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Genome-Scale Metabolic Network Reconstruction

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Bacterial Pangenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1231))

Abstract

Bacterial metabolism is an important source of novel products/processes for everyday life and strong efforts are being undertaken to discover and exploit new usable substances of microbial origin. Computational modeling and in silico simulations are powerful tools in this context since they allow the exploration and a deeper understanding of bacterial metabolic circuits. Many approaches exist to quantitatively simulate chemical reaction fluxes within the whole microbial metabolism and, regardless of the technique of choice, metabolic model reconstruction is the first step in every modeling pipeline. Reconstructing a metabolic network consists in drafting the list of the biochemical reactions that an organism can carry out together with information on cellular boundaries, a biomass assembly reaction, and exchange fluxes with the external environment. Building up models able to represent the different functional cellular states is universally recognized as a tricky task that requires intensive manual effort and much additional information besides genome sequence. In this chapter we present a general protocol for metabolic reconstruction in bacteria and the main challenges encountered during this process.

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Author information

Authors and Affiliations

  1. Department of Biology, University of Florence, via Madonna del Piano 6, I-50019 Sesto Fiorentino, Florence, Italy

    Marco Fondi

  2. Computer Laboratory, University of Cambridge, Cambridge, UK

    Pietro Liò

Authors
  1. Marco Fondi
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  2. Pietro Liò
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Corresponding author

Correspondence to Marco Fondi .

Editor information

Editors and Affiliations

  1. Department of Biology, University of Florence, Florence, Italy

    Alessio Mengoni

  2. EMBL-EBI, Cambridge, United Kingdom

    Marco Galardini

  3. Department of Biology, University of Florence, Florence, Italy

    Marco Fondi

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Fondi, M., Liò, P. (2015). Genome-Scale Metabolic Network Reconstruction. In: Mengoni, A., Galardini, M., Fondi, M. (eds) Bacterial Pangenomics. Methods in Molecular Biology, vol 1231. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1720-4_15

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  • DOI: https://doi.org/10.1007/978-1-4939-1720-4_15

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1719-8

  • Online ISBN: 978-1-4939-1720-4

  • eBook Packages: Springer Protocols

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