Towards predicting gut microbial metabolism: Integration of flux balance analysis and untargeted metabolomics

Ellen Kuang, Matthew Marney, Daniel Cuevas, Robert A. Edwards, Erica M. Forsberg

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)
9 Downloads (Pure)


Genomics-based metabolic models of microorganisms currently have no easy way of corroborating predicted biomass with the actual metabolites being produced. This study uses untargeted mass spectrometry-based metabolomics data to generate a list of accurate metabolite masses produced from the human commensal bacteria Citrobacter sedlakii grown in the presence of a simple glucose carbon source. A genomics-based flux balance metabolic model of this bacterium was previously generated using the bioinformatics tool PyFBA and phenotypic growth curve data. The high-resolution mass spectrometry data obtained through timed metabolic extractions were integrated with the predicted metabolic model through a program called MS_FBA. This program correlated untargeted metabolomics features from C. sedlakii with 218 of the 699 metabolites in the model using an exact mass match, with 51 metabolites further confirmed using predicted isotope ratios. Over 1400 metabolites were matched with additional metabolites in the ModelSEED database, indicating the need to incorporate more specific gene annotations into the predictive model through metabolomics-guided gap filling.

Original languageEnglish
Article number156
Number of pages11
Issue number4
Publication statusPublished - Apr 2020
Externally publishedYes

Bibliographical note

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (


  • Bioinformatics
  • Flux balance analysis
  • Mass spectrometry
  • Metabolomics
  • Microbiome
  • Multiomics


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