Evidence map›Paper›PMID 40270679›Full record

ArticleFrontiers in bioinformatics2025

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

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 and 23 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

33 authors.

Julia M Kelliher *Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Leah Y D Johnson *Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Francisca E RodriguezBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Jaclyn K SaundersDepartment of Marine Sciences, University of Georgia, Athens, GA, United States.
Marie E KroegerIn-Pipe Technology, Wood Dale, IL, United States.
Buck HansonBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Aaron J RobinsonBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Winston E AnthonyPacific Northwest National Laboratory, Richland, WA, United States.
Marc W Van GoethemBiological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
Anders KiledalDepartment of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, United States.
Ahmed A ShiblPublic Health Research Center, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
Amanda Araujo Serrao de AndradeDepartment of Biological Sciences, University of Calgary, Calgary, AB, Canada.
Cassandra L EttingerDepartment of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States.
Chhedi Lal GuptaICMR-CRMCH, National Institute of Immunohaematology, Chandrapur Unit, Chandrapur, Maharashtra, India.
Chris R P RobinsonDepartment of Biology, Indiana University, Bloomington, IN, United States.
Cristal ZunigaDepartment of Biology, Cell, and Molecular Biology, San Diego State University, San Diego, CA, United States.
Daniel SprockettDepartment of Microbiology and Immunology, Wake Forest University School of Medicine, Winston-Salem, NC, United States.
Douglas Terra MachadoBioinformatics Laboratory, National Laboratory for Scientific Computing, Quitandinha, Rio de Janeiro, Brazil.
Emilie J SkoogScripps Institution of Oceanography, UC San Diego, La Jolla, CA, United States.
Iyanu OduwoleGraduate School of Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, TN, United States.
Jason A RothmanDepartment of Microbiology and Plant Pathology, University of California: Riverside, Riverside, CA, United States.
Kaelan PrimeBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Katherine R LaneMassachusetts Institute of Technology, Cambridge, MA, United States.
Leandro Nascimento LemosIlum School of Science, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil.
Lisa KarstensDivision of Oncological Sciences, Department of Obstetrics and Gynecology, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States.
Mark McCauleyThe Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, United States.
Mitiku Mihiret SeyoumDepartment of Poultry Science, University of Arkansas, Fayetteville, AR, United States.
Moamen M ElmassryDepartment of Molecular Biology, Princeton University, Princeton, NJ, United States.
Mustafa GuzelDepartment of Food Engineering, Hitit University, Corum, Türkiye.
Reid LongleyBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Simon RouxLawrence Berkeley National Laboratory, Berkeley, CA, United States.
Thomas M PitotDepartment of Biochemistry, Microbiology, and Bioinformatics, Université Laval, Québec, QC, Canada.
Emiley A Eloe-FadroshLawrence Berkeley National Laboratory, Berkeley, CA, United States.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

data reusedata standardsFAIR datametadatamicrobiomemulti-omicssurvey

Identifiers

PMID40270679
PMCPMC12015674

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.