Metabolic network reconstruction and dynamic models of Fibrobacter succinogenes S85

The folder contains the metabolic network and mathematical models developed in the article

Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacterium Fibrobacter succinogenes S85. Fakih et al., 2022. bioRxiv. https://doi.org/10.1101/2022.10.18.512662

The folder DynamicModel includes the MATLAB implementation of the dynamic models of F. succinogenes S85 to represent its metabolism on glucose, cellobiose, and cellulose.

The folder NetworkReconstruction contains all the files of the reconstruction of the metabolic network of F. succinogenes S85 in the AuReMe workspace.

Supplementary material A

▫   Table S1 Biomass composition

▫   Table S2 List of seeds and targets

▫   Table S3 Comparison between the two draft models obtained via annotation

Supplementary material B

▫   Data set S1 Blast results for gene-reaction association

▫   Data set S2 List of active pathways

▫   Data set S3 List of spontaneous, transport reactions

▫   Data set S4 Lumped biomass reaction

▫   Data set S5 Reduced model