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 Krecké; Diane Merten; Hulda S. Haraldsdóttir; Almut Heinken; Laurent Heirendt; Stefanía Magnúsdóttir; Dmitry A. Ravcheev; Swagatika Sahoo; Piotr Gawron; Lucia Friscioni; Beatriz García Santa Cruz; Mabel Prendergast; Alberto Puente; Mariana Figueiredo Rodrigues; Akansha Roy; Mouss Rouquaya; Luca Wiltgen; Alise Žagare; Elisabeth John; Maren Krueger; Inna Kuperstein; Andrei Y. Zinovyev; Reinhard Schneider

doi:10.1093/nar/gky992

Systems BiologyNucleic Acids ResearchOct 10, 2018

Peer-reviewed journal article

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

Alberto Noronha iD, Jennifer Modamio iD, Yohan Jarosz iD, Elisabeth Guerard iD, Nicolas Sompairac iD, German Preciat iD, Anna Dröfn Daníelsdóttir, Max Krecké iD, Diane Merten iD, Hulda S. Haraldsdóttir iD, Almut Heinken iD, Laurent Heirendt iD, Stefanía Magnúsdóttir iD, Dmitry A. Ravcheev iD, Swagatika Sahoo iD, Piotr Gawron iD, Lucia Friscioni, Beatriz García Santa Cruz iD, Mabel Prendergast iD, Alberto Puente, Mariana Figueiredo Rodrigues iD, Akansha Roy, Mouss Rouquaya, Luca Wiltgen iD, Alise Žagare iD, , Ines Thiele iD

Abstract

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 Mendelian diseases, 818 microbes, 632,685 microbial genes, and 8,790 food items. The VMHs 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 VMHs utility. The VMH represents a novel, interdisciplinary database for data interpretation and hypothesis generation to the biomedical community.

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