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 resea...
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Frontiers Media S.A.
2025-04-01
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| author | Julia M. Kelliher Julia M. Kelliher Leah Y. D. Johnson Francisca E. Rodriguez Jaclyn K. Saunders Marie E. Kroeger Buck Hanson Aaron J. Robinson Winston E. Anthony Marc W. Van Goethem Anders Kiledal Ahmed A. Shibl Amanda Araujo Serrao de Andrade Cassandra L. Ettinger Chhedi Lal Gupta Chhedi Lal Gupta Chris R. P. Robinson Cristal Zuniga Cristal Zuniga Daniel Sprockett Douglas Terra Machado Emilie J. Skoog Iyanu Oduwole Jason A. Rothman Kaelan Prime Katherine R. Lane Leandro Nascimento Lemos Lisa Karstens Mark McCauley Mitiku Mihiret Seyoum Moamen M. Elmassry Mustafa Guzel Reid Longley Simon Roux Thomas M. Pitot Emiley A. Eloe-Fadrosh |
| author_facet | Julia M. Kelliher Julia M. Kelliher Leah Y. D. Johnson Francisca E. Rodriguez Jaclyn K. Saunders Marie E. Kroeger Buck Hanson Aaron J. Robinson Winston E. Anthony Marc W. Van Goethem Anders Kiledal Ahmed A. Shibl Amanda Araujo Serrao de Andrade Cassandra L. Ettinger Chhedi Lal Gupta Chhedi Lal Gupta Chris R. P. Robinson Cristal Zuniga Cristal Zuniga Daniel Sprockett Douglas Terra Machado Emilie J. Skoog Iyanu Oduwole Jason A. Rothman Kaelan Prime Katherine R. Lane Leandro Nascimento Lemos Lisa Karstens Mark McCauley Mitiku Mihiret Seyoum Moamen M. Elmassry Mustafa Guzel Reid Longley Simon Roux Thomas M. Pitot Emiley A. Eloe-Fadrosh |
| author_sort | Julia M. Kelliher |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-9c96f61b92d846d9a0d28d9476e7a0ae |
| institution | DOAJ |
| issn | 2673-7647 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioinformatics |
| spelling | doaj-art-9c96f61b92d846d9a0d28d9476e7a0ae2025-08-20T03:06:13ZengFrontiers Media S.A.Frontiers in Bioinformatics2673-76472025-04-01510.3389/fbinf.2025.15857171585717A cost and community perspective on the barriers to microbiome data reuseJulia M. Kelliher0Julia M. Kelliher1Leah Y. D. Johnson2Francisca E. Rodriguez3Jaclyn K. Saunders4Marie E. Kroeger5Buck Hanson6Aaron J. Robinson7Winston E. Anthony8Marc W. Van Goethem9Anders Kiledal10Ahmed A. Shibl11Amanda Araujo Serrao de Andrade12Cassandra L. Ettinger13Chhedi Lal Gupta14Chhedi Lal Gupta15Chris R. P. Robinson16Cristal Zuniga17Cristal Zuniga18Daniel Sprockett19Douglas Terra Machado20Emilie J. Skoog21Iyanu Oduwole22Jason A. Rothman23Kaelan Prime24Katherine R. Lane25Leandro Nascimento Lemos26Lisa Karstens27Mark McCauley28Mitiku Mihiret Seyoum29Moamen M. Elmassry30Mustafa Guzel31Reid Longley32Simon Roux33Thomas M. Pitot34Emiley A. Eloe-Fadrosh35Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United StatesDepartment of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, MI, United StatesBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United StatesBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United StatesDepartment of Marine Sciences, University of Georgia, Athens, GA, United StatesIn-Pipe Technology, Wood Dale, IL, United StatesBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United StatesBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United StatesPacific Northwest National Laboratory, Richland, WA, United StatesBiological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi ArabiaDepartment of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, United StatesPublic Health Research Center, New York University Abu Dhabi, Abu Dhabi, United Arab EmiratesDepartment of Biological Sciences, University of Calgary, Calgary, AB, Canada0Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States1ICMR-CRMCH, National Institute of Immunohaematology, Chandrapur Unit, Chandrapur, Maharashtra, India2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India3Department of Biology, Indiana University, Bloomington, IN, United States4Department of Biology, Cell, and Molecular Biology, San Diego State University, San Diego, CA, United States5DOE Great Lakes Bioenergy Research Center, San Diego State University, San Diego, CA, United States6Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston-Salem, NC, United States7Bioinformatics Laboratory, National Laboratory for Scientific Computing, Quitandinha, Rio de Janeiro, Brazil8Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, United States9Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, TN, United States0Department of Microbiology and Plant Pathology, University of California: Riverside, Riverside, CA, United StatesBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States1Massachusetts Institute of Technology, Cambridge, MA, United States2Ilum School of Science, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil3Division of Oncological Sciences, Department of Obstetrics and Gynecology, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States4The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, United States5Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States6Department of Molecular Biology, Princeton University, Princeton, NJ, United States7Department of Food Engineering, Hitit University, Corum, TürkiyeBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States8Lawrence Berkeley National Laboratory, Berkeley, CA, United States9Department of Biochemistry, Microbiology, and Bioinformatics, Université Laval, Québec, QC, Canada8Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesMicrobiome 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.https://www.frontiersin.org/articles/10.3389/fbinf.2025.1585717/fullmicrobiomemulti-omicsdata reuseFAIR datasurveymetadata |
| spellingShingle | Julia M. Kelliher Julia M. Kelliher Leah Y. D. Johnson Francisca E. Rodriguez Jaclyn K. Saunders Marie E. Kroeger Buck Hanson Aaron J. Robinson Winston E. Anthony Marc W. Van Goethem Anders Kiledal Ahmed A. Shibl Amanda Araujo Serrao de Andrade Cassandra L. Ettinger Chhedi Lal Gupta Chhedi Lal Gupta Chris R. P. Robinson Cristal Zuniga Cristal Zuniga Daniel Sprockett Douglas Terra Machado Emilie J. Skoog Iyanu Oduwole Jason A. Rothman Kaelan Prime Katherine R. Lane Leandro Nascimento Lemos Lisa Karstens Mark McCauley Mitiku Mihiret Seyoum Moamen M. Elmassry Mustafa Guzel Reid Longley Simon Roux Thomas M. Pitot Emiley A. Eloe-Fadrosh A cost and community perspective on the barriers to microbiome data reuse Frontiers in Bioinformatics microbiome multi-omics data reuse FAIR data survey metadata |
| title | A cost and community perspective on the barriers to microbiome data reuse |
| title_full | A cost and community perspective on the barriers to microbiome data reuse |
| title_fullStr | A cost and community perspective on the barriers to microbiome data reuse |
| title_full_unstemmed | A cost and community perspective on the barriers to microbiome data reuse |
| title_short | A cost and community perspective on the barriers to microbiome data reuse |
| title_sort | cost and community perspective on the barriers to microbiome data reuse |
| topic | microbiome multi-omics data reuse FAIR data survey metadata |
| url | https://www.frontiersin.org/articles/10.3389/fbinf.2025.1585717/full |
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