Constructing and Analyzing Metabolic Flux Models of Microbial Communities

  • José P. Faria
  • Tahmineh Khazaei
  • Janaka N. Edirisinghe
  • Pamela Weisenhorn
  • Samuel M. D. Seaver
  • Neal Conrad
  • Nomi Harris
  • Matthew DeJongh
  • Christopher S. HenryEmail author
Part of the Springer Protocols Handbooks book series (SPH)


Here we provide a broad overview of current research in modeling the growth and behavior of microbial communities, while focusing primarily on metabolic flux modeling techniques, including the reconstruction of individual species models, reconstruction of mixed-bag models, and reconstruction of multi-species models. We describe how flux balance analysis may be applied with these various model types to explore the interactions of a microbial community with its environment, as well as the interactions of individual species with each other. We demonstrate all discussed model reconstruction and analysis approaches using the Department of Energy’s Systems Biology Knowledgebase (KBase), constructing and importing genome-scale metabolic models of Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii, and subsequently combining them into a community model of the gut microbiome. We also use KBase to explore how these species interact with each other and with the gut environment, exploring the trade-offs in information provided by applying each metabolic flux modeling approach. Overall, we conclude that no single approach is better than the others, and often there is much to be gained by applying multiple approaches synergistically when exploring the ecology of a microbial community.


Bacteroides thetaiotaomicron Ecology Faecalibacterium prausnitzii Flux balance analysis Genome-scale modeling Microbial communities 



This work was supported by the US Department of Energy, Office of Biological and Environmental Research; under contract DE-AC02-06CH11357 as a part of the DOE Knowledgebase project (MD, JE, SS, NC, and NH), and by the National Science Foundation grant number EFMA-1137089 (CSH, PW, JF, and TK).


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • José P. Faria
    • 1
    • 2
  • Tahmineh Khazaei
    • 3
  • Janaka N. Edirisinghe
    • 1
    • 4
  • Pamela Weisenhorn
    • 4
    • 7
  • Samuel M. D. Seaver
    • 1
    • 4
  • Neal Conrad
    • 4
  • Nomi Harris
    • 5
  • Matthew DeJongh
    • 6
  • Christopher S. Henry
    • 1
    • 4
    Email author
  1. 1.Computation InstituteUniversity of ChicagoChicagoUSA
  2. 2.Computing, Environment and Life Sciences, Argonne National LaboratoryArgonneUSA
  3. 3.Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUSA
  4. 4.Mathematics and Computer Science DivisionArgonne National LaboratoryArgonneUSA
  5. 5.Lawrence Berkley National LabBerkleyUSA
  6. 6.Computer Science DepartmentHope CollegeHollandUSA
  7. 7.BiosciencesArgonne National LaboratoryArgonneUSA

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