Data needed to reproduce the results from the manuscript " Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models" by Noushin Hadadi, Vikash Pandey, Anush Chiappino-Pepe, Marian Morales, Hector Gallart-Ayala, Florence Mehl, Julijana Ivanisevic, Vladimir Sentchilo and Jan R. van der Meer. The dataset includes: Models folder that contains TFA reconstructions/models as well as REMI models where we integrated different type of constraints based on gene expression data and metabolomics data using the REMI method. We provide scripts and simulation data so that one can reproduce the reported results. Scripts folder contains scripts for generating models, alternative analysis, and biomass building blocks (BBBs) analysis. Stationary vs exponential comparison Sand vs liquid comparison BBB Analysis Simdata folder contains the mat files of alternative solutions obtained from REMi models, BBB analysis for exponential vs stationary and sand vs liquid as well as the edgR analysis results of the differentially expressed genes.