is a Data Source.
BugSigDB is a community-editable database of manually curated microbial signatures from published differential abundance studies of host-associated microbiomes. Each signature lists the taxa reported as increased or decreased between two conditions and is annotated with study geography, health outcome, host body site and experimental, epidemiological and statistical methods using controlled vocabulary. The initial release held more than 2,500 signatures from more than 600 studies on three host species. The site is a Semantic MediaWiki. Data are exported hourly to GitHub and released periodically on Zenodo, and the bugsigdbr Bioconductor package gives access from R.
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Waldron Lab
Github: waldronlab
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| bugsigdb.site | BugSigDB web site | bugsigdb.org | Graphical Interface | http | Semantic MediaWiki site for browsing,... |
| bugsigdb.full_dump | BugSigDB full dump | full_dump.csv (3.1 MB) | Product | csv | Hourly export of all complete BugSigD... |
| bugsigdb.gmt | BugSigDB signature GMT files | BugSigDBExports | Product | tsv | Hourly exports of BugSigDB signatures... |
| bugsigdb.zenodo | BugSigDB stable releases | zenodo.5606165 | Product | csv | Periodic manually reviewed stable dat... |
| bugsigdb.bugsigdbr | bugsigdbr | bugsigdbr | Programming Interface | http | bugsigdbr, an R/Bioconductor package ... |
| 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... |
BugSigDB is a curated database of microbial signatures from published differential abundance studies. A signature is the set of taxa a study reported as increased or decreased between two groups, with the study design, the host, the body site and the outcome recorded in controlled vocabulary.
The Nature Biotechnology paper describes more than 2,500 signatures from more than 600 studies on three host species. The database is community-editable and grows past those numbers. Records are organized as studies, experiments and signatures.
The wiki at https://bugsigdb.org/ is the curation interface. The
BugSigDBExports repository
holds hourly exports: a full CSV dump and GMT files for each taxonomic level
and identifier type. Stable, manually reviewed releases are archived on Zenodo
under the concept DOI 10.5281/zenodo.5606165. The bugsigdbr package on
Bioconductor reads these exports from R.
The wiki returned HTTP 403 from the curation network on 2026-09-16 and I did
not read it directly. The export repository README and its .zenodo.json
metadata were the sources for this page.
The Zenodo metadata in the export repository declares CC-BY-4.0.
MicroMap loads BugSigDB signatures as one of its association sources.
Created: September 16, 2026 | Last modified: September 23, 2026