ArticleNucleic acids research2021
HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 2 of them syntheses that pooled it.
What it found
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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
40 citing papers in PubMed, 2 syntheses or guidelines pooled it, 69 citations in OpenAlex.
- Meta-analysis of 22,710 human microbiome metagenomes defines an oral-to-gut microbial enrichment score and associations with host health and disease.Nature communications · 2025Pooled it
- Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach.mSystems · 2023Pooled it
- ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics.bioRxiv : the preprint server for biology · 2026Article
- Metalog: curated and harmonised contextual data for global metagenomics samples.Nucleic acids research · 2026Article
- PRIME: a database for 16S rRNA microbiome data with phenotypic reference and comprehensive metadata.Nucleic acids research · 2026Article
- ResMicroDb: a comprehensive database and analysis platform for the human respiratory microbiome.Nucleic acids research · 2026Article
- Contrasting associations between microbiota respiratory strategies and seafloor macrofauna.ISME communications · 2026Article
- The BeeBiome data portal provides easy access to bee microbiome information.BMC bioinformatics · 2025Article
- NIBN Japan Microbiome Database, a database for exploring the correlations between human microbiome and health.Scientific reports · 2025Article
- Article
- A human gut bacterium antagonizes neighboring bacteria by altering their protein-folding ability.Cell host & microbe · 2025Article
- Article
- Visualizing metagenomic and metatranscriptomic data: A comprehensive review.Computational and structural biotechnology journal · 2024Review
- Review
- Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.PLoS computational biology · 2024Article
- Discovery and structural mechanism of DNA endonucleases guided by RAGATH-18-derived RNAs.Cell research · 2024Article
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Study of the intestinal microbiota composition and the effect of treatment with intensive chemotherapy in patients recovered from acute leukemia.Scientific reports · 2024Article
- The African Human Microbiome Portal: a public web portal of curated metagenomic metadata.Database : the journal of biological databases and curation · 2024Article
- A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions.Frontiers in microbiology · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomics became a standard strategy to comprehend the functional potential of microbial communities, including the human microbiome. Currently, the number of metagenomes in public repositories is increasing exponentially. The Sequence Read Archive (SRA) and the MG-RAST are the two main repositories for metagenomic data. These databases allow scientists to reanalyze samples and explore new hypotheses. However, mining samples from them can be a limiting factor, since the metadata available in these repositories is often misannotated, misleading, and decentralized, creating an overly complex environment for sample reanalysis. The main goal of the HumanMetagenomeDB is to simplify the identification and use of public human metagenomes of interest. HumanMetagenomeDB version 1.0 contains metadata of 69 822 metagenomes. We standardized 203 attributes, based on standardized ontologies, describing host characteristics (e.g. sex, age and body mass index), diagnosis information (e.g. cancer, Crohn's disease and Parkinson), location (e.g. country, longitude and latitude), sampling site (e.g. gut, lung and skin) and sequencing attributes (e.g. sequencing platform, average length and sequence quality). Further, HumanMetagenomeDB version 1.0 metagenomes encompass 58 countries, 9 main sample sites (i.e. body parts), 58 diagnoses and multiple ages, ranging from just born to 91 years old. The HumanMetagenomeDB is publicly available at https://webapp.ufz.de/hmgdb/.
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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.