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In this work, we present a computational method to investigate gut microbiota-host metabolic interactions. Due to the diversity of species present in the gut that may contribute to the metabolism of certain substrates and the subsequent community level interactions between the different bacterial species and the host cells, an atomic level approach is taken. In particular, the Kyoto Encyclopedia ... read moreof Genes and Genomes (KEGG) is used to assemble various metabolic models representing different proportions of murine host cells and various bacterial phyla (Kanehisa Laboratories, 2015). Pathways between common dietary nutrients that would be present in the GI tract to bioactive gut metabolites of interest are then investigated using a reachability analysis and a “random-walks” pathfinding algorithm. Finally, an atom tracing function is implored to determine the conservation of atoms along the pathway, and model results are compared against each other. It is the hope that such an analysis will lead to new insights to the atomic level contribution of various gut flora to the synthesis of bioactive gut metabolites.read less
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