Metadata harmonization–Standards are the key for a better usage of omics data for integrative microbiome analysis
Tomislav Cernava, Daria Rybakova, François Buscot, Thomas Clavel, Alice C. McHardy, Fernando Meyer, Folker Meyer, Jörg Overmann, Bärbel Stecher, Angela Sessitsch, Michael Schloter, Gabriele Berg, The MicrobiomeSupport Team, Paulo Arruda, Thomas Bartzanas, Tanja Kostić, Paula Iara Brennan, Bárbara Bort Biazotti, Marie‐Christine Champomier‐Vergès, Trevor C. Charles, Mairéad Coakley, Paul D. Cotter, Don A. Cowan, Kathleen D’hondt, Ilario Ferrocino, Kristina Foterek, Gema Herrero-Corral, Carly Huitema, Janet Jansson, Shuang‐Jiang Liu, Paula Malloy, Emmanuelle Maguin, Lidia Hanna Markiewicz, Ryan McClure, A. Moser, Jolien Roovers, Matthew J. Ryan, Inga Sarand, Bettina Schelkle, Annelein Meisner, Ulrich Schurr, Joseph Selvin, Effie Tsakalidou, Martin Wagner, Steven A. Wakelin, Wiesław Wiczkowski, Hanna Winkler, Juanjuan Xiao, C.J. Bunthof, Rafael Soares Correa de Souza, Yolanda Sanz, Lene Lange, Hauke Smidt
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.