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The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease [article]

Alberto Noronha, Jennifer Modamio, Yohan Jarosz, Nicolas Sompairac, German Preciat Gonzalez, Anna Drofn Danielsdottir, Max Krecke, Diane Merten, Hulda S. Haraldsdottir, Almut Heinken, Laurent Heirendt, Stefania Magnusdottir (+20 others)
2018 biorxiv/medrxiv   pre-print

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A multitude of factors contribute to complex diseases and can be measured with "omics" methods. Databases facilitate data interpretation for underlying mechanisms. Here, we describe the Virtual Metabolic Human (VMH, http://vmh.life) database encapsulating current knowledge of human metabolism within five interlinked resources "Human metabolism", "Gut microbiome", "Disease", "Nutrition", and "ReconMaps". The VMH captures 5,180 unique metabolites, 17,730 unique reactions, 3,288 human genes, 255
more » ... ndelian diseases, 818 microbes, 632,685 microbial genes, and 8,790 food items. The VMH's unique features are i) the hosting the metabolic reconstructions of human and gut microbes amenable for metabolic modeling; ii) seven human metabolic maps for data visualization; iii) a nutrition designer; iv) a user-friendly webpage and application-programming interface to access its content; and v) user feedback option for community engagement. We demonstrate with four examples the VMH's utility. The VMH represents a novel, interdisciplinary database for data interpretation and hypothesis generation to the biomedical community.
doi:10.1101/321331 fatcat:abra7kq6ivbp5gtwxcihvupite
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Alberto Noronha, Jennifer Modamio, Yohan Jarosz, Nicolas Sompairac, German Preciat Gonzalez, Anna Drofn Danielsdottir, Max Krecke, Diane Merten, Hulda S. Haraldsdottir, Almut Heinken, Laurent Heirendt, Stefania Magnusdottir, Dmitry A. Ravcheev, Swagatika Sahoo, Piotr Gawron, Elisabeth Guerard, Lucia Fiscioni, Beatriz Garcia, Mabel Prendergast, Alberto Puente, Mariana Rodrigues, Akansha Roy, Mouss Rouquaya, Luca Wiltgen, Alise Zagare, Elisabeth John, Maren Krueger, Inna Kuperstein, Andrei Zinovyev, Reinhard Schneider, Ronan M.T. Fleming, Ines Thiele. "The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease." biorxiv/medrxiv (2018)