Metadata harmonization–Standards are the key for a better usage of omics data for integrative microbiome analysis
Environmental Microbiome, vol. 17, pp. 33
Abstract
BACKGROUND: Tremendous amounts of data generated from microbiome research studies during the last decades require not only standards for sampling and preparation of omics data but also clear concepts of how the metadata is prepared to ensure re-use for integrative and interdisciplinary microbiome analysis. RESULTS: In this Commentary, we present our views on the key issues related to the current system for metadata submission in omics research, and propose the development of a global metadata system. Such a system should be easy to use, clearly structured in a hierarchical way, and should be compatible with all existing microbiome data repositories, following common standards for minimal required information and common ontology. Although minimum metadata requirements are essential for microbiome datasets, the immense technological progress requires a flexible system, which will have to be constantly improved and re-thought. While FAIR principles (Findable, Accessible, Interoperable, and Reusable) are already considered, international legal issues on genetic resource and sequence sharing provided by the Convention on Biological Diversity need more awareness and engagement of the scientific community. CONCLUSIONS: The suggested approach for metadata entries would strongly improve retrieving and re-using data as demonstrated in several representative use cases. These integrative analyses, in turn, would further advance the potential of microbiome research for novel scientific discoveries and the development of microbiome-derived products.
Authors 51
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Tomislav Cernava corresponding
Affiliation as printed
Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria. tomislav.cernava@tugraz.at
TU Graz - Graz University of Technology [Graz] (Rechbauerstr. 12, 8010 Graz - Austria)
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Affiliation as printed
Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
TU Graz - Graz University of Technology [Graz] (Rechbauerstr. 12, 8010 Graz - Austria)
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Helmholtz Centre for Environmental Research · German Centre for Integrative Biodiversity Research
Affiliation as printed
2Soil Ecology Department, Helmholtz Centre for Environmental Research (UFZ), Halle (Saale), Germany
3German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
UFZ - Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (04318 Leipzig, Germany - Germany)
iDiv - German Centre for Integrative Biodiversity Research (Deutscher Platz 5e, 04103 Leipzig - Germany)
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Universitätsklinikum Aachen · RWTH Aachen University
Affiliation as printed
Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
UKA - Universitätsklinikum RWTH Aachen - University Hospital Aachen [Aachen, Germany] (Universitätsklinikum Aachen, AöR - Pauwelsstraße 30 - 52074 Aachen - Germany)
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Medizinische Hochschule Hannover · German Center for Infection Research · Helmholtz Centre for Infection Research · Technische Universität Braunschweig
Affiliation as printed
Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
Cluster of Excellence RESIST (EXC2155), Hannover Medical School, Hannover, Germany
Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
German Center for Infection Research (DZIF), Hannover-Braunschweig site, Hannover, Germany
DZIF - German Center for Infection Research - Partner Site Bonn-Cologne (Partner Site Bonn-Cologne, Bonn - Germany)
MHH - Medizinische Hochschule Hannover = Hannover Medical School (Carl-Neuberg-Straße 1, 30625 Hannover, - Germany)
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Helmholtz Centre for Infection Research · University of Duisburg-Essen · Technische Universität Braunschweig
Affiliation as printed
Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
Universität Duisburg-Essen, Essen, Germany
HZI - Helmholtz Centre for Infection Research (Inhoffenstraße 7, 38124 Braunschweig - Germany)
Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig] (38092 Braunschweig - Germany)
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Helmholtz Centre for Infection Research · University of Duisburg-Essen · Technische Universität Braunschweig
Affiliation as printed
Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
Universität Duisburg-Essen, Essen, Germany
Universität Duisburg-Essen = University of Duisburg-Essen [Essen] (Universitätsstraße 2, 45141 Essen - Germany)
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German Center for Infection Research · Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures · Technische Universität Braunschweig
Affiliation as printed
Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
Technical University of Braunschweig, Braunschweig, Germany
DSMZ - Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (Inhoffenstraße 7B, 38124 Braunschweig - Germany)
DZIF - German Center for Infection Research - partner site Hannover-Braunschweig (Germany)
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German Center for Infection Research · Max-von-Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie · Ludwig-Maximilians-Universität München
Affiliation as printed
German Center for Infection Research (DZIF), Munich, Germany
Max Von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
DZIF - German Center for Infection Research, Partnersite Munich (Germany)
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AIT Austrian Institute of Technology GmbH
Affiliation as printed
Bioresources Unit, AIT Austrian Institute of Technology, Tulln, Austria
AIT - Austrian Institute of Technology [Vienna] (Donau-City-Straße 1 1220 Vienna - Austria)
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Affiliation as printed
Helmholtz Zentrum München, Oberschleissheim, Germany
IBB - Institute of Biomathematics and Biometry - Helmholtz Zentrum München (Ingolstädter Landstraße 1 D-85764 Neuherberg - Germany)
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Gabriele Berg corresponding
University of Potsdam · Graz University of Technology · Leibniz Institute for Agricultural Engineering and Bioeconomy
Affiliation as printed
Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria. gabriele.berg@tugraz.at
Leibniz-Institute for Agricultural Engineering Potsdam (ATB), Potsdam, Germany. gabriele.berg@tugraz.at
University of Potsdam, Potsdam, Germany. gabriele.berg@tugraz.at
TU Graz - Graz University of Technology [Graz] (Rechbauerstr. 12, 8010 Graz - Austria)
University of Potsdam = Universität Potsdam (Am Neuen Palais 10, House 9 14469 Potsdam - Germany)
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Agricultural University of Athens
Affiliation as printed
Agricultural University of Athens (Athènes - Greece)
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Microbiologie de l’alimentation au service de la santé
Affiliation as printed
MICALIS - MICrobiologie de l'ALImentation au Service de la Santé (Domaine de Vilvert 78352 JOUY-EN-JOSAS CEDEX - France)
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Affiliation as printed
University of Waterloo [Waterloo] (200 University Avenue West, Waterloo, ON, Canada N2L 3G1 - Canada)
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Universidade Estadual de Campinas (UNICAMP)
Affiliation as printed
UNICAMP - Universidade Estadual de Campinas = University of Campinas (Cidade Universitária 'Zeferino Vaz' CEP 13083-970 | Campinas-SP - Brazil)
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Microbiologie de l’alimentation au service de la santé
Affiliation as printed
MICALIS - MICrobiologie de l'ALImentation au Service de la Santé (Domaine de Vilvert 78352 JOUY-EN-JOSAS CEDEX - France)
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Affiliation as printed
Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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Affiliation as printed
Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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