ArticleNucleic acids research2025
Tier-based standards for FAIR sequence data and metadata sharing in microbiome research.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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.
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.
Who cites it
4 citing papers in PubMed.
- Gut and respiratory microbiomes in asthma and allergic diseases: a narrative review of mechanistic insights, gut-lung axis interactions and therapeutic opportunities.Translational pediatrics · 2026Review
- Enhanced semantic classification of microbiome sample origins using large language models (LLMs).GigaScience · 2026Article
- Metalog: curated and harmonised contextual data for global metagenomics samples.Nucleic acids research · 2026Article
- Oral dysbiosis: methodological evolution, the mobile resistome and the future of machine learning in dentistry.Journal of oral microbiology · 2026Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Microbiome research is a growing, data-driven field within the life sciences. While policies exist for sharing microbiome sequence data and using standardized metadata schemes, compliance among researchers varies. To promote open research data best practices in microbiome research and adjacent communities, we (i) propose two tiered badge systems to evaluate data/metadata sharing compliance, and (ii) developed an automated evaluation tool to determine adherence to data reporting standards in publications with amplicon and metagenome sequence data. In a systematic evaluation of publications (n = 2929) spanning human gut microbiome research, and case studies of soil and gut microbiota (n = 370), we found nearly half do not meet minimum standards for sequence data availability. Moreover, poor standardization of metadata creates a high barrier to harmonization and cross-study comparison. Using this badge system and evaluation tool, our proof-of-concept work exposes (i) the ineffectiveness of sequence data availability statements and (ii) the lack of consistent metadata reporting. We highlight the need for improved practices and infrastructure that reduce barriers to data submission and maximize reproducibility in microbiome research. We anticipate that our tiered badge framework will promote dialogue regarding data sharing practices and facilitate data reuse, supporting best practices that make microbiome data Findable, Accessible, Interoperable, and Reusable (FAIR).
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What OpenQuestion holds
Registered trials
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.