94% of researchers rate our articles as excellent or good
Learn more about the work of our research integrity team to safeguard the quality of each article we publish.
Find out more
PERSPECTIVE article
Front. Bioinform.
Sec. Genomic Analysis
Volume 5 - 2025 | doi: 10.3389/fbinf.2025.1585717
This article is part of the Research Topic Expert Opinions in Genomic Analysis View all 4 articles
A cost & community perspective on the barriers to microbiome data reuse
Provisionally accepted
Julia Mae Kelliher 1,2*
Leah Johnson 1
Francisca E Rodriguez 1 Jaclyn K Saunders 3
Marie Kroger 4
Buck Timothy Hanson 1
Aaron Robinson 1
Winston Anthony 5 Marc W Van Goethem 6 Anders Kiledal 7
Ahmed A Shibl 8 Amanda Araujo Serrao de Andrade 9
Cassie L Ettinger 10
Chhedi Lal Gupta 11,12 Chris R P Robinson 13
Cristal Zuniga 14,15 Daniel Sprockett 16
Douglas Terra Machado 17
Emilie J Skoog 18 Iyanu Oduwole 19 Jason A Rothman 10 Kaelan Prime 1 Katherine R Lane 20
Leandro Nascimento Lemos 21
Lisa Karstens 22
Mark Mccauley 23
Mitiku Mihiret Seyoum 24
Moamen M Elmassry 25 Mustafa Guzel 26
Reid Longley 1
Simon Roux 27 Thomas M Pitot 28
Emiley A Eloe-Fadrosh 27*- 1 Los Alamos National Laboratory (DOE), Los Alamos, United States
- 2 Michigan State University, East Lansing, Michigan, United States
- 3 University of Georgia, Athens, Georgia, United States
- 4 In-Pipe Technology, Wood Dale, United States
- 5 Pacific Northwest National Laboratory (DOE), Richland, Washington, United States
- 6 King Abdullah University of Science and Technology, Thuwal, Makkah, Saudi Arabia
- 7 University of Michigan, Ann Arbor, Michigan, United States
- 8 New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- 9 University of Calgary, Calgary, Alberta, Canada
- 10 University of California, Riverside, Riverside, California, United States
- 11 National Institute of Immunohaematology, Indian Council of Medical Research, Mumbai, Maharashtra, India
- 12 Academy of Scientific and Innovative Research (AcSIR), New Delhi, National Capital Territory of Delhi, India
- 13 Indiana University, Bloomington, Indiana, United States
- 14 San Diego State University, San Diego, California, United States
- 15 Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States
- 16 Wake Forest University, Winston-Salem, North Carolina, United States
- 17 National Laboratory for Scientific Computing (LNCC), Petrópolis, Rio de Janeiro, Brazil
- 18 Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
- 19 The University of Tennessee, Knoxville, Knoxville, Tennessee, United States
- 20 Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
- 21 National Center for Research in Energy and Materials (Brazil), Campinas, São Paulo, Brazil
- 22 Oregon Health and Science University, Portland, Oregon, United States
- 23 Wetland and Aquatic Research Center, United States Geological Survey (USGS), Baton Rouge, Louisiana, United States
- 24 University of Arkansas, Fayetteville, North Carolina, United States
- 25 Princeton University, Princeton, New Jersey, United States
- 26 Hittite University, Çorum, Corum, Türkiye
- 27 Berkeley Lab (DOE), Berkeley, California, United States
- 28 Laval University, Quebec, Quebec, Canada
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 & 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 evidencebased recommendations for how to address data sharing and reuse challenges with concrete actions for future work.
Keywords: microbiome, multi-omics, Data reuse, FAIR Data, Survey, metadata, data standards
Received: 01 Mar 2025; Accepted: 17 Mar 2025.
Copyright: © 2025 Kelliher, Johnson, Rodriguez, Saunders, Kroger, Hanson, Robinson, Anthony, Van Goethem, Kiledal, Shibl, Andrade, Ettinger, Gupta, Robinson, Zuniga, Sprockett, Machado, Skoog, Oduwole, Rothman, Prime, Lane, Lemos, Karstens, Mccauley, Seyoum, Elmassry, Guzel, Longley, Roux, Pitot and Eloe-Fadrosh. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Julia Mae Kelliher, Los Alamos National Laboratory (DOE), Los Alamos, United States
Emiley A Eloe-Fadrosh, Berkeley Lab (DOE), Berkeley, California, United States
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.