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 Carolyn McHardy, Fernando Meyer, Folker Meyer, Jörg Overmann, Bärbel Stecher, Angela Sessitsch, Michael Schloter, Gabriele Berg, Paulo Arruda, Thomas Bartzanas, Tanja Kostic, Paula Iara Brennan, Bárbara Bort Biazotti, Marie Christine Champomier-Verges, Trevor Charles, Mairead CoakleyPaul Cotter, Don Cowan, Kathleen D’Hondt, Ilario Ferrocino, Kristina Foterek, Gema Herrero-Corral, Carly Huitema, Janet Jansson, Shuang Jiang Liu, Paula Malloy, Emmanuelle Maguin, Lidia Markiewicz, Ryan Mcclure, Andreas Moser, Jolien Roovers, Matthew Ryan, Inga Sarand, Bettina Schelkle, Annelein Meisner, Ulrich Schurr, Joseph Selvin, Effie Tsakalidou, Martin Wagner, Steve Wakelin, Wiesław Wiczkowski, Hanna Winkler, Juanjuan Xiao, Christine J. Bunthof, Rafael Soares Correa de Souza, Hauke Smidt

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

10 Citations (Scopus)


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.

Original languageEnglish
Article number33
JournalEnvironmental Microbiomes
Issue number1
Publication statusPublished - 24 Jun 2022


  • Convention on biological diversity
  • Data storage
  • FAIR
  • Metadata
  • Microbiome
  • Omics technologies
  • Repositories


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