Data from: Dynamic simulations of microbial communitiesunder perturbations: opportunities formicrobiome engineering

<p>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.</p> <p>Each case study (i.e. microbial community) has the following structure, corresponding to the different steps performed by our system MDPbiomeGEM:<br> 1. InputGEM: Genome-scale metabolic models (GEM) and medium composition<br> 2. OutputMMODES: simulated microbial community timeseries by MMODES<br> 3. MmodesToMDPbiome: transformation of output from MMODES in input to MDPbiome<br> 4. OutRobustClustering: identification of microbiome states<br> 5. OutputMDPbiome: output of MDPbiome, with prediction of microbiome state changes and interventions</p> <p>a. Human gut microbiome (BifFae): the microbes in this community are <em>Bifidobacterium adolescentis L2-32</em> (<em>i</em>Bif452) and <em>Faecalibacterium prausnitizii A2-135</em> (<em>i</em>Fap484), 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.</p> <p>b. Soil microbiome (Atrazine): the microbes in this community are <em>P. aurescens, H. stevensii</em>, <em>Halobacillus sp</em>. 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).&nbsp;Model construction was lead by&nbsp;Raphy Zarecki. With the exception of <em>P.aurescens TC1</em> [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.</p> <p>&nbsp;</p> <p>&nbsp;</p>