ArticleCommunications biology2020
The archives are half-empty: an assessment of the availability of microbial community sequencing data.
Article in Communications biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled 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.
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
18 citing papers in PubMed, 1 synthesis or guideline pooled it, 40 citations in OpenAlex.
- Prevalence and predictors of data and code sharing in the medical and health sciences: systematic review with meta-analysis of individual participant data.BMJ (Clinical research ed.) · 2023Pooled it
- FAIRer DNA sequence data with q2-ena-uploader: a QIIME 2 plugin for data deposition in the European Nucleotide Archive.Microbiology resource announcements · 2026Article
- HVRLocator: a computationally efficient tool for identifying hypervariable regions in large 16S rRNA datasets.GigaScience · 2026Article
- Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data.Molecular ecology resources · 2025Article
- Meta-omics reveals subgingival plaque reconstruction dynamics.Journal of oral microbiology · 2025Article
- The African Human Microbiome Portal: a public web portal of curated metagenomic metadata.Database : the journal of biological databases and curation · 2024Article
- Multiple graphical views for automatically generating SQL for the MycoDiversity DB; making fungal biodiversity studies accessible.Biodiversity data journal · 2024Article
- The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes.Animal microbiome · 2023Article
- Curated and harmonized gut microbiome 16S rRNA amplicon data from dietary fiber intervention studies in humans.Scientific data · 2023Article
- The use of different 16S rRNA gene variable regions in biogeographical studies.Environmental microbiology reports · 2023Article
- Universal drivers of cheese microbiomes.iScience · 2023Article
- Current Challenges and Pitfalls in Soil Metagenomics.Microorganisms · 2022Article
- Machine Learning Data Analysis Highlights the Role ofBiomedicines · 2022Article
- SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata.Database : the journal of biological databases and curation · 2022Article
- DNA Metabarcoding for the Characterization of Terrestrial Microbiota-Pitfalls and Solutions.Microorganisms · 2021Review
- Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies.Frontiers in genetics · 2021Article
- Dataset search in biodiversity research: Do metadata in data repositories reflect scholarly information needs?PloS one · 2021Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As DNA sequencing has become more popular, the public genetic repositories where sequences are archived have experienced explosive growth. These repositories now hold invaluable collections of sequences, e.g., for microbial ecology, but whether these data are reusable has not been evaluated. We assessed the availability and state of 16S rRNA gene amplicon sequences archived in public genetic repositories (SRA, EBI, and DDJ). We screened 26,927 publications in 17 microbiology journals, identifying 2015 16S rRNA gene sequencing studies. Of these, 7.2% had not made their data public at the time of analysis. Among a subset of 635 studies sequencing the same gene region, 40.3% contained data which was not available or not reusable, and an additional 25.5% contained faults in data formatting or data labeling, creating obstacles for data reuse. Our study reveals gaps in data availability, identifies major contributors to data loss, and offers suggestions for improving data archiving practices.
Indexed as
Identifiers
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.