is a Data Source.
GMrepo (Gut Microbiome Data Repository) is a curated and consistently annotated database of human gut metagenomes and 16S rRNA amplicon datasets. Samples are grouped by manually curated host phenotype (health and disease, coded with MeSH) and their microbial contents are re-annotated with a common pipeline so that projects can be compared across datasets. Version 3 (2026) holds 890 projects and 118,965 runs, 302 annotated diseases and 1,299 marker taxa for 167 phenotype pairs, with a Marker Consistency Index summarizing how reproducible each marker is across studies. Data are served through the web site and a RESTful API.
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Chen Lab (evolgeniusteam)
Github: evolgeniusteam
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| gmrepo.site | GMrepo web site | gmrepo.humangut.info | Graphical Interface | http | Web interface for browsing curated pr... |
| gmrepo.api | GMrepo RESTful API | GMrepoProgrammableAccess | Programming Interface | http | RESTful API giving programmable acces... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| micromap.api | MicroMap API | docs | Programming Interface | http | was derived from | REST API and MCP server over the prod... |
GMrepo is a curated repository of human gut metagenomes and amplicon datasets. It re-annotates the microbial content of public samples with one pipeline and curates the host metadata by hand, so that samples from different projects can be compared by phenotype.
GMrepo v3 (2026) holds 890 projects and 118,965 runs, of which 87,048 are 16S rRNA and 31,917 are shotgun metagenomes. It annotates 302 diseases with MeSH and reports 1,299 marker taxa, 726 species and 573 genera, across 167 phenotype pairs drawn from 275 curated projects. A Marker Consistency Index gives the share of studies in which a marker changes in the same direction.
The web site is at https://gmrepo.humangut.info/. A RESTful API under
https://gmrepo.humangut.info/api/ answers POST requests for project lists,
phenotype associations and per-run taxonomic profiles. Example clients are in
the GMrepoProgrammableAccess
repository. Earlier versions served bulk files under /Downloads/. On
2026-09-16 that path returned the site’s HTML shell and not a file, so no bulk
download product is listed. I did not find a stated data license.
mBodyMap is a sister database from the same group that covers microbes across body sites beyond the gut.
MicroMap loads GMrepo as one of its gut microbiome sources.
Created: September 16, 2026 | Last modified: September 23, 2026