ArticleEnvironmental microbiome2022
Metadata harmonization-Standards are the key for a better usage of omics data for integrative microbiome analysis.
Article in Environmental microbiome, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Problems With GO Enrichment as an Endpoint for Ecological Omics Interpretation.Molecular ecology · 2026Article
- Multidisciplinary Delphi consensus statement on minimal standards for clinical metadata and end points in microbiome studies.Nature reviews. Gastroenterology & hepatology · 2026Review
- IDBac: an open-access web platform to identify bacteria and analyze relationships in culture collections using MALDI-TOF mass spectrometry.Nature communications · 2026Article
- Applying Artificial Intelligence and machine learning in precision nutrition.Nature communications · 2026Review
- Meat-Borne Bacterial Pathogen Detection: Conventional, Molecular and Emerging AI-Based Strategies.Diagnostics (Basel, Switzerland) · 2026Review
- Towards standardization in pig microbiome research based on a comprehensive twenty-year review.Animal microbiome · 2026Review
- Large-scale manual curation and harmonization of metadata from metagenomic and cancer genomic repositories: challenges and solutions.Database : the journal of biological databases and curation · 2026Article
- Standardized and batch effect-independent technologies enable global collaboration in microbiome research.The ISME journal · 2026Article
- PRIME: a database for 16S rRNA microbiome data with phenotypic reference and comprehensive metadata.Nucleic acids research · 2026Article
- The Mpox contextual data specification package: a data curation toolkit to support collaborative pathogen genomic surveillance.Microbial genomics · 2026Article
- Standardizing microbiome research: interlaboratory validation of SOPs for sample preparation and DNA extraction from food and environmental ecosystems.Environmental microbiome · 2025Article
- Large-scale Manual Curation and Harmonization of Metadata from Metagenomic and Cancer Genomic Repositories: Challenges and Solutions.bioRxiv : the preprint server for biology · 2025Article
- Advancing Intervertebral Disc Biology via Omics: Implications for Nucleus Pulposus Progenitor Cell-Based Regeneration.JOR spine · 2025Review
- STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies.Nature microbiology · 2025Review
- IDBac: an open-access web platform and compendium for the identification of bacteria by MALDI-TOF mass spectrometry.bioRxiv : the preprint server for biology · 2025Article
- Tier-based standards for FAIR sequence data and metadata sharing in microbiome research.Nucleic acids research · 2025Article
- Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research?Poultry science · 2025Review
- Leveraging the microbiome to combat antibiotic resistant gynecological infections.npj antimicrobials and resistance · 2025Review
- Article
- Genomic dissection of the antimicrobial resistance epidemiology ofFrontiers in microbiology · 2025Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
backgroundTremendous amounts of data generated from microbiome research studies during the last decades require not only standards for sampling and preparation of omics data but also clear concepts of how the metadata is prepared to ensure re-use for integrative and interdisciplinary microbiome analysis.
resultsIn this Commentary, we present our views on the key issues related to the current system for metadata submission in omics research, and propose the development of a global metadata system. Such a system should be easy to use, clearly structured in a hierarchical way, and should be compatible with all existing microbiome data repositories, following common standards for minimal required information and common ontology. Although minimum metadata requirements are essential for microbiome datasets, the immense technological progress requires a flexible system, which will have to be constantly improved and re-thought. While FAIR principles (Findable, Accessible, Interoperable, and Reusable) are already considered, international legal issues on genetic resource and sequence sharing provided by the Convention on Biological Diversity need more awareness and engagement of the scientific community.
conclusionsThe suggested approach for metadata entries would strongly improve retrieving and re-using data as demonstrated in several representative use cases. These integrative analyses, in turn, would further advance the potential of microbiome research for novel scientific discoveries and the development of microbiome-derived products.
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