Flux balance analysis for overproduction of organic acids by Synechocystis sp. PCC 6803 under dark anoxic condition

AbstractThe human gut harbors an enormous number of symbiotic microbes, which is vital for human health. However, interactions within the complex microbiota community and between the microbiota and its host are challenging to elucidate, limiting development in the treatment for a variety of diseases associated with microbiota dysbiosis. Using in silico simulation methods based on flux balance analysis, those interactions can be better investigated. Flux balance analysis uses an annotated genome-scale reconstruction of a metabolic network to determine the distribution of metabolic fluxes that represent the complete metabolism of a bacterium in a certain metabolic environment such as the gut. Simulation of a set of bacterial species in a shared metabolic environment can enable the study of the effect of numerous perturbations, such as dietary changes or addition of a probiotic species in a personalized manner. This review aims to introduce to experimental biologists the possible applications of flux balance analysis in the host-microbiota interaction field and discusses its potential use to improve human health.

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Why does yeast ferment? A flux balance analysis study

Biochemical Society Transactions ◽

10.1042/bst0381225 ◽

2010 ◽

Vol 38 (5) ◽

pp. 1225-1229 ◽

Cited By ~ 23

Author(s):

Evangelos Simeonidis ◽

Ettore Murabito ◽

Kieran Smallbone ◽

Hans V. Westerhoff

Keyword(s):

Flux Balance Analysis ◽

Energy Cost ◽

Yeast Fermentation ◽

Minimal Amount ◽

Aerobic Growth ◽

Analysis Study ◽

Flux Balance ◽

Balance Analysis ◽

Genome Scale ◽

Excess Glucose

Advances in biological techniques have led to the availability of genome-scale metabolic reconstructions for yeast. The size and complexity of such networks impose limits on what types of analyses one can perform. Constraint-based modelling overcomes some of these restrictions by using physicochemical constraints to describe the potential behaviour of an organism. FBA (flux balance analysis) highlights flux patterns through a network that serves to achieve a particular objective and requires a minimal amount of data to make quantitative inferences about network behaviour. Even though FBA is a powerful tool for system predictions, its general formulation sometimes results in unrealistic flux patterns. A typical example is fermentation in yeast: ethanol is produced during aerobic growth in excess glucose, but this pattern is not present in a typical FBA solution. In the present paper, we examine the issue of yeast fermentation against respiration during growth. We have studied a number of hypotheses from the modelling perspective, and novel formulations of the FBA approach have been tested. By making the observation that more respiration requires the synthesis of more mitochondria, an energy cost related to mitochondrial synthesis is added to the FBA formulation. Results, although still approximate, are closer to experimental observations than earlier FBA analyses, at least on the issue of fermentation.

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Critical assessment of genome-scale metabolic models of Arabidopsis thaliana

Molecular Omics ◽

10.1039/d1mo00351h ◽

2022 ◽

Author(s):

Javad Zamani ◽

Sayed-Amir Marashi ◽

Tahmineh Lohrasebi ◽

Mohammad-Ali Malboobi ◽

Esmail Foroozan

Keyword(s):

Arabidopsis Thaliana ◽

Flux Balance Analysis ◽

Critical Assessment ◽

Flux Balance ◽

Balance Analysis ◽

Metabolic Models ◽

Living Organisms ◽

Genome Scale

Genome-scale metabolic models (GSMMs) have enabled researchers to perform systems-level studies of living organisms. As a constraint-based technique, flux balance analysis (FBA) aids computation of reaction fluxes and prediction of...

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