Community-Driven Metadata Standards for Agricultural Microbiome Research

J. P. Dundore-Arias, E. A. Eloe-Fadrosh, L. M. Schriml, G. A. Beattie, F. P. Brennan, P. E. Busby, R. B. Calderon, S. C. Castle, J. B. Emerson, S. E. Everhart, K. Eversole, K. E. Frost, J. R. Herr, A. I. Huerta, A. S. Iyer-Pascuzzi, A. K. Kalil, J. E. Leach, J. Leonard, J. E. Maul, B. PrithivirajM. Potrykus, N. R. Redekar, J. A. Rojas, K. A.T. Silverstein, D. J. Tomso, S. G. Tringe, B. A. Vinatzer, L. L. Kinkel

Research output: Contribution to journalReview articlepeer-review


Accelerating the pace of microbiome science to enhance crop productivity and agroecosystem health will require transdisciplinary studies, comparisons among datasets, and synthetic analyses of research from diverse crop management contexts. However, despite the widespread availability of crop-associated microbiome data, variation in field sampling and laboratory processing methodologies, as well as metadata collection and reporting, significantly constrains the potential for integrative and comparative analyses. Here we discuss the need for agriculture-specific metadata standards for microbiome research, and propose a list of “required” and “desirable” metadata categories and ontologies essential to be included in a future minimum information metadata standards checklist for describing agricultural microbiome studies. We begin by briefly reviewing existing metadata standards relevant to agricultural microbiome research, and describe ongoing efforts to enhance the potential for integration of data across research studies. Our goal is not to delineate a fixed list of metadata requirements. Instead, we hope to advance the field by providing a starting point for discussion, and inspire researchers to adopt standardized procedures for collecting and reporting consistent and well-annotated metadata for agricultural microbiome research.

Original languageEnglish (US)
Pages (from-to)115-121
Number of pages7
JournalPhytobiomes Journal
Issue number2
StatePublished - Feb 20 2020

Bibliographical note

Funding Information:
Funding: This material was supported in part by the National Science Foundation under grant number 1714276. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.


  • Genomics
  • Meta-analysis
  • Metagenomics
  • Microbiome
  • Omics
  • Ontologies
  • Phytobiome
  • Synthetic

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