Systems Biology of Microbial Communities

  • Ali Navid
  • Cheol-Min Ghim
  • Andrew T. Fenley
  • Sooyeon Yoon
  • Sungmin Lee
  • Eivind Almaas
Part of the Methods in Molecular Biology book series (MIMB, volume 500)


Microbes exist naturally in a wide range of environments in communities where their interactions are significant, spanning the extremes of high acidity and high temperature environments to soil and the ocean. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.


Microbial community Rate equation Agent-based modeling Population dynamics Quorum sensing Biofilm 



This work was performed under the auspices of the US Department of Energy by Lawrence Livermore National Laboratory (LLNL) under Contract DE-AC52-07NA27344, and supported by the LLNL Laboratory Directed Research and Development program on grant 06-ERD-061.


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Copyright information

© Humana Press 2009

Authors and Affiliations

  • Ali Navid
  • Cheol-Min Ghim
  • Andrew T. Fenley
  • Sooyeon Yoon
  • Sungmin Lee
  • Eivind Almaas
    • 1
  1. 1.Biosciences and Biotechnology DivisionLawrence Livermore National LaboratoryLivermoreUSA

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