Renz2021 - genome-scale metabolic model (iDPM21RW) of Dolosigranulum pigrum 83VPs KB5

  public model
Model Identifier
MODEL2012220003
Short description
Dolosigranulum pigrum is a quite recently discovered Gram-positive coccus. It has gained increasing attention due to its negative correlation with Staphylococcus aureus, which is one of the most successful modern pathogens causing severe infections with tremendous morbidity and mortality due to its multiple resistances. As the possible mechanisms behind its inhibition of S. aureus remain unclear, a genome-scale metabolic model (GEM) is of enormous interest and high importance to better study its role in this fight. This article presents the first GEM of D. pigrum, which was curated using automated reconstruction tools and extensive manual curation steps to yield a high-quality GEM. It was evaluated and validated using all currently available experimental data of D. pigrum. With this model, already predicted auxotrophies and biosynthetic pathways could be verified. The model was used to define a minimal medium for further laboratory experiments and to predict various carbon sources’ growth capacities. This model will pave the way to better understand D. pigrum’s role in the fight against S. aureus.
Format
COMBINE archive (0.1)
Related Publication
  • First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies
  • Alina Renz, Lina Widerspick, Andreas Dräger
  • Metabolites , 4/ 2021 , Volume 11 , Issue 4 , pages: 232 , DOI: 10.3390/metabo11040232
  • 1 Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany 2 Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany 3 Cluster of Excellence ‘Controlling Microbes to Fight Infections,’ University of Tübingen, 72076 Tübingen, Germany 4 German Center for Infection Research (DZIF), Partner site Tübingen, 72076 Tübingen, Germany
  • Dolosigranulum pigrum is a quite recently discovered Gram-positive coccus. It has gained increasing attention due to its negative correlation with Staphylococcus aureus, which is one of the most successful modern pathogens causing severe infections with tremendous morbidity and mortality due to its multiple resistances. As the possible mechanisms behind its inhibition of S. aureus remain unclear, a genome-scale metabolic model (GEM) is of enormous interest and high importance to better study its role in this fight. This article presents the first GEM of D. pigrum, which was curated using automated reconstruction tools and extensive manual curation steps to yield a high-quality GEM. It was evaluated and validated using all currently available experimental data of D. pigrum. With this model, already predicted auxotrophies and biosynthetic pathways could be verified. The model was used to define a minimal medium for further laboratory experiments and to predict various carbon sources’ growth capacities. This model will pave the way to better understand D. pigrum’s role in the fight against S. aureus.
Contributors
Andreas Dräger, Kausthubh Ramachandran

Metadata information


Curation status
Non-curated

Modelling approach(es)

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Model files

iDPM21RW.omex iDPM21RW: Genome-scale metabolic model of Dolosigranulum pigrum 83VPs KB5 1.07 MB Preview | Download

  • Model originally submitted by : Andreas Dräger
  • Submitted: 13-Apr-2021 08:35:48
  • Last Modified: 13-Apr-2021 08:35:48
Revisions
  • Version: 5 public model Download this version
    • Submitted on: 13-Apr-2021 08:35:48
    • Submitted by: Kausthubh Ramachandran
    • With comment: Updated model submission name and short description as per the BioModels submission guidelines