ReviewNature microbiology2023
Challenges and opportunities in sharing microbiome data and analyses.
Review in Nature microbiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 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
37 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Gut microbiota-associated predictors as biomarkers of neoadjuvant treatment response in rectal cancer-a systematic review.British journal of cancer · 2026Pooled it
- Artificial intelligence in human microbiome research: from data integration to explainable translation.Archives of microbiology · 2026Review
- Artificial intelligence driven diet-intestinal microbiota-host health integration: A four-dimensional paradigm for advancing host wellness research.iMetaOmics · 2026Review
- The need for standardization and improved open (meta)data practices in metaproteomics.Microbiome · 2026Article
- Uneven global coverage of halophilic metagenomes limits comparative analyses of microbial adaptation to saline environments.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Advancing FAIR data towards comparable, organized, predictive AI-ready data for community validation.Communications biology · 2026Review
- Environmental effectiveness of the National Action Plan to Contain Antimicrobial Resistance: evidence from Chinese soil.National science review · 2026Article
- AI-empowered human microbiome research.Gut · 2026Review
- Assessing the performance of multimodal large language models in experimental information extraction from liquid-liquid phase separation literature.Scientific reports · 2026Article
- Towards standardization in pig microbiome research based on a comprehensive twenty-year review.Animal microbiome · 2026Review
- PRIME: a database for 16S rRNA microbiome data with phenotypic reference and comprehensive metadata.Nucleic acids research · 2026Article
- The gut microbiome in colorectal cancer: molecular paradigms and translational frontiers.Frontiers in bioengineering and biotechnology · 2026Review
- The gut-brain axis in Alzheimer's disease: early detection, microbial metabolites, mechanisms, and therapeutic opportunities.Frontiers in molecular biosciences · 2026Review
- State of omics-based microbial diagnostics of CRC.Gut microbes · 2025Review
- STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies.Nature microbiology · 2025Review
- Key Challenges in Plant Microbiome Research in the Next Decade.Microorganisms · 2025Review
- Credible inferences in microbiome research: ensuring rigour, reproducibility and relevance in the era of AI.Nature reviews. Gastroenterology & hepatology · 2025Review
- Identifying Optimal Machine Learning Approaches for Human Gut Microbiome (Shotgun Metagenomics) and Metabolomics Integration with Stable Feature Selection.bioRxiv : the preprint server for biology · 2025Article
- MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.Nucleic acids research · 2025Article
- Dissecting microbial communities with single-cell transcriptome analysis.Science (New York, N.Y.) · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Microbiome data, metadata and analytical workflows have become 'big' in terms of volume and complexity. Although the infrastructure and technologies to share data have been established, the interdisciplinary and multi-omic nature of the field can make resources difficult to identify and use. Following best practices for data deposition requires substantial effort, with sometimes little obvious reward. Gaps remain where microbiome-specific resources for data sharing or reproducibility do not yet exist. We outline available best practices, challenges to their adoption and opportunities in data sharing in microbiome research. We showcase examples of best practices and advocate for their enforcement and incentivization for data sharing. This includes recognition of data curation and sharing endeavours by individuals, institutions, journals and funders. Opportunities for progress include enabling microbiome-specific databases to incorporate future methods for data analysis, integration and reuse.
Indexed as
Identifiers
37783751What 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.