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

Alberto Noronha, Jennifer Modamio, Yohan Jarosz, Elisabeth Guerard, Nicolas Sompairac, German Preciat, Anna Dröfn Daníelsdóttir, Max Krecke, Diane Merten, Hulda S Haraldsdóttir, Almut Heinken, Laurent Heirendt, Stefanía Magnúsdóttir, Dmitry A Ravcheev, Swagatika Sahoo, Piotr Gawron, Lucia Friscioni, Beatriz Garcia, Mabel Prendergast, Alberto Puente, Mariana Rodrigues. Akansha Roy, Mouss Rouquaya, Luca Wiltgen, Alise Žagare, Elisabeth John, Maren Krueger, Inna Kuperstein, Andrei Zinovyev, Reinhard Schneider, Ronan M T Fleming, and Ines Thiele

Nucleic Acids Res (2019) 47 (D1): D614–D624, doi:10.1093/nar/gky992

The VMH integrates the metabolic reconstructions of human (Recon3D) and gut microbes (AGORA) representing a vast and unique knowledge base for metabolic pathways. Both resources have a shared nomenclature which allows exploring potential interactions between gut microbes and host metabolism. These reconstructions can also be used for metabolic modeling experiments. The VMH functions as a knowledge hub. It interlinks “Human metabolism”, “Gut microbiome”, “Disease”, “Nutrition”, and “ReconMaps”, allowing for cross-linked analysis. Emphasis has been placed on connecting VMH’s entities with external resources facilitating access to further metabolic, genetic, clinical, nutritional, and toxicological information. The VMH enables the visualization of simulation and experimental data in the context of the human metabolic network. Seven comprehensive Google-like maps of human metabolism are available in the “ReconMaps” resource.

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