Input and output files of the application of our MDPbiomeGEM system (available at https://github.com/beatrizgj/MDPbiomeGEM) to different microbial communities, in particular from human gut microbiome and soil microbiome. Each case study (i.e. microbial community) has the following structure, corresponding to the different steps performed by our system MDPbiomeGEM: 1. InputGEM: Genome-scale metabolic models (GEM) and medium composition 2. OutputMMODES: simulated microbial community timeseries by MMODES 3. MmodesToMDPbiome: transformation of output from MMODES in input to MDPbiome 4. OutRobustClustering: identification of microbiome states 5. OutputMDPbiome: output of MDPbiome, with prediction of microbiome state changes and interventions a. Human gut microbiome (BifFae): the microbes in this community are Bifidobacterium adolescentis L2-32 (iBif452) and Faecalibacterium prausnitizii A2-135 (iFap484), whose GEMs were taken from the original publication [El-Semman et al.,2014] (https://doi.org/10.1186/1752-0509-8-41). We upload here those GEMs adjusted to satisfy the scenario we model, that is described in our manuscript. b. Soil microbiome (Atrazine): the microbes in this community are P. aurescens, H. stevensii, Halobacillus sp. The GEMs used in this consortium were kindly provided by the authors of [Xu et al.,2019] (https://doi.org/10.1038/s41396-018-0288-5). Model construction was lead by Raphy Zarecki. With the exception of P.aurescens TC1 [Ofaim et al.,2019] (http://dx.doi.org/10.1101/536011) they had not yet been made publicly available. With the permission of the authors of the original models [Xu et al.,2019], we upload here those GEMs adjusted to satisfy the scenario we model, that is described in our manuscript.