skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

Journal Article · · Processes
DOI:https://doi.org/10.3390/pr2040711· OSTI ID:1418704

Sponsoring Organization:
USDOE
Grant/Contract Number:
Biological and Environmental Research (FWP 56820); Biological and Environmental Research (FWP 56812); Laboratory Directed Research and Development
OSTI ID:
1418704
Journal Information:
Processes, Journal Name: Processes Vol. 2 Journal Issue: 4; ISSN 2227-9717
Publisher:
MDPI AGCopyright Statement
Country of Publication:
Switzerland
Language:
English

References (118)

Parallel Extreme Ray and Pathway Computation book January 2010
Microbial interactions: from networks to models journal July 2012
Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota journal December 2013
Prokaryotes: The unseen majority journal June 1998
Interactions in the microbiome: communities of organisms and communities of genes journal January 2014
Environments that Induce Synthetic Microbial Ecosystems journal November 2010
d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities journal November 2013
Error and attack tolerance of complex networks journal July 2000
Antimicrobial resistance in bacterial biofilms journal January 2006
Distilling Free-Form Natural Laws from Experimental Data journal April 2009
An improved algorithm for stoichiometric network analysis: theory and applications journal November 2004
Experimental methods and modeling techniques for description of cell population heterogeneity journal November 2011
You Are What You Host: Microbiome Modulation of the Aging Process journal January 2014
Phylogeny of Microorganisms Populating a Thick, Subaerial, Predominantly Lithotrophic Biofilm at an Extreme Acid Mine Drainage Site journal September 2000
Species Distribution Models: Ecological Explanation and Prediction Across Space and Time journal December 2009
Prediction of dynamic behavior of mutant strains from limited wild-type data journal March 2012
Metabolic modeling of a mutualistic microbial community journal January 2007
Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics journal May 2014
Computing the shortest elementary flux modes in genome-scale metabolic networks journal September 2009
Stochastic thermodynamics of chemical reaction networks journal January 2007
Relationship between Thermodynamic Driving Force and One-Way Fluxes in Reversible Processes journal January 2007
A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities journal January 2011
An improved cellular automaton method to model multispecies biofilms journal October 2013
Engineering ecosystems and synthetic ecologies journal January 2012
Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition journal January 2012
Modeling Microbial Dynamics in Heterogeneous Environments: Growth on Soil Carbon Sources journal December 2011
Challenges for Complex Microbial Ecosystems: Combination of Experimental Approaches with Mathematical Modeling journal January 2013
Time, Structure, and Fluctuations journal September 1978
Modeling product formation in anaerobic mixed culture fermentations journal January 2006
Quantifying the importance of local niche-based and stochastic processes to tropical tree community assembly journal April 2012
A Primer on Metagenomics journal February 2010
From Plant Traits to Plant Communities: A Statistical Mechanistic Approach to Biodiversity journal November 2006
Moving pictures of the human microbiome journal January 2011
A thermodynamically-based model for predicting microbial growth and community composition coupled to system geochemistry: Application to uranium bioreduction journal March 2010
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology journal January 2011
Identification of Functionally Relevant Populations in Enhanced Biological Phosphorus Removal Processes Based On Intracellular Polymers Profiles and Insights into the Metabolic Diversity and Heterogeneity journal April 2012
Soil biodiversity and soil community composition determine ecosystem multifunctionality journal March 2014
Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism journal February 2014
A predictive model of community assembly that incorporates intraspecific trait variation journal August 2012
Large-scale computation of elementary flux modes with bit pattern trees journal August 2008
Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures journal October 2010
Population balance modeling. Promise for the future journal February 2002
Evolutionary Dynamics of Biological Games journal February 2004
Evolutionary game theory: Theoretical concepts and applications to microbial communities journal October 2010
Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass journal August 2013
Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis journal October 2012
Competitive and cooperative metabolic interactions in bacterial communities journal September 2011
Enhanced Biofilm Formation and Increased Resistance to Antimicrobial Agents and Bacterial Invasion Are Caused by Synergistic Interactions in Multispecies Biofilms journal June 2006
Modeling microbial community structure and functional diversity across time and space journal May 2012
The role of physiological heterogeneity in microbial population behavior journal September 2010
Stochastic Simulation of Chemical Kinetics journal May 2007
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments journal July 2010
Dynamic models of metabolism: Review of the cybernetic approach journal February 2012
Maximum entropy production and plant optimization theories journal May 2010
Bistability versus Bimodal Distributions in Gene Regulatory Processes from Population Balance journal August 2011
The microbiome: stress, health and disease journal November 2013
Toward quantitative understanding on microbial community structure and functioning: a modeling-centered approach using degradation of marine oil spills as example journal March 2014
Emergent cooperation in microbial metabolism journal January 2010
Predicting bacterial community assemblages using an artificial neural network approach journal April 2012
Estimating the Dimension of a Model journal March 1978
Modeling metabolic systems: the need for dynamics journal November 2013
Snowdrift game dynamics and facultative cheating in yeast journal April 2009
Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation journal March 2009
Reduction of a set of elementary modes using yield analysis journal February 2009
A thermodynamic analysis of the anaerobic oxidation of methane in marine sediments journal December 2008
A hybrid model of anaerobic E. coli GJT001: Combination of elementary flux modes and cybernetic variables journal September 2008
Gut microbiome and metabolic diseases journal November 2013
Dynamic modeling of microbial cell populations journal October 2003
What is microbial community ecology? journal August 2009
Comparative Metagenomics of Microbial Communities journal April 2005
The functional design of the rotary enzyme ATP synthase is consistent with maximum entropy production journal October 2006
Scale-Free Networks journal May 2003
A bunch of tiny individuals—Individual-based modeling for microbes journal January 2009
Overview of Mathematical Approaches Used to Model Bacterial Chemotaxis II: Bacterial Populations journal July 2008
Super-individuals a simple solution for modelling large populations on an individual basis journal July 1995
In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study journal January 2009
Systematic development of hybrid cybernetic models: Application to recombinant yeast co-consuming glucose and xylose journal August 2009
Mathematical Description of Microbial Biofilms journal January 2010
OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities journal February 2012
Stochastic and deterministic assembly processes in subsurface microbial communities journal March 2012
A road map for the development of community systems (CoSy) biology journal March 2012
Modeling microbial communities: Current, developing, and future technologies for predicting microbial community interaction journal July 2012
Individual-based Modelling: An Essential Tool for Microbiology journal April 2008
BacSim, a simulator for individual-based modelling of bacterial colony growth journal December 1998
Dynamic modeling of aerobic growth of Shewanella oneidensis. Predicting triauxic growth, flux distributions, and energy requirement for growth journal January 2013
Minimal cut sets in a metabolic network are elementary modes in a dual network journal December 2011
Microbial communities in industrial environment journal June 2009
The generation and maintenance of diversity in microbial communities journal March 2011
Large-scale in silico modeling of metabolic interactions between cell types in the human brain journal November 2010
A structured and dynamic framework to advance traits-based theory and prediction in ecology journal March 2010
Ecosystem functioning and maximum entropy production: a quantitative test of hypotheses journal May 2010
The design of long-term effective uranium bioremediation strategy using a community metabolic model journal April 2012
Towards novel approaches to modelling biotic interactions in multispecies assemblages at large spatial extents: Modelling multispecies interactions journal December 2011
Advances in modeling trait-based plant community assembly journal October 2013
Computational systems biology and in silico modeling of the human microbiome journal May 2012
Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease journal December 2011
Community Flux Balance Analysis for Microbial Consortia at Balanced Growth journal May 2013
Microbial physiology-based model of ethanol metabolism in subsurface sediments journal July 2011
Attractants and repellents influence methylation and demethylation of methyl-accepting chemotaxis proteins in an extract of Escherichia coli. journal December 1979
Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks journal June 2011
Analysis of optimality in natural and perturbed metabolic networks journal November 2002
In Silico Geobacter sulfurreducens Metabolism and Its Representation in Reactive Transport Models journal November 2008
Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model journal March 2011
Scale-Free Networks: A Decade and Beyond journal July 2009
On enhancing productivity of bioethanol with multiple species journal January 2012
Integrating cybernetic modeling with pathway analysis provides a dynamic, systems-level description of metabolic control journal June 2008
Deciphering microbial interactions and detecting keystone species with co-occurrence networks journal May 2014
Classification of metagenomic sequences: methods and challenges journal September 2012
Metabolic networks evolve towards states of maximum entropy production journal November 2011
Exacting predictions by cybernetic model confirmed experimentally: Steady state multiplicity in the chemostat journal July 2012
What is flux balance analysis? journal March 2010
Cybernetic models based on lumped elementary modes accurately predict strain-specific metabolic function journal October 2010
Gene-centric approach to integrating environmental genomics and biogeochemical models journal January 2014
Microbial community structure and its functional implications journal May 2009
Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism journal November 2008
Dynamic modelling of mixotrophic microalgal photobioreactor systems with time-varying yield coefficient for the lipid consumption journal June 2014
Dynamic metabolic modeling of a microaerobic yeast co-culture: predicting and optimizing ethanol production from glucose/xylose mixtures journal January 2013
iDynoMiCS: next-generation individual-based modelling of biofilms: iDynoMiCS for Biofilm Modelling journal March 2011