A cost and community perspective on the barriers to microbiome data reuse

Microbiome research is becoming a mature field with a wealth of data amassed from diverse ecosystems, yet the ability to fully leverage multi-omics data for reuse remains challenging. To provide a view into researchers' behavior and attitudes towards data reuse, we surveyed over 700 microbiome researchers to evaluate data sharing and reuse challenges. We found that many researchers are impeded by difficulties with metadata records, challenges with processing and bioinformatics, and problems with data repository submissions. We also explored the cost constraints of data reuse at each step of the data reuse process to better understand "pain points" and to provide a more quantitative perspective from sixteen active researchers. The bioinformatics and data processing step was estimated to be the most time consuming, which aligns with some of the most frequently reported challenges from the community survey. From these two approaches, we present evidence-based recommendations for how to address data sharing and reuse challenges with concrete actions for future work.

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Publication Details

Journal
Frontiers in Bioinformatics
Published
2025-04-09
DOI
https://doi.org/10.3389/fbinf.2025.1585717
Citations
2
Primary Topic
Research Data Management Practices
Type
article
Field-Weighted Citation Impact
6.49

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article

A cost and community perspective on the barriers to microbiome data reuse

Mitiku Mihiret Seyoum, Marie Kroeger, E. Anders Kiledal, Lisa Karstens et al.
2 citations
Frontiers in Bioinformatics
Research Data Management Practices
6.49
article

A cost and community perspective on the barriers to microbiome data reuse

Mitiku Mihiret Seyoum, Marie Kroeger, E. Anders Kiledal, Lisa Karstens, Chhedi Lal Gupta, Alexandre de Melo Andrade, Simon Roux, Mustafa Güzel, Julia M. Kelliher, Ahmed A. Shibl, Mark McCauley, Daniel D. Sprockett, L. Johnson, Moamen M. Elmassry, Thomas M. Pitot, Leandro Nascimento Lemos, Marc W. Van Goethem, Douglas Terra Machado, Emiley A. Eloe‐Fadrosh, Emilie J. Skoog, Jaclyn K. Saunders, Aaron Robinson, Jason A. Rothman, Katherine R. Lane, Francisca E. Rodriguez, Winston Anthony, Cassandra L. Ettinger, Cristal Zúñiga, Buck Hanson, Reid Longley, Iyanu Oduwole, Kaelan Prime, Chris R. P. Robinson
article en
2 citations

Abstract

Microbiome research is becoming a mature field with a wealth of data amassed from diverse ecosystems, yet the ability to fully leverage multi-omics data for reuse remains challenging. To provide a view into researchers' behavior and attitudes towards data reuse, we surveyed over 700 microbiome researchers to evaluate data sharing and reuse challenges. We found that many researchers are impeded by difficulties with metadata records, challenges with processing and bioinformatics, and problems with data repository submissions. We also explored the cost constraints of data reuse at each step of the data reuse process to better understand "pain points" and to provide a more quantitative perspective from sixteen active researchers. The bioinformatics and data processing step was estimated to be the most time consuming, which aligns with some of the most frequently reported challenges from the community survey. From these two approaches, we present evidence-based recommendations for how to address data sharing and reuse challenges with concrete actions for future work.

Frontiers in BioinformaticsVol. 5
University of California, Riverside (US), New York University Abu Dhabi (AE), Los Alamos National Laboratory (US), Pacific Northwest National Laboratory (US), Lawrence Berkeley National Laboratory (US), Scripps Institution of Oceanography (US), Oregon Health & Science University (US), University of Georgia (US), University of Calgary (CA), Princeton University (US), San Diego State University (US), University of Michigan (US), Hitit Üniversitesi (TR), Great Lakes Bioenergy Research Center (US), University of Florida (US), University of California San Diego (US), ICMR - National Institute of Immunohaemotology (IN), Indiana University Bloomington (US), Brazilian Center for Research in Energy and Materials (BR), Institute of Wood Science and Technology (IN), Brazilian Biosciences National Laboratory (BR), Université Laval (CA), Wake Forest University (US), Massachusetts Institute of Technology (US), King Abdullah University of Science and Technology (SA), University of Tennessee at Knoxville (US), University of Arkansas at Fayetteville (US), Michigan State University (US), Academy of Scientific and Innovative Research (IN)
U.S. Department of Energy, Office of Science, Biological and Environmental Research, Lawrence Berkeley National Laboratory, Los Alamos National Laboratory, Pacific Northwest National Laboratory
Openalex Percentile: Top 4%
Research Data Management Practices
6.49
DOIOpen Access PDFOpenAlex
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