Evidence map›Paper›PMID 40253432›Full record

ArticleEnvironmental microbiome2025

Microbiome data management in action workshop: Atlanta, GA, USA, June 12-13, 2024.

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 and 27 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Environmental microbiome, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

37 authors.

Julia M KelliherNew Mexico Consortium, Los Alamos, NM, USA. jkelliher@lanl.gov.ORCID http://orcid.org/0000-0003-4100-9119
Mashael AljumaahCenter for Gastrointestinal Biology and Disease (CGIBD), School of Medicine, UNC Microbiome Core, University of North Carolina, Chapel Hill, NC, USA.ORCID http://orcid.org/0000-0003-2477-7239
Sarah R BordensteinDepartments of Biology & Entomology, Pennsylvania State University, University Park, PA, USA.ORCID http://orcid.org/0000-0001-6092-1950
J Rodney BristerNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-2249-975X
Patrick S G ChainBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.ORCID http://orcid.org/0000-0003-3949-3634
Jose Pablo Dundore-AriasDepartment of Biology and Chemistry, California State University, Monterey Bay, Seaside, CA, USA.ORCID http://orcid.org/0000-0002-4944-0125
Joanne B EmersonDepartment of Plant Pathology, University of California Davis, Davis, CA, USA.ORCID http://orcid.org/0000-0001-9983-5566
Vanessa Moreira C FernandesDepartment of Biological Sciences, Florida Atlantic University, Boca Raton, FL, USA.ORCID http://orcid.org/0000-0001-5340-5464
Roberto FloresNational Institute on Aging, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-9856-8010
Antonio GonzalezDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Zoe A HansenDepartment of Plant Pathology, University of Minnesota, Saint Paul, MN, USA.ORCID http://orcid.org/0000-0002-6238-0104
Eneida L HatcherNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0009-0004-8858-9645
Scott A JacksonNational Institute of Standards and Technology, Gaithersburg, MD, USA.ORCID http://orcid.org/0000-0003-4891-8323
Christina A KelloggU.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL, USA.ORCID http://orcid.org/0000-0002-6492-9455
Ramana MadupuBiological Systems Science Division, Department of Energy, Office of Biological & Environmental Research, Germantown, MD, USA.
Cassandra Maria Luz MillerDepartment of Biology, University of New Mexico, Albuquerque, NM, USA.ORCID http://orcid.org/0000-0002-2368-9301
Chloe MirzayiCUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA.ORCID http://orcid.org/0000-0002-9817-2868
Ahmed M MoustafaDivision of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0002-9949-6936
Christopher MungallLawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-6601-2165
Aaron OliverScripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-0410-8284
Nonia ParientePublic Library of Science, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-3666-5683
Jennifer Pett-RidgePhysical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.ORCID http://orcid.org/0000-0002-4439-2398
Sydne RecordDepartment of Wildlife, Fisheries, and Conservation Biology, University of Maine, Orono, ME, USA.ORCID http://orcid.org/0000-0001-7293-2155
Linta RejiDepartment of Geophysical Sciences, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0002-1337-6782
Anna-Louise ReysenbachCenter for Life in Extreme Environments, Portland State University, Portland, OR, USA.ORCID http://orcid.org/0000-0001-9130-7750
Virginia I RichCenter of Microbiome Science, The Ohio State University, Columbus, OH, USA.ORCID http://orcid.org/0000-0003-0558-102X
Lorna RichardsonEMBL-European Bioinformatics Institute, Hinxton, UK.ORCID http://orcid.org/0000-0002-3655-5660
Lynn M SchrimlInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0001-8910-9851
Reed S ShabmanOffice of Data Science and Emerging Technologies, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0003-3272-3484
Maria A SierraTri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA.ORCID http://orcid.org/0000-0003-4115-034X
Matthew B SullivanCenter of Microbiome Science, The Ohio State University, Columbus, OH, USA.ORCID http://orcid.org/0000-0001-8398-8234
Punithavathi SundaramurthyBenioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-2036-2557
Katherine M ThibaultNational Ecological Observatory Network, Battelle, Boulder, CO, USA.ORCID http://orcid.org/0000-0003-3477-6424
Luke R ThompsonNorthern Gulf Institute, Mississippi State University, Starkville, MS, USA.ORCID http://orcid.org/0000-0002-3911-1280
Scott TigheVermont Integrative Genomics, University of Vermont, Burlington, VT, USA.ORCID http://orcid.org/0000-0002-3988-0741
Ethell VereenScience, Technology, Engineering and Mathematics Division, Morehouse College, Atlanta, GA, USA.ORCID http://orcid.org/0000-0003-4758-6021
Emiley A Eloe-FadroshLawrence Berkeley National Laboratory, Berkeley, CA, USA. eaeloefadrosh@lbl.gov.ORCID http://orcid.org/0000-0002-8162-1276

Funding

Directorate for Biological Sciences 2422717
6 · The paper itself

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.

Indexed as

ChecklistData managementData reuseData stewardshipEnvironmental MicrobiomeGuidelinesMicrobiomeStandardsWorkshop

Identifiers

PMID40253432
PMCPMC12009515

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.