Daniel Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11488-z	journal	August 2019
Theoretical results concerning light absorption in a discrete medium, and application to specific absorption of phytoplankton Morel, André; Bricaud, Annick Deep Sea Research Part A. Oceanographic Research Papers, Vol. 28, Issue 11 https://doi.org/10.1016/0198-0149(81)90039-X	journal	November 1981
Generic modelling of cooperative growth patterns in bacterial colonies Ben-Jacob, Eshel; Schochet, Ofer; Tenenbaum, Adam Nature, Vol. 368, Issue 6466 https://doi.org/10.1038/368046a0	journal	March 1994
Constraint-based stoichiometric modelling from single organisms to microbial communities Gottstein, Willi; Olivier, Brett G.; Bruggeman, Frank J. Journal of The Royal Society Interface, Vol. 13, Issue 124 https://doi.org/10.1098/rsif.2016.0627	journal	November 2016
Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models Lewis, Nathan E.; Hixson, Kim K.; Conrad, Tom M. Molecular Systems Biology, Vol. 6, Issue 1 https://doi.org/10.1038/msb.2010.47	journal	January 2010
Mechanically Driven Growth of Quasi-Two-Dimensional Microbial Colonies Farrell, F. D. C.; Hallatschek, O.; Marenduzzo, D. Physical Review Letters, Vol. 111, Issue 16 https://doi.org/10.1103/PhysRevLett.111.168101	journal	October 2013
Investment in secreted enzymes during nutrient-limited growth is utility dependent Cezairliyan, Brent; Ausubel, Frederick M. Proceedings of the National Academy of Sciences, Vol. 114, Issue 37 https://doi.org/10.1073/pnas.1708580114	journal	August 2017
An Ecological Network of Polysaccharide Utilization among Human Intestinal Symbionts Rakoff-Nahoum, Seth; Coyne, Michael J.; Comstock, Laurie E. Current Biology, Vol. 24, Issue 1 https://doi.org/10.1016/j.cub.2013.10.077	journal	January 2014
Synthetic cooperation in engineered yeast populations Shou, W.; Ram, S.; Vilar, J. M. G. Proceedings of the National Academy of Sciences, Vol. 104, Issue 6 https://doi.org/10.1073/pnas.0610575104	journal	January 2007
Community Flux Balance Analysis for Microbial Consortia at Balanced Growth Khandelwal, Ruchir A.; Olivier, Brett G.; Röling, Wilfred F. M. PLoS ONE, Vol. 8, Issue 5 https://doi.org/10.1371/journal.pone.0064567	journal	May 2013
COBRApy: COnstraints-Based Reconstruction and Analysis for Python Ebrahim, Ali; Lerman, Joshua A.; Palsson, Bernhard O. BMC Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1186/1752-0509-7-74	journal	January 2013
A protocol for generating a high-quality genome-scale metabolic reconstruction Thiele, Ines; Palsson, Bernhard Ø Nature Protocols, Vol. 5, Issue 1 https://doi.org/10.1038/nprot.2009.203	journal	January 2010
Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH) Borer, Benedict; Ataman, Meriç; Hatzimanikatis, Vassily PLOS Computational Biology, Vol. 15, Issue 6 https://doi.org/10.1371/journal.pcbi.1007127	journal	June 2019
The Integrative Human Microbiome Project Consortium, iHMP Nature, Vol. 569, Issue 7758, p. 641-648 https://doi.org/10.1038/s41586-019-1238-8	journal	May 2019
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease Noronha, Alberto; Modamio, Jennifer; Jarosz, Yohan Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky992	journal	October 2018
Global Trends in Marine Plankton Diversity across Kingdoms of Life Ibarbalz, Federico M.; Henry, Nicolas; Brandão, Manoela C. Cell, Vol. 179, Issue 5 https://doi.org/10.1016/j.cell.2019.10.008	journal	November 2019
KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4163	journal	July 2018
The microbial habitat in soil: Scale, heterogeneity and functional consequences Nunan, Naoise Journal of Plant Nutrition and Soil Science, Vol. 180, Issue 4 https://doi.org/10.1002/jpln.201700184	journal	May 2017
Synthetic microbial communities Großkopf, Tobias; Soyer, Orkun S. Current Opinion in Microbiology, Vol. 18 https://doi.org/10.1016/j.mib.2014.02.002	journal	April 2014
Bioprinting microbial communities to examine interspecies interactions in time and space Hynes, William F.; Chacón, Jeremy; Segrè, Daniel Biomedical Physics & Engineering Express, Vol. 4, Issue 5 https://doi.org/10.1088/2057-1976/aad544	journal	August 2018
Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data Zomorrodi, Ali R.; Maranas, Costas D. BMC Systems Biology, Vol. 4, Issue 1 https://doi.org/10.1186/1752-0509-4-178	journal	December 2010
Analysis of optimality in natural and perturbed metabolic networks Segre, D.; Vitkup, D.; Church, G. M. Proceedings of the National Academy of Sciences, Vol. 99, Issue 23 https://doi.org/10.1073/pnas.232349399	journal	November 2002
Metabolic gene–deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes Fong, Stephen S.; Palsson, Bernhard Ø Nature Genetics, Vol. 36, Issue 10 https://doi.org/10.1038/ng1432	journal	September 2004
Modeling of spatiotemporal patterns in bacterial colonies Lacasta, A. M.; Cantalapiedra, I. R.; Auguet, C. E. Physical Review E, Vol. 59, Issue 6 https://doi.org/10.1103/PhysRevE.59.7036	journal	June 1999
Natural variability of phytoplanktonic absorption in oceanic waters: Influence of the size structure of algal populations Bricaud, Annick Journal of Geophysical Research, Vol. 109, Issue C11 https://doi.org/10.1029/2004JC002419	journal	January 2004
Modeling metabolism of the human gut microbiome Magnúsdóttir, Stefanía; Thiele, Ines Current Opinion in Biotechnology, Vol. 51 https://doi.org/10.1016/j.copbio.2017.12.005	journal	June 2018
Microbial communities associated with plants: learning from nature to apply it in agriculture Andreote, Fernando Dini; Pereira e. Silva, Michele de Cássia Current Opinion in Microbiology, Vol. 37 https://doi.org/10.1016/j.mib.2017.03.011	journal	June 2017
Challenges in microbial ecology: building predictive understanding of community function and dynamics Widder, Stefanie; Allen, Rosalind J.; Pfeiffer, Thomas The ISME Journal, Vol. 10, Issue 11 https://doi.org/10.1038/ismej.2016.45	journal	March 2016
Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa Biofilm Formation Biggs, Matthew B.; Papin, Jason A. PLoS ONE, Vol. 8, Issue 10 https://doi.org/10.1371/journal.pone.0078011	journal	October 2013
What is flux balance analysis? Orth, Jeffrey D.; Thiele, Ines; Palsson, Bernhard Ø Nature Biotechnology, Vol. 28, Issue 3 https://doi.org/10.1038/nbt.1614	journal	March 2010
On the deformability of an empirical fitness landscape by microbial evolution Bajić, Djordje; Vila, Jean C. C.; Blount, Zachary D. Proceedings of the National Academy of Sciences, Vol. 115, Issue 44 https://doi.org/10.1073/pnas.1808485115	journal	October 2018
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth Ibarra, Rafael U.; Edwards, Jeremy S.; Palsson, Bernhard O. Nature, Vol. 420, Issue 6912 https://doi.org/10.1038/nature01149	journal	November 2002
FLYCOP: metabolic modeling-based analysis and engineering microbial communities García-Jiménez, Beatriz; García, José Luis; Nogales, Juan Bioinformatics, Vol. 34, Issue 17 https://doi.org/10.1093/bioinformatics/bty561	journal	September 2018
An objective function exploiting suboptimal solutions in metabolic networks Wintermute, Edwin H.; Lieberman, Tami D.; Silver, Pamela A. BMC Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1186/1752-0509-7-98	journal	January 2013
Non-additive microbial community responses to environmental complexity Pacheco, Alan R.; Osborne, Melisa L.; Segrè, Daniel Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-22426-3	journal	April 2021

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