Construction of EcN model iHM1533 based on 55 reference strains. The pipeline for comparison of EcN to the reference strains and construction of the draft model was based on the work of Norsigian et al. [1].
Notebook 1. Generation of panmodel and panreactome of all reference strains
Notebook 2.1 Comparison of EcN genome to reference genomes based on protein and DNA homology
Notebook 2.2 Analysis of the genome comparison in 2.1
Notebook 2.3 Visualisation of the genome comparison in a heatmap
Notebook 3.1 Generation of the draft model based on iML1515 with addition from other reference models, based on genome comparison (protein)
Notebook 3.2 Addition of reactions based on DNA genome comparison (none found to be added)
Notebook 3.3 Reactions added from EcN model iDK1463
Notebook 4.1 Correction of duplicate reactions and removal of unbound energy-generating fluxes
Notebook 4.2 Correction of mass and charge balances, correction of incorrect formulas of metabolites
Notebook 4.3 Use gapfilling to identify reactions missing for the metabolism of carbon sources
Notebook 4.4 Use gapfilling to identify reactions correcting blocked reactions
Notebook 4.5 Correct errors found during gene essentiality and biology analysis
Notebook 4.6 Addition of secondary metabolite biosynthetic pathways
Notebook 4.7 Update of reaction and metabolite annotation and removal of genes and metabolites not linked to reactions
Notebook 4.8 Update of the biomass objective function using BOFdat [2]
Notebook 4.9 Analysis of final model
Notebook 5.1 Comparison of iHM1533 and iDK1463 to biology data
Notebook 5.2 Comparison of flux predictions of iHM1533 to 13C data
Notebook 5.2b Comparison of flux predictions of iHM1533 to 13C data with flux variability analysis
Notebook 5.3 Gene essentiality analysis on M9 media
Notebook 5.3b Gene essentiality analysis on Gut Microbiome Media (GMM)
Notebook 6.1 FSEOF analysis of secondary metabolite biosynthesis pathways
[1] Norsigian, C.J., Fang, X., Seif, Y. et al. A workflow for generating multi-strain genome-scale metabolic models of prokaryotes. Nat Protoc 15, 1–14 (2020). https://doi.org/10.1038/s41596-019-0254-3
[2] Lachance, J. C., Lloyd, C. J., Monk, J. M., Yang, L., Sastry, A. V., Seif, Y., ... & Jacques, P. É. (2019). BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. PLoS computational biology, 15(4), e1006971.