Model Identifier
MODEL2407310001
Short description
This genome-scale metabolic model (GEM) of Corynebacterium tuberculostearicum strain DSM 44922 (Taxon ID 38304) was initially built with CarveMe version 1.5.1 based on the genome assembly with NCBI accession GCF_013408445.1 and then underwent a series of careful semi-automatic and manual curation. It is the first model curated using the Python tool MCC for mass and charge curation.
Format
COMBINE archive (0.1)
Related Publication
  • MCC: automated mass and charge curation at the genome scale applied to C. tuberculostearicum Click here to expand
  • Reihaneh Mostolizadeh, Finn Mier, Andreas Dräger
  • Microbiology Spectrum , 11/ 2025 Preprint
  • 1Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany 2Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany 3Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karl University of Tübingen, Tübingen, Germany 4Data Analytics and Bioinformatics, Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany 5Quantitative Biology Center (QBiC), Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany 6German Center for Infection Research (DZIF), Tübingen, Germany
  • For many years, antibiotics reliably protected mankind against bacterial infections, including the respiratory tract colonizer Corynebacterium tuberculostearicum. However, the spread of antimicrobial resistance necessitates the search for new treatment options, where the microbiota may play a crucial role. One way to investigate the complex nature of bacteria and their interactions with human hosts or microbiota is through genome-scale metabolic models (GEMs). Constructing GEMs is labor-intensive and time-consuming. We introduce the Python package Mass and Charge Curation (MCC), which implements a new automated algorithm to facilitate mass and charge balancing—one of the most time-consuming reconstruction steps. This package manipulates reconstructions by consolidating data from multiple resources and updating the notes field with relevant changes. It also visually compares draft and curated models, ensuring high-quality metabolic reconstructions. Using MCC, we developed a metabolic reconstruction of C. tuberculostearicum strain DSM 44922. The model was improved based on standardization policies, resulting in a functional, well-annotated, high-quality product. We also simulated the organism’s growth in Systems Network Model 3. The high-quality model iCTUB2024RM consistently resembles growth behavior under realistic conditions in an artificial human nasal environment, enhancing the understanding of C. tuberculostearicum and its potential impact on health and disease. The curation process of this model led to the development of the MCC package, which facilitates the mass and charge balancing of arbitrary flux balance constraints models in the SBML format.
Contributors
Submitter of the first revision: Andreas Dräger
Submitter of this revision: Andreas Dräger
Annotation Curator: Andreas Dräger

Metadata information

is (1 statement)
BioModels Database MODEL2407310001

Curation status
Non-curated
Modelling approach(es)
constraint-based model
This model has been published without a web link to the reference publication.

Connected external resources