Microbiome data management in action workshop: Atlanta, GA, USA, June 12–13, 2024
Abstract Microbiome research is revolutionizing human and environmental health, but the value and reuse of microbiome data are significantly hampered by the limited development and adoption of data standards. While several ongoing efforts are aimed at improving microbiome data management, significan...
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2025-04-01
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| Series: | Environmental Microbiome |
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| Online Access: | https://doi.org/10.1186/s40793-025-00702-9 |
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| author | Julia M. Kelliher Mashael Aljumaah Sarah R. Bordenstein J. Rodney Brister Patrick S. G. Chain Jose Pablo Dundore-Arias Joanne B. Emerson Vanessa Moreira C. Fernandes Roberto Flores Antonio Gonzalez Zoe A. Hansen Eneida L. Hatcher Scott A. Jackson Christina A. Kellogg Ramana Madupu Cassandra Maria Luz Miller Chloe Mirzayi Ahmed M. Moustafa Christopher Mungall Aaron Oliver Nonia Pariente Jennifer Pett-Ridge Sydne Record Linta Reji Anna-Louise Reysenbach Virginia I. Rich Lorna Richardson Lynn M. Schriml Reed S. Shabman Maria A. Sierra Matthew B. Sullivan Punithavathi Sundaramurthy Katherine M. Thibault Luke R. Thompson Scott Tighe Ethell Vereen Emiley A. Eloe-Fadrosh |
| author_facet | Julia M. Kelliher Mashael Aljumaah Sarah R. Bordenstein J. Rodney Brister Patrick S. G. Chain Jose Pablo Dundore-Arias Joanne B. Emerson Vanessa Moreira C. Fernandes Roberto Flores Antonio Gonzalez Zoe A. Hansen Eneida L. Hatcher Scott A. Jackson Christina A. Kellogg Ramana Madupu Cassandra Maria Luz Miller Chloe Mirzayi Ahmed M. Moustafa Christopher Mungall Aaron Oliver Nonia Pariente Jennifer Pett-Ridge Sydne Record Linta Reji Anna-Louise Reysenbach Virginia I. Rich Lorna Richardson Lynn M. Schriml Reed S. Shabman Maria A. Sierra Matthew B. Sullivan Punithavathi Sundaramurthy Katherine M. Thibault Luke R. Thompson Scott Tighe Ethell Vereen Emiley A. Eloe-Fadrosh |
| author_sort | Julia M. Kelliher |
| collection | DOAJ |
| description | Abstract Microbiome research is revolutionizing human and environmental health, but the value and reuse of microbiome data are significantly hampered by the limited development and adoption of data standards. While several ongoing efforts are aimed at improving microbiome data management, significant gaps still remain in terms of defining and promoting adoption of consensus standards for these datasets. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines for human microbiome research have been endorsed and successfully utilized by many research organizations, publishers, and funding agencies, and have been recognized as a consensus community standard. No equivalent effort has occurred for environmental, synthetic, and non-human host-associated microbiomes. To address this growing need within the microbiome research community, we convened the Microbiome Data Management in Action Workshop (June 12–13, 2024, in Atlanta, GA, USA), to bring together key decision makers in microbiome science including researchers, publishers, funders, and data repositories. The 50 attendees, representing the diverse and interdisciplinary nature of microbiome research, discussed recent progress and challenges, and brainstormed actionable recommendations and paths forward for coordinated environmental microbiome data management and the modifications necessary for the STORMS guidelines to be applied to environmental, non-human host, and synthetic microbiomes. The outcomes of this workshop will form the basis of a formalized data management roadmap to be implemented across the field. These best practices will drive scientific innovation now and in years to come as these data continue to be used not only in targeted reanalyses but in large-scale models and machine learning efforts. |
| format | Article |
| id | doaj-art-b6edff100d464e7094d530ebc0ccbb26 |
| institution | DOAJ |
| issn | 2524-6372 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Environmental Microbiome |
| spelling | doaj-art-b6edff100d464e7094d530ebc0ccbb262025-08-20T03:18:53ZengBMCEnvironmental Microbiome2524-63722025-04-012011810.1186/s40793-025-00702-9Microbiome data management in action workshop: Atlanta, GA, USA, June 12–13, 2024Julia M. Kelliher0Mashael Aljumaah1Sarah R. Bordenstein2J. Rodney Brister3Patrick S. G. Chain4Jose Pablo Dundore-Arias5Joanne B. Emerson6Vanessa Moreira C. Fernandes7Roberto Flores8Antonio Gonzalez9Zoe A. Hansen10Eneida L. Hatcher11Scott A. Jackson12Christina A. Kellogg13Ramana Madupu14Cassandra Maria Luz Miller15Chloe Mirzayi16Ahmed M. Moustafa17Christopher Mungall18Aaron Oliver19Nonia Pariente20Jennifer Pett-Ridge21Sydne Record22Linta Reji23Anna-Louise Reysenbach24Virginia I. Rich25Lorna Richardson26Lynn M. Schriml27Reed S. Shabman28Maria A. Sierra29Matthew B. Sullivan30Punithavathi Sundaramurthy31Katherine M. Thibault32Luke R. Thompson33Scott Tighe34Ethell Vereen35Emiley A. Eloe-Fadrosh36New Mexico ConsortiumCenter for Gastrointestinal Biology and Disease (CGIBD), School of Medicine, UNC Microbiome Core, University of North CarolinaDepartments of Biology & Entomology, Pennsylvania State UniversityNational Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBioscience Division, Los Alamos National LaboratoryDepartment of Biology and Chemistry, California State UniversityDepartment of Plant Pathology, University of California DavisDepartment of Biological Sciences, Florida Atlantic UniversityNational Institute on Aging, National Institutes of HealthDepartment of Pediatrics, University of California San DiegoDepartment of Plant Pathology, University of MinnesotaNational Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthNational Institute of Standards and TechnologyU.S. Geological Survey, St. Petersburg Coastal and Marine Science CenterBiological Systems Science Division, Department of Energy, Office of Biological & Environmental ResearchDepartment of Biology, University of New MexicoCUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public HealthDivision of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of PhiladelphiaLawrence Berkeley National LaboratoryScripps Institution of Oceanography, University of California San DiegoPublic Library of SciencePhysical and Life Sciences Directorate, Lawrence Livermore National LaboratoryDepartment of Wildlife, Fisheries, and Conservation Biology, University of MaineDepartment of Geophysical Sciences, University of ChicagoCenter for Life in Extreme Environments, Portland State UniversityCenter of Microbiome Science, The Ohio State UniversityEMBL-European Bioinformatics InstituteInstitute for Genome Sciences, University of Maryland School of MedicineOffice of Data Science and Emerging Technologies, National Institute of Allergy and Infectious Diseases, National Institutes of HealthTri-Institutional Computational Biology and Medicine Program, Weill Cornell MedicineCenter of Microbiome Science, The Ohio State UniversityBenioff Center for Microbiome Medicine, University of California San FranciscoNational Ecological Observatory NetworkNorthern Gulf Institute, Mississippi State UniversityVermont Integrative Genomics, University of VermontScience, Technology, Engineering and Mathematics Division, Morehouse CollegeLawrence Berkeley National LaboratoryAbstract Microbiome research is revolutionizing human and environmental health, but the value and reuse of microbiome data are significantly hampered by the limited development and adoption of data standards. While several ongoing efforts are aimed at improving microbiome data management, significant gaps still remain in terms of defining and promoting adoption of consensus standards for these datasets. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines for human microbiome research have been endorsed and successfully utilized by many research organizations, publishers, and funding agencies, and have been recognized as a consensus community standard. No equivalent effort has occurred for environmental, synthetic, and non-human host-associated microbiomes. To address this growing need within the microbiome research community, we convened the Microbiome Data Management in Action Workshop (June 12–13, 2024, in Atlanta, GA, USA), to bring together key decision makers in microbiome science including researchers, publishers, funders, and data repositories. The 50 attendees, representing the diverse and interdisciplinary nature of microbiome research, discussed recent progress and challenges, and brainstormed actionable recommendations and paths forward for coordinated environmental microbiome data management and the modifications necessary for the STORMS guidelines to be applied to environmental, non-human host, and synthetic microbiomes. The outcomes of this workshop will form the basis of a formalized data management roadmap to be implemented across the field. These best practices will drive scientific innovation now and in years to come as these data continue to be used not only in targeted reanalyses but in large-scale models and machine learning efforts.https://doi.org/10.1186/s40793-025-00702-9MicrobiomeEnvironmental MicrobiomeStandardsData managementData stewardshipData reuse |
| spellingShingle | Julia M. Kelliher Mashael Aljumaah Sarah R. Bordenstein J. Rodney Brister Patrick S. G. Chain Jose Pablo Dundore-Arias Joanne B. Emerson Vanessa Moreira C. Fernandes Roberto Flores Antonio Gonzalez Zoe A. Hansen Eneida L. Hatcher Scott A. Jackson Christina A. Kellogg Ramana Madupu Cassandra Maria Luz Miller Chloe Mirzayi Ahmed M. Moustafa Christopher Mungall Aaron Oliver Nonia Pariente Jennifer Pett-Ridge Sydne Record Linta Reji Anna-Louise Reysenbach Virginia I. Rich Lorna Richardson Lynn M. Schriml Reed S. Shabman Maria A. Sierra Matthew B. Sullivan Punithavathi Sundaramurthy Katherine M. Thibault Luke R. Thompson Scott Tighe Ethell Vereen Emiley A. Eloe-Fadrosh Microbiome data management in action workshop: Atlanta, GA, USA, June 12–13, 2024 Environmental Microbiome Microbiome Environmental Microbiome Standards Data management Data stewardship Data reuse |
| title | Microbiome data management in action workshop: Atlanta, GA, USA, June 12–13, 2024 |
| title_full | Microbiome data management in action workshop: Atlanta, GA, USA, June 12–13, 2024 |
| title_fullStr | Microbiome data management in action workshop: Atlanta, GA, USA, June 12–13, 2024 |
| title_full_unstemmed | Microbiome data management in action workshop: Atlanta, GA, USA, June 12–13, 2024 |
| title_short | Microbiome data management in action workshop: Atlanta, GA, USA, June 12–13, 2024 |
| title_sort | microbiome data management in action workshop atlanta ga usa june 12 13 2024 |
| topic | Microbiome Environmental Microbiome Standards Data management Data stewardship Data reuse |
| url | https://doi.org/10.1186/s40793-025-00702-9 |
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