title: Understanding the interactions between bacteria in the human gut through metabolic modeling.
abstract: The human gut microbiome plays an influential role in maintaining human health, and it is a potential target for prevention and treatment of disease. Genome-scale metabolic models (GEMs) can provide an increased understanding of the mechanisms behind the effects of diet, the genotype-phenotype relationship and microbial robustness. Here we reconstructed GEMs for three key species, (Bacteroides thetaiotamicron, Eubacterium rectale and Methanobrevibacter smithii) as relevant representatives of three main phyla in the human gut (Bacteroidetes, Firmicutes and Euryarchaeota). We simulated the interactions between these three bacteria in different combinations of gut ecosystems and compared the predictions with the experimental results obtained from colonization of germ free mice. Furthermore, we used our GEMs for analyzing the contribution of each species to the overall metabolism of the gut microbiota based on transcriptome data and demonstrated that these models can be used as a scaffold for understanding bacterial interactions in the gut.
authors: Department of Chemical and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.
authors: Saeed
authors: S
authors: Shoaie
authors: Fredrik
authors: F
authors: Karlsson
authors: Adil
authors: A
authors: Mardinoglu
authors: Intawat
authors: I
authors: Nookaew
authors: Sergio
authors: S
authors: Bordel
authors: Jens
authors: J
authors: Nielsen
mesh_terms: D018407:Bacterial Physiological Phenomena; D003198:Computer Simulation; D041981:Gastrointestinal Tract / Q000382:microbiology*; D016680:Genome, Bacterial / Q000502:physiology*; D006801:Humans; D054892:Metagenome / Q000502:physiology*; D064307:Microbiota / Q000502:physiology*; D008954:Models, Biological
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