External resources
Other teams have curated human microbiome metadata before us. Where their annotations join our samples through archive accessions, we include them with the source named on every value.
How these values are used
Values from these resources are route R2 evidence rows with evidence_source = external.<resource>; the locator points to the record at the source and the quote is the source's raw value. A sample's own archive attribute and the study's own supplementary tables take precedence. Please cite the resource's reference when you use values that carry its evidence source. Maintainers who prefer different terms can open an issue.
African Human Microbiome Portal (H3ABioNet) · BugSigDB · curatedMetagenomicData 3 (cMD 3) · GMrepo v3 · HMP / iHMP data portal · HumanMetagenomeDB · mBodyMap · Meta2DB (LLNL) · MicrobeAtlas · MicrobiomeDB (VEuPathDB)
https://microbiome.h3abionet.org/ — African human microbiome samples, metadata only (14,889 records, 70 BioProjects, 72 articles)
What it offers. Harmonised, ontology-coded metadata (demographics, body site, disease) for African cohorts; filtered downloads.
How we join it. BioProject / BioSample accession.
In this release. 3,163 values for 1,571 samples in 5 catalog projects.
Database 2024 · No formal licence; portal disclaimer: research purposes only. Export whole_data.tar.gz 2024-05-30.
projects using African Human Microbiome Portal (H3ABioNet) (5)
PRJEB24771 · PRJNA415207 · PRJNA450025 · PRJNA491626 · PRJNA762668
https://bugsigdb.org/ — curated microbial signatures from published studies, all body sites (thousands of signatures from > 1,000 studies)
What it offers. Study-level curation: condition, body site, sequencing type, cohort location, linked PMID/DOI (CC-BY).
How we join it. PMID / DOI → registry_study_papers → study.
In this release. 7,794 values for 7,587 samples in 36 catalog projects.
Geistlinger et al. 2023 Nat Biotechnol · CC-BY-4.0 (BugSigDBExports full dump 2026-09-28).
projects using BugSigDB (36)
PRJEB13835 · PRJEB28847 · PRJEB29237 · PRJEB37731 · PRJEB44275 · PRJEB49521 · PRJEB65418 · PRJEB72531 · PRJEB79034 · PRJEB81434 · PRJNA1001944 · PRJNA1033532 · PRJNA1043252 · PRJNA1050658 · PRJNA1061168 · PRJNA1135717 · PRJNA188481 · PRJNA328258 · PRJNA354235 · PRJNA356225 · PRJNA431482 · PRJNA449784 · PRJNA451479 · PRJNA529487 · PRJNA588035 · PRJNA689961 · PRJNA695570 · PRJNA728908 · PRJNA763023 · PRJNA765566 · PRJNA826539 · PRJNA849795 · PRJNA905444 · PRJNA911205 · PRJNA912151 · PRJNA985875
https://waldronlab.io/curatedMetagenomicData/ — human shotgun metagenomes, all body sites; manually curated per-sample metadata (> 22,000 samples, 94 studies, 42 countries (cMD 3))
What it offers. Per-sample curated age, sex, BMI, country, disease, antibiotics and study condition; MetaPhlAn/HUMAnN profiles; NCBI accessions per sample.
How we join it. sample_metadata NCBI_accession (SRR/ERR run ids, ';'-separated) → registry runs → BioSample; study_name → PMID / BioProject.
In this release. 79,145 values for 22,777 samples in 108 catalog projects.
Pasolli et al. 2017 Nat Methods; cMD 3 — Nature Communications 2025 · Artistic-2.0 (repository DESCRIPTION); source: curatedMetagenomicDataCuration commit 8059a76 (2026-09-28).
projects using curatedMetagenomicData 3 (cMD 3) (108)
PRJDB15956 · PRJEB10878 · PRJEB11532 · PRJEB1220 · PRJEB12357 · PRJEB12449 · PRJEB13870 · PRJEB15371 · PRJEB1690 · PRJEB17632 · PRJEB1775 · PRJEB17784 · PRJEB1786 · PRJEB18780 · PRJEB20800 · PRJEB21528 · PRJEB22893 · PRJEB27005 · PRJEB27928 · PRJEB29127 · PRJEB29373 · PRJEB32631 · PRJEB32762 · PRJEB36820 · PRJEB37249 · PRJEB38625 · PRJEB39223 · PRJEB42013 · PRJEB43119 · PRJEB4336 · PRJEB45799 · PRJEB47909 · PRJEB49516 · PRJEB51776 · PRJEB5224 · PRJEB53401 · PRJEB53403 · PRJEB59350 · PRJEB6337 · PRJEB6456 · PRJEB6997 · PRJEB7369 · PRJEB7774 · PRJEB8094 · PRJEB9150 · PRJEB9576 · PRJNA1043247 · PRJNA217052 · PRJNA231909 · PRJNA268964 · PRJNA278393 · PRJNA289586 · PRJNA290380 · PRJNA290729 · PRJNA297252 · PRJNA299502 · PRJNA300541 · PRJNA319574 · PRJNA322188 · PRJNA327106 · PRJNA328899 · PRJNA339914 · PRJNA340216 · PRJNA352475 · PRJNA354235 · PRJNA356102 · PRJNA356225 · PRJNA373901 · PRJNA375935 · PRJNA376566 · PRJNA379120 · PRJNA379741 · PRJNA389927 · PRJNA392180 · PRJNA397112 · PRJNA397906 · PRJNA399742 · PRJNA421881 · PRJNA422434 · PRJNA429097 · PRJNA431482 · PRJNA475246 · PRJNA48479 · PRJNA485056 · PRJNA486009 · PRJNA491335 · PRJNA504891 · PRJNA516054 · PRJNA521455 · PRJNA527208 · PRJNA529124 · PRJNA529400 · PRJNA531203 · PRJNA531273 · PRJNA547591 · PRJNA561510 · PRJNA588035 · PRJNA612291 · PRJNA613947 · PRJNA656577 · PRJNA682730 · PRJNA690543 · PRJNA692830 · PRJNA749645 · PRJNA762360 · PRJNA770295 · PRJNA797994 · PRJNA832909
https://gmrepo.humangut.info/ — human gut, 16S and shotgun; phenotype-centred curation (890 projects, 118,965 runs/samples (87,048 16S · 31,917 WGS), 302 diseases (v3))
What it offers. Per-run curated phenotype (MeSH disease), age, sex, BMI, country, health status; project-level markers; RESTful API and downloads.
How we join it. run accession (SRR/ERR/DRR) and project id (PRJNA…) → registry runs / studies.
In this release. 38,294 values for 20,185 samples in 153 catalog projects.
Wu et al. 2020, Dai et al. 2022, Liu et al. 2026 NAR (v3) · No licence published; the site asks for citation of Dai et al. 2022 (GMrepo v2). Live API, 2026-09-28.
projects using GMrepo v3 (153)
PRJDB16312 · PRJDB3601 · PRJDB7767 · PRJEB12123 · PRJEB1220 · PRJEB12947 · PRJEB15257 · PRJEB15371 · PRJEB1775 · PRJEB18755 · PRJEB19090 · PRJEB2054 · PRJEB21793 · PRJEB21933 · PRJEB22481 · PRJEB23052 · PRJEB23207 · PRJEB24557 · PRJEB26795 · PRJEB37924 · PRJEB38997 · PRJEB40200 · PRJEB4336 · PRJEB45443 · PRJEB46398 · PRJEB47458 · PRJEB51635 · PRJEB52930 · PRJEB54728 · PRJEB55534 · PRJEB57770 · PRJEB6092 · PRJEB62571 · PRJEB63351 · PRJEB64515 · PRJEB7949 · PRJEB80379 · PRJEB8094 · PRJNA1024678 · PRJNA1037036 · PRJNA1043252 · PRJNA1044118 · PRJNA1077400 · PRJNA1080251 · PRJNA1096289 · PRJNA1111312 · PRJNA177201 · PRJNA215106 · PRJNA222611 · PRJNA237362 · PRJNA272371 · PRJNA285502 · PRJNA289586 · PRJNA296946 · PRJNA298489 · PRJNA301903 · PRJNA314903 · PRJNA32089 · PRJNA349463 · PRJNA356225 · PRJNA373879 · PRJNA380118 · PRJNA386502 · PRJNA387903 · PRJNA389280 · PRJNA390646 · PRJNA394687 · PRJNA395744 · PRJNA396794 · PRJNA397219 · PRJNA397906 · PRJNA398089 · PRJNA400072 · PRJNA401385 · PRJNA401977 · PRJNA413659 · PRJNA414540 · PRJNA422434 · PRJNA428202 · PRJNA429097 · PRJNA429990 · PRJNA431482 · PRJNA438164 · PRJNA447983 · PRJNA448876 · PRJNA449784 · PRJNA453965 · PRJNA473126 · PRJNA478949 · PRJNA479838 · PRJNA48479 · PRJNA492716 · PRJNA494824 · PRJNA503484 · PRJNA509999 · PRJNA510445 · PRJNA521587 · PRJNA530971 · PRJNA531273 · PRJNA542578 · PRJNA543967 · PRJNA546034 · PRJNA553191 · PRJNA562766 · PRJNA604850 · PRJNA624223 · PRJNA629755 · PRJNA633576 · PRJNA645402 · PRJNA650244 · PRJNA660883 · PRJNA671239 · PRJNA672125 · PRJNA674716 · PRJNA688881 · PRJNA692325 · PRJNA695570 · PRJNA702617 · PRJNA716780 · PRJNA730640 · PRJNA754518 · PRJNA755357 · PRJNA762199 · PRJNA762484 · PRJNA765566 · PRJNA792685 · PRJNA793776 · PRJNA795985 · PRJNA801051 · PRJNA808649 · PRJNA818062 · PRJNA821237 · PRJNA822660 · PRJNA824338 · PRJNA833034 · PRJNA836336 · PRJNA851554 · PRJNA858062 · PRJNA862077 · PRJNA883179 · PRJNA893406 · PRJNA917645 · PRJNA932948 · PRJNA941376 · PRJNA942468 · PRJNA955235 · PRJNA961076 · PRJNA976404 · PRJNA986283 · PRJNA994318 · PRJNA994433 · PRJNA999028 · PRJNA999593
https://portal.hmpdacc.org/ — HMP1 and iHMP cohorts (multi-site, longitudinal) (> 30,000 files across the HMP programmes)
What it offers. Rich subject and visit metadata for the HMP cohorts (partly controlled access).
How we join it. SRS / SRR accessions and BioProjects of the HMP studies.
In this release. 4,083 values for 2,317 samples in 2 catalog projects.
Human Microbiome Project Consortium 2012; iHMP 2019 · IBDMDB hmp2_metadata_2018-08-20.csv (public) and the archived HMP DACC HMASM-690 table (Wayback 2024-04-15); portal API retired.
projects using HMP / iHMP data portal (2)
https://webapp.ufz.de/hmgdb/ — human metagenomes from SRA and MG-RAST, all body sites (69,822 metagenomes, 203 standardised attributes (v1.0))
What it offers. Standardised host attributes (body site, age, sex, disease, country) from archive metadata, ontology terms.
How we join it. SRA sample / run accession.
In this release. 62 values for 37 samples in 3 catalog projects.
Kasmanas et al. 2021 NAR · No licence statement published (© HumanMetagenomeDB & TerrestrialMetagenomeDB team). Release 1.1 (June 2020), fetched 2026-09-28.
projects using HumanMetagenomeDB (3)
https://mbodymap.microbiome.cloud/ — human microbes across body sites with health/disease associations; per-run curated phenotypes (tens of thousands of runs across 20+ body sites (see site))
What it offers. Per-run body site, phenotype and disease annotation; taxon–disease associations.
How we join it. run accession, project id.
In this release. 1,671 values for 1,663 samples in 2 catalog projects.
Jin et al. 2022 NAR · No licence statement; the Help page asks for citation. Download files dated 2021-09-26.
projects using mBodyMap (2)
https://gdo-meta2db.llnl.gov/ — curated shotgun metagenomic feature sets with labelled health-state metadata (see Zenodo record 17315984)
What it offers. Labelled sample metadata (health state) for shotgun studies; Centrifuge-based profiles.
How we join it. SRA run accession.
In this release. 7,066 values for 3,510 samples in 35 catalog projects.
Meta2DB 2024 bioRxiv / 2026 · CC-BY-4.0 (Zenodo record 17315984, 2025-10-13).
projects using Meta2DB (LLNL) (35)
PRJDB4176 · PRJEB11419 · PRJEB21612 · PRJEB24557 · PRJEB35615 · PRJEB47976 · PRJEB53401 · PRJEB53403 · PRJNA255439 · PRJNA289586 · PRJNA307231 · PRJNA311208 · PRJNA327106 · PRJNA385215 · PRJNA400072 · PRJNA401385 · PRJNA530971 · PRJNA602729 · PRJNA602731 · PRJNA602732 · PRJNA624223 · PRJNA634145 · PRJNA638403 · PRJNA638404 · PRJNA638405 · PRJNA689961 · PRJNA698223 · PRJNA743718 · PRJNA751448 · PRJNA759070 · PRJNA759642 · PRJNA798058 · PRJNA806955 · PRJNA826539 · PRJNA878603
https://microbeatlas.org/ — all microbiome samples in SRA (amplicon and metagenomic), all biomes (2,390,937 samples, 52,950 studies)
What it offers. Harmonised SSU-rRNA community profiles, extracted metadata keywords, environmental ontology and geographic coordinates per sample.
How we join it. SRA sample / run accession.
In this release. 32 values for 32 samples in 1 catalog projects.
Cell 2026 · No licence statement found on the site; citation requested. Bulk metadata 2026-01-29.
projects using MicrobeAtlas (1)
https://microbiomedb.org/ — curated microbiome studies (mostly 16S, some shotgun), human and other hosts (dozens of studies with rich sample metadata)
What it offers. Deeply curated per-sample metadata with ontology terms, downloadable per study.
How we join it. SRA accessions where deposited.
In this release. 3,975 values for 2,215 samples in 7 catalog projects.
Oliveira et al. 2018 NAR · VEuPathDB data-use statement: data provided freely for public use, cite the resource. Build 37 (May 2024).
projects using MicrobiomeDB (VEuPathDB) (7)
PRJNA294605 · PRJNA396794 · PRJNA417343 · PRJNA48479 · PRJNA489090 · PRJNA510445 · PRJNA675301
Also consulted, not incorporated (out of scope or no per-sample archive-linked metadata): EMBERS (LLM extraction of metadata from 26,435 gut-microbiome papers) · Human Microbiome Compendium (MicroBioMap) · MGnify (EBI Metagenomics) · PRIME · gutMEGA, gutMDisorder, Disbiome, HMDAD, GutMetaNet, HGMT.