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

Alberto Noronha(University of Luxembourg), Jennifer Modamio(University of Luxembourg), Yohan Jarosz(University of Luxembourg), Elisabeth Guerard(University of Luxembourg), Nicolas Sompairac(Inserm), German Preciat(University of Luxembourg), Anna Dröfn Daníelsdóttir(University of Luxembourg), Max Krecké(University of Luxembourg), Diane Merten(University of Luxembourg), Hulda S. Haraldsdóttir(University of Luxembourg), Almut Heinken(University of Luxembourg), Laurent Heirendt(University of Luxembourg), Stefanía Magnúsdóttir(University of Luxembourg), Dmitry A. Ravcheev(University of Luxembourg), Swagatika Sahoo(University of Luxembourg), Piotr Gawron(University of Luxembourg), Lucia Friscioni(University of Luxembourg), Beatriz García Santa Cruz(University of Luxembourg), Mabel Prendergast(University of Luxembourg), Alberto Puente(University of Luxembourg), Mariana Figueiredo Rodrigues(University of Luxembourg), Akansha Roy(University of Luxembourg), Mouss Rouquaya(University of Luxembourg), Luca Wiltgen(University of Luxembourg), Alise Žagare(University of Luxembourg), Elisabeth John(University of Luxembourg), Maren Krueger(University of Luxembourg), Inna Kuperstein(Inserm), Andreï Zinovyev(Inserm), Reinhard Schneider(University of Luxembourg), Ronan M. T. Fleming(University of Luxembourg), Ines Thiele(University of Luxembourg)
Nucleic Acids Research
October 10, 2018
10.1093/nar/gky992
Cited by 423Open Access
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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, www.vmh.life) database encapsulating current knowledge of human metabolism within five interlinked resources 'Human metabolism', 'Gut microbiome', 'Disease', 'Nutrition', and 'ReconMaps'. The VMH captures 5180 unique metabolites, 17 730 unique reactions, 3695 human genes, 255 Mendelian diseases, 818 microbes, 632 685 microbial genes and 8790 food items. The VMH's unique features are (i) the hosting of 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; (v) user feedback option for community engagement and (vi) the connection of its entities to 57 other web resources. The VMH represents a novel, interdisciplinary database for data interpretation and hypothesis generation to the biomedical community.

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