Skip to main content

The Chemistry of Microbiomes Proceedings of a Seminar Series (2017) / Chapter Skim
Currently Skimming:

12 Genome-Scale Metabolic Modeling and Its Application to Microbial Communities - Jennifer L. Reed
Pages 85-92

The Chapter Skim interface presents what we've algorithmically identified as the most significant single chunk of text within every page in the chapter.
Select key terms on the right to highlight them within pages of the chapter.


From page 85...
... The remaining sections describe how constraint-based models are built from genomic information, and how these models have been used to answer qualitative and quantitative questions regarding cellular metabolism for individual species and microbial communities. RECONSTRUCTING METABOLIC NETWORKS AND BUILDING CONSTRAINT-BASED MODELS Constraint-based metabolic models are built from an organism's genome-scale metabolic network reconstruction.
Read the entire page →
From page 86...
... These models can be used to predict nutrient utilization, minimal medium requirements, product secretion, pathway utilization, gene essentiality, synthetic lethality, and missing reactions from network reconstructions. The amount of data needed to generate qualitative predictions is typically lower than that for quantitative predictions; however, the types of data needed depend on the questions being asked.
Read the entire page →
From page 87...
... Missing reactions and isozymes in draft models can be identified by resolving discrepancies where the models predict no growth, but cells grow experimentally. Previously, mispredictions associated with carbon source utilization, gene essentiality, and synthetic lethality have been used to add reactions and genes to the metabolic models (Reed et al., 2006; Henry et al., 2009; Zomorrodi and Maranas, 2010)
Read the entire page →
From page 88...
... Individual models have been successfully used to design genetic and environmental perturbations to achieve desired phenotypes; however, to extend such approaches to design microbial communities and manipulate their behaviors will require knowledge of which objective functions accurately predict intracellular and extracellular fluxes in co-culture. Another challenge deals with building metabolic models from genomic and metagenomic data.
Read the entire page →
From page 89...
... Since cellular behaviors are dependent on chemical concentrations in their local environments, future microbiome models should also include approaches to predict concentration gradients in response to flow, diffusion, and microbial metabolism. Constraint-based models can be used to study a diverse range of organisms and microbial communities, including synthetic and natural communities associated with ocean, marine, and human environments.
Read the entire page →
From page 90...
... 2007. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli.
Read the entire page →
From page 91...
... 2014. Adaptive evolution of synthetic cooperating communities improves growth performance.
Read the entire page →

Key Terms

  • microbial communities
  • multispecies models
  • individual species
  • syst biol
  • mol syst

  • metabolic networks
  • capacity constraints
  • qualitative predictions
  • flux distributions
  • biomass production

  • acad sci
  • escherichia coli
  • sci usa
  • secretion rates
  • metabolic network

  • metabolic engineering
  • accurately predict
  • natural communities
  • answer qualitative
  • extracellular fluxes

  • missing reactions
  • product secretion
  • quantitative predictions
  • gene essentiality
  • nutrient uptake

  • enzyme capacity
  • objective functions
  • proc natl
  • natl acad
  • intracellular fluxes


    • This material may be derived from roughly machine-read images, and so is provided only to facilitate research.
    More information on Chapter Skim is available.