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Constructing and Analyzing Metabolic Flux Models of Microbial Communities

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Hydrocarbon and Lipid Microbiology Protocols

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

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.

Author contributed equally with all other contributors

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Acknowledgements

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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    Authors and Affiliations

    1. Computation Institute, University of Chicago, Chicago, IL, 60637, USA

      José P. Faria, Janaka N. Edirisinghe, Samuel M. D. Seaver & Christopher S. Henry

    2. Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL, 60439, USA

      José P. Faria

    3. Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA

      Tahmineh Khazaei

    4. Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA

      Janaka N. Edirisinghe, Pamela Weisenhorn, Samuel M. D. Seaver, Neal Conrad & Christopher S. Henry

    5. Lawrence Berkley National Lab, Berkley, CA, 94720, USA

      Nomi Harris

    6. Computer Science Department, Hope College, Holland, MI, 49423, USA

      Matthew DeJongh

    7. Biosciences, Argonne National Laboratory, Argonne, IL, 60439, USA

      Pamela Weisenhorn

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    1. José P. Faria
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    Correspondence to Christopher S. Henry .

    Editor information

    Editors and Affiliations

    1. Dept. Biological Sciences, University of Essex Dept. Biological Sciences, Colchester, Essex, United Kingdom

      Terry J. McGenity

    2. Braunschweig, Germany

      Kenneth N. Timmis

    3. Department of Biology, University of the Balearic Islands and Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Palma de Mallorca, Spain

      Balbina Nogales

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    Faria, J.P. et al. (2016). Constructing and Analyzing Metabolic Flux Models of Microbial Communities. In: McGenity, T., Timmis, K., Nogales , B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2016_215

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    • DOI: https://doi.org/10.1007/8623_2016_215

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    • Publisher Name: Springer, Berlin, Heidelberg

    • Print ISBN: 978-3-662-50449-9

    • Online ISBN: 978-3-662-50450-5

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