ArticleNucleic acids research2026
GMrepo v3: a curated human gut microbiome database with expanded disease coverage and enhanced cross-dataset biomarker analysis.
Article in Nucleic acids research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Artificial intelligence driven diet-intestinal microbiota-host health integration: A four-dimensional paradigm for advancing host wellness research.iMetaOmics · 2026Review
- Longitudinal dynamics of the maternal gut virome associate with metabolic features of preterm birth.Nature communications · 2026Article
- Microbiome and aging: Trajectories of microbiome age across human ecosystems and their systemic effects.iMeta · 2026Review
- Review
- Towards microbiome-informed strategies for predicting and preventing pregnancy complications.Reproduction & fertility · 2026Review
- The 2026 Nucleic Acids Research database issue and the online molecular biology database collection.Nucleic acids research · 2026Article
- Decoding the microbial blueprint of pancreatic cancer.Frontiers in medicine · 2026Review
- Shared and condition-associated gut microbiota alterations in older adults with depression and constipation: evidence from the American Gut Project.Frontiers in microbiology · 2026Article
- CRC-TrustBench: benchmarking cross-study and cross-country generalization in gut metagenomic colorectal cancer prediction.Frontiers in microbiology · 2026Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
GMrepo (Gut Microbiome Data Repository) is a curated and consistently annotated database of human gut metagenomes, designed to improve data reusability and enable cross-project and cross-disease comparisons. In this latest release, GMrepo v3 has been expanded to 890 projects and 118 965 runs/samples, including 87 048 16S rRNA and 31 917 metagenomic datasets. The number of annotated diseases has increased from 133 to 302, allowing more comprehensive disease-related microbiome analyses. We systematically identified microbial markers between phenotype pairs (e.g. healthy versus diseased) at the project level and compared them across datasets to detect reproducible signatures. As of this release, GMrepo v3 includes 1299 marker taxa (726 species and 573 genera) associated with 167 phenotype pairs, derived from 275 carefully curated projects. To assess marker stability, we developed the Marker Consistency Index (MCI), which summarizes the prevalence and directional consistency of markers across studies. Among 400 markers showing altered abundances in ≥10 projects, 143 were consistently enriched in healthy controls (MCI > 75%), while 85 were enriched in diseases (MCI < 25%). A marker-centric interface enables users to explore marker behavior across diseases. The GMrepo v3 database is freely accessible 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.