Metabolism of the Gut Microbiome : New Insights through Genome-Scale Metabolic Modeling

We are building a Human Metabolic Atlas, a novel web-based database and modelling tool that can be used by medical and pharmaceutical researchers to analyse clinical data with the objectives of identifying biomarkers associated with disease development and improving health care. The central technology in the Human Metabolic Atlas is genome-scale metabolic modelling (GEMs), which will be made tissue-specific by using different types of experimental data, e.g. from the Human Protein Atlas. These models will immediately allow for context-dependent analysis of clinical data, providing much more information than traditional statistical correlation analysis, and hence advance the identification of biomarkers that can be used for early diagnosis of metabolic related diseases. As part of the Human Metabolic Atlas we are developing GEMs for the gut microbiome. In this context we are using metagenomics for identification of different metabolic functions that are associated with human diseases. Here we are using metagenomics sequencing data from the gut microbiome of patients with different diseases, e.g. arteriosclerosis and type 2 diabetes. Through the combination of the bacterial GEMs and metagenomics data we have identified enriched metabolic functions in the microbiome, and based on this we point to novel prospective biomarkers for disease development. We are further integrating metagenomics information into predictive metabolic models that have the prospect for simulation of how the gut microbiome will respond to diet.