Reconstruction and Analysis of Central Metabolism in Microbes

  • Janaka N. EdirisingheEmail author
  • José P. Faria
  • Nomi L. Harris
  • Benjamin H. Allen
  • Christopher S. HenryEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1716)


Genome-scale metabolic models (GEMs) generated from automated reconstruction pipelines often lack accuracy due to the need for extensive gapfilling and the inference of periphery metabolic pathways based on lower-confidence annotations. The central carbon pathways and electron transport chains are among the most well-understood regions of microbial metabolism, and these pathways contribute significantly toward defining cellular behavior and growth conditions. Thus, it is often useful to construct a simplified core metabolic model (CMM) that is comprised of only the high-confidence central pathways. In this chapter, we discuss methods for producing core metabolic models (CMM) based on genome annotations. With its reduced scope compared to GEMs, CMM reconstruction focuses on accurate representation of the central metabolic pathways related to energy biosynthesis and accurate energy yield predictions. We demonstrate the reconstruction and analysis of CMMs using the DOE Systems Biology Knowledgebase (KBase). The complete workflow is available at

Key words

Central metabolism Core metabolic models Metabolic model reconstruction Flux balance analysis Biochemical pathways Model comparison 


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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  • Janaka N. Edirisinghe
    • 1
    • 2
    Email author
  • José P. Faria
    • 1
    • 2
  • Nomi L. Harris
    • 3
  • Benjamin H. Allen
    • 4
  • Christopher S. Henry
    • 1
    • 2
    Email author
  1. 1.Computation InstituteUniversity of ChicagoChicagoUSA
  2. 2.Mathematics and Computer Science DivisionArgonne National LaboratoryArgonneUSA
  3. 3.Environmental Genomics and Systems Biology DivisionE. O. Lawrence Berkeley National LaboratoryBerkeleyUSA
  4. 4.Biosciences DivisionOak Ridge National LaboratoryOak RidgeUSA

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