Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine
Fig 2
The workflow to generate the iNTS_SL1344 GEM.
We reconstructed the iNTS_SL1344 GEM (2,735 reactions) starting from functional genome annotation with the KEGG database and the published GEM of the strain LT2, STM_v1_0 (2,545 reactions). This process outputted three reaction databases (DB1: 1,803 reactions, DB2: 364 reactions and DB3: 1,468 reactions) that were used for the network curation. We then used the STM_v1_0 as a basis and we characterized pathways to connect extracellular metabolites to the SL1344 metabolism. The expanded network was then compared against growth assays data and curated using the draft GEMs generated in the first step of the workflow and optimization methods. Finally, advanced bioinformatics methods were used to predict catalyzing genes for the newly added biochemistry.