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. 2022 Jun 24;17(1):33.
doi: 10.1186/s40793-022-00425-1.

Metadata harmonization-Standards are the key for a better usage of omics data for integrative microbiome analysis

Tomislav Cernava #  1 , Daria Rybakova #  2 , François Buscot  3   4 , Thomas Clavel  5 , Alice Carolyn McHardy  6   7   8   9 , Fernando Meyer  6   7 , Folker Meyer  10 , Jörg Overmann  11   12 , Bärbel Stecher  13   14 , Angela Sessitsch  15 , Michael Schloter #  16 , Gabriele Berg #  17   18   19 ; MicrobiomeSupport Team
Collaborators, Affiliations

Metadata harmonization-Standards are the key for a better usage of omics data for integrative microbiome analysis

Tomislav Cernava et al. Environ Microbiome. .

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.

Keywords: Convention on biological diversity; Data storage; FAIR; Metadata; Microbiome; Omics technologies; Repositories.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Example of the hierarchically built structure of the questions in the metadata application allowing for an easy and non-redundant ontology search for plant-associated microbiomes
Fig. 2
Fig. 2
An overview of FAIR principles ( adapted from [56] that could be implemented in metadata requirements to facilitate search and re-use of deposited microbiome data in the future
See this image and copyright information in PMC

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