ArticleNucleic acids research2022
GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 papers, 2 of them syntheses that pooled it.
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Who cites it
113 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- 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
- Meta-analysis of the Microbial Diversity Cultured in Bioreactors Simulating the Gut Microbiome.Microbial ecology · 2024Pooled it
- Trial
- GutMIND: A multi-cohort machine learning framework for integrative characteristics of the microbiota-gut-brain axis in neuropsychiatric disorders.Gut microbes · 2026Article
- Article
- Human gut flagellome profiling using FlaPro reveals TLR5-related phenotype-specific alterations in IBD.Gut microbes · 2026Article
- Compositional and functional differences of gut microbiome and metabolome inform pathogenesis of cholestatic liver disease.Gut microbes · 2026Article
- Insights into the dynamics of antibiotic resistance genes in the human gut microbiome across populations.Gut pathogens · 2026Article
- Deciphering themSphere · 2026Article
- Prevalence aware feature selection improves biomarker identification in microbiome studies.Bioinformatics (Oxford, England) · 2026Article
- Clinical potential of the gut microbiome in oncology: a scoping review of treatment response, toxicity and biomarker development.Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer · 2026Article
- AI-empowered human microbiome research.Gut · 2026Review
- Machine learning model to identify gut microbiome-derived metabolites as potential biomarkers of autism spectrum disorder: a pilot study.BMC psychiatry · 2026Article
- Gut microbial metabolic disorder in depression: insights from computational modeling and mediation analysis.BMC microbiology · 2026Article
- MDPD reveals specific microbial signatures in human pulmonary diseases.Briefings in bioinformatics · 2026Article
- ABaCo: addressing heterogeneity challenges in metagenomic data integration with adversarial generative models.Nucleic acids research · 2026Article
- Gut microbiota-dependent 24-hydroxycholesterol metabolism contributes to capsaicin-induced amelioration of Alzheimer's disease-like pathology in mice.Nature communications · 2026Article
- Gut Bacteria Improve Depressive Symptoms by Degrading Cortisol into Androgen.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Transformer Models, Graph Networks, and Generative AI in Gut Microbiome Research: A Narrative Review.Bioengineering (Basel, Switzerland) · 2026Review
- Cross-cohort resistome and virulome gradients structure the colorectal cancer microbiome.NPJ biofilms and microbiomes · 2026Article
53 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purposes are to increase the reusability and accessibility of human gut metagenomic data, and enable cross-project and phenotype comparisons. To achieve these goals, we performed manual curation on the meta-data and organized the datasets in a phenotype-centric manner. GMrepo v2 contains 353 projects and 71,642 runs/samples, which are significantly increased from the previous version. Among these runs/samples, 45,111 and 26,531 were obtained by 16S rRNA amplicon and whole-genome metagenomics sequencing, respectively. We also increased the number of phenotypes from 92 to 133. In addition, we introduced disease-marker identification and cross-project/phenotype comparison. We first identified disease markers between two phenotypes (e.g. health versus diseases) on a per-project basis for selected projects. We then compared the identified markers for each phenotype pair across datasets to facilitate the identification of consistent microbial markers across datasets. Finally, we provided a marker-centric view to allow users to check if a marker has different trends in different diseases. So far, GMrepo includes 592 marker taxa (350 species and 242 genera) for 47 phenotype pairs, identified from 83 selected projects. GMrepo v2 is freely available at: https://gmrepo.humangut.info.
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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.