All human shotgun metagenomes (registry) human_all
Every ENA study with ≥ 1 human-host shotgun-DNA metagenome run; archive-only metadata (route R1), Sandpiper profiles, papers and authors.
Membership rule (config/scope.yaml): . Memberships derive deterministically from host, body sites, life stages and assay; a study can belong to several scopes.
4,675
studies
929,502
runs
782,606
BioSamples
621,742
BioSamples with harvested attributes — site known 51 %, age 16 %, sex 19 %
446,164
runs with a Sandpiper profile (48 %)
4,669
classified · 6 pending
Open in the registry explorer (pre-filtered) All scopes
Body sites and life stages within the scope
Primary body site (body_site_primary)
| value | studies | runs |
|---|---|---|
| gut_stool | 2,720 | 668,906 |
| blood_tissue | 385 | 32,935 |
| respiratory_lower | 369 | 36,008 |
| oral | 321 | 32,144 |
| unknown_site | 265 | 20,675 |
| vaginal_urogenital | 155 | 30,748 |
| skin | 149 | 26,464 |
| multi_site | 100 | 54,671 |
| other_site | 86 | 6,030 |
| nasal_nasopharyngeal | 73 | 16,275 |
| eye_ear | 45 | 4,358 |
| milk | 7 | 288 |
Primary life stage (life_stage_primary)
| value | studies | runs |
|---|---|---|
| unknown_age | 2,402 | 318,033 |
| adult | 1,387 | 312,099 |
| infant | 410 | 190,786 |
| child | 325 | 42,839 |
| elderly | 56 | 8,926 |
| mixed_ages | 46 | 51,190 |
| neonate | 24 | 3,591 |
| adolescent | 20 | 1,641 |
Assay (assay)
| value | studies | runs |
|---|---|---|
| shotgun_dna | 4,549 | 874,862 |
| mixed | 105 | 43,742 |
| amplicon | 10 | 4,895 |
| amplicon_misfiled | 8 | 5,525 |
| other | 3 | 478 |
Classification stage (classification_stage)
| value | studies | runs |
|---|---|---|
| sonnet_x2 | 2,774 | 445,376 |
| deterministic_prior | 1,121 | 335,243 |
| opus_adjudicated | 681 | 117,614 |
| curator_audit | 57 | 15,968 |
| owner_decision | 21 | 9,982 |
| deterministic_rule | 15 | 5,146 |
| pending | 6 | 173 |
Largest studies by BioSamples (top 25)
| study | title | BioSamples | runs | sites | stages | assay | stage |
|---|---|---|---|---|---|---|---|
| PRJNA416160 ENA | The Environmental Determinants of Diabetes in the Young (TEDDY) Parent Study | 21,012 | 43,327 | gut_stool;blood_tissue | neonate;infant;child | shotgun_dna | sonnet_x2 |
| PRJEB75464 ENA | PREDICT 3 UK22A | 12,353 | 12,353 | gut_stool | adult | shotgun_dna | deterministic_prior |
| PRJNA400115 ENA | TEDDY Microbiome | 12,266 | 13,245 | gut_stool | infant;neonate;child | shotgun_dna | deterministic_prior |
| PRJEB75462 ENA | PREDICT 3 US21 | 11,797 | 11,797 | gut_stool | unknown_age | shotgun_dna | sonnet_x2 |
| PRJNA1460779 ENA | The Vaginal Microbiome as a Reservoir for Uropathogens: A Population-Scale Metagenomic Study of Women... | 10,003 | 10,003 | vaginal_urogenital | adult | shotgun_dna | deterministic_prior |
| PRJEB51353 ENA | Human gut metagenomes of SCAPIS Uppsala and Malmo | 9,819 | 9,977 | gut_stool | adult | shotgun_dna | deterministic_prior |
| PRJEB75463 ENA | PREDICT 3 US22A | 8,469 | 8,469 | gut_stool | adult | shotgun_dna | deterministic_prior |
| PRJEB11419 ENA | American Gut Project | 8,060 | 13,995 | gut_stool;oral;skin;nasal_nasopharyngeal;other_site | infant;adult;elderly | mixed | opus_adjudicated |
| PRJEB108612 ENA | MOMmy-Microbiome_Epigenome_Neurodevelopment | 5,328 | 5,328 | gut_stool | infant | shotgun_dna | deterministic_prior |
| PRJEB23147 ENA | Human_colon_16S | 5,249 | 5,969 | gut_stool | adult | shotgun_dna | sonnet_x2 |
| PRJNA1468137 ENA | Maternal influences on infant gut microbiome and health | 4,749 | 4,749 | gut_stool;vaginal_urogenital;milk | infant;adult | shotgun_dna | deterministic_prior |
| PRJNA1347413 ENA | Metagenomic data from the ASPREE-XT study | 4,711 | 4,711 | gut_stool | adult;elderly | shotgun_dna | deterministic_prior |
| PRJEB108450 ENA | Exploring Fecal Microbiome in the CHILD COVID-19 sub-project | 4,102 | 4,348 | gut_stool | child;adult | shotgun_dna | deterministic_rule |
| PRJEB32762 ENA | iMSMS Baranzini data | 3,765 | 4,797 | gut_stool | adult | mixed | sonnet_x2 |
| PRJEB60398 ENA | Data-driven prediction of colonization outcomes for complex microbial communities | 3,564 | 3,994 | gut_stool | unknown_age | shotgun_dna | sonnet_x2 |
| PRJNA838575 ENA | CHILD Infant Stool Raw sequence reads | 2,934 | 2,934 | gut_stool | infant;child | shotgun_dna | deterministic_prior |
| PRJEB37731 ENA | Effects of the menstrual cycle and hormonal contraceptives on the human microbiome | 2,825 | 2,825 | gut_stool;oral;vaginal_urogenital | adult | mixed | sonnet_x2 |
| PRJEB40903 ENA | DNA extraction comparison testing 2019-2020 | 2,770 | 2,770 | gut_stool;skin;oral | adult | shotgun_dna | opus_adjudicated |
| PRJEB46788 ENA | Codiversification of gut microbiota with humans | 2,750 | 2,750 | gut_stool | infant;child;adult | shotgun_dna | deterministic_prior |
| PRJEB70237 ENA | HELMi infant and parental stool WGS metagenomes | 2,664 | 2,664 | gut_stool | infant | shotgun_dna | deterministic_prior |
| PRJEB97686 ENA | BMT CTN 1801 microbiome data | 2,631 | 5,024 | gut_stool | adult | shotgun_dna | deterministic_prior |
| PRJEB44559 ENA | Inferring_pneumococcal_transmission_routes_to_infants_during_a_cluster_randomised_vaccine_trial_in_Nha_Tran... | 2,499 | 2,499 | nasal_nasopharyngeal | infant | shotgun_dna | sonnet_x2 |
| PRJNA1357304 ENA | Shotgun metagenomic sequencing of stool microbiomes relating to "Characterising the gut phageome and its... | 2,472 | 2,472 | gut_stool | unknown_age | shotgun_dna | opus_adjudicated |
| PRJEB110772 ENA | Gut microbiota associates with frailty in older women | 2,398 | 2,398 | gut_stool | adult;elderly | shotgun_dna | deterministic_prior |
| PRJEB45799 ENA | The person-to-person transmission landscape of the gut and oral microbiomes | 2,394 | 2,394 | gut_stool;oral | infant | shotgun_dna | deterministic_prior |
Counts are computed from data/registry_studies.parquet at build time (release R2026.25).