Respiratory tract respiratory
Nasal / nasopharyngeal and lower-respiratory shotgun metagenomes.
Membership rule (config/scope.yaml): nasal_nasopharyngeal in body_sites OR respiratory_lower in body_sites. Memberships derive deterministically from host, body sites, life stages and assay; a study can belong to several scopes.
827
studies
117,408
runs
100,048
BioSamples
67,745
BioSamples with harvested attributes — site known 54 %, age 13 %, sex 14 %
24,611
runs with a Sandpiper profile (21 %)
824
classified · 3 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 |
|---|---|---|
| respiratory_lower | 492 | 49,716 |
| nasal_nasopharyngeal | 195 | 19,150 |
| multi_site | 51 | 33,922 |
| gut_stool | 36 | 8,735 |
| blood_tissue | 19 | 1,721 |
| oral | 17 | 1,806 |
| unknown_site | 8 | 1,623 |
| skin | 4 | 481 |
| other_site | 3 | 171 |
| eye_ear | 2 | 83 |
Primary life stage (life_stage_primary)
| value | studies | runs |
|---|---|---|
| unknown_age | 622 | 72,407 |
| adult | 80 | 7,628 |
| child | 62 | 8,590 |
| infant | 33 | 26,487 |
| mixed_ages | 14 | 1,381 |
| neonate | 8 | 477 |
| elderly | 5 | 258 |
| adolescent | 3 | 180 |
Assay (assay)
| value | studies | runs |
|---|---|---|
| shotgun_dna | 534 | 77,214 |
| other | 122 | 10,973 |
| amplicon_misfiled | 82 | 9,994 |
| isolate_genome | 34 | 1,165 |
| amplicon | 27 | 984 |
| mixed | 17 | 16,538 |
| unknown | 6 | 260 |
| rna | 5 | 280 |
Classification stage (classification_stage)
| value | studies | runs |
|---|---|---|
| sonnet_x2 | 617 | 81,419 |
| opus_adjudicated | 154 | 25,583 |
| deterministic_prior | 41 | 6,607 |
| owner_decision | 8 | 2,913 |
| deterministic_rule | 3 | 166 |
| pending | 3 | 38 |
| curator_audit | 1 | 682 |
Largest studies by BioSamples (top 25)
| study | title | BioSamples | runs | sites | stages | assay | stage |
|---|---|---|---|---|---|---|---|
| PRJEB11419 ENA | American Gut Project | 8,060 | 13,995 | gut_stool;oral;skin;nasal_nasopharyngeal;other_site | infant;adult;elderly | mixed | opus_adjudicated |
| PRJEB98607 ENA | The_Respiratory_Virus_and_Microbiome_Initiative_DR | 6,647 | 6,647 | respiratory_lower | unknown_age | amplicon_misfiled | sonnet_x2 |
| PRJEB60095 ENA | Cardamom | 2,860 | 2,860 | nasal_nasopharyngeal;gut_stool | infant | other | sonnet_x2 |
| 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 |
| PRJNA48479 ENA | Human Microbiome Project (HMP) Metagenomic WGS Projects, deeper sequencing of the human microbiome... | 2,103 | 11,164 | multi_site;oral;gut_stool;nasal_nasopharyngeal | unknown_age | shotgun_dna | sonnet_x2 |
| PRJNA1084017 ENA | Laboratory validation of a respiratory metagenomic sequencing assay | 1,876 | 1,876 | respiratory_lower | unknown_age | shotgun_dna | sonnet_x2 |
| PRJEB23944 ENA | Understanding_the_biological_factors_underpinning_the_structure_of_the_nasal_microbiota | 1,723 | 1,723 | nasal_nasopharyngeal | unknown_age | shotgun_dna | sonnet_x2 |
| PRJEB102181 ENA | method development for a SISPA or Phi based winter virus study | 1,292 | 1,292 | nasal_nasopharyngeal;respiratory_lower | unknown_age | shotgun_dna | sonnet_x2 |
| PRJNA1195144 ENA | Sequencing of pediatric respiratory syncytial virus isolates from Houston | 1,251 | 1,251 | respiratory_lower;nasal_nasopharyngeal | child | shotgun_dna | sonnet_x2 |
| PRJEB71147 ENA | Nasopharyngeal_metagenomics_South_African_children | 1,123 | 1,124 | nasal_nasopharyngeal | child | shotgun_dna | sonnet_x2 |
| PRJNA818777 ENA | the metagenomic sequencing data of 450 respiratory samples Metagenome | 934 | 934 | respiratory_lower | unknown_age | shotgun_dna | sonnet_x2 |
| PRJNA964705 ENA | Nasal and fecal communities of cows, farmers, and non-farmers. Raw sequence reads | 891 | 891 | gut_stool;nasal_nasopharyngeal | unknown_age | shotgun_dna | sonnet_x2 |
| PRJNA1465085 ENA | Metagenomic profiling and whole-genome sequencing of clinical samples from 853 patients with... | 853 | 853 | respiratory_lower | unknown_age | shotgun_dna | sonnet_x2 |
| PRJNA46337 ENA | The Neonatal Microbiome and Necrotizing Enterocolitis | 827 | 1,153 | gut_stool;respiratory_lower | infant;neonate;child | amplicon_misfiled | owner_decision |
| PRJDB34973 ENA | Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluids Improves Pathogen Detection and... | 803 | 803 | respiratory_lower | unknown_age | shotgun_dna | sonnet_x2 |
| PRJEB14801 ENA | Puerto Rico and Plantanal | 767 | 767 | skin;gut_stool;oral;nasal_nasopharyngeal;multi_site | infant | amplicon | owner_decision |
| PRJNA948840 ENA | Upper respiratory and gut microbiomes of children and adolescents with SARS-CoV-2 infection (BRAVE Kids study) | 727 | 727 | gut_stool;nasal_nasopharyngeal | child;adolescent;adult | shotgun_dna | deterministic_prior |
| PRJNA977832 ENA | Microbiomes detected by bronchoalveolar lavage fluid metagenomic next-generation sequencing among... | 718 | 718 | respiratory_lower | unknown_age | shotgun_dna | sonnet_x2 |
| PRJNA1392013 ENA | Infant nasal metagenome | 704 | 704 | nasal_nasopharyngeal | infant;neonate | shotgun_dna | deterministic_prior |
| PRJEB96268 ENA | Airway metagenomes from the BWPR cohort – initial dataset | 694 | 694 | oral;respiratory_lower | adult;elderly | shotgun_dna | sonnet_x2 |
| PRJEB20836 ENA | Cystic_fibrosis_pathogens | 693 | 1,352 | respiratory_lower | unknown_age | shotgun_dna | sonnet_x2 |
| PRJEB90577 ENA | PediCAP metagenomics and metaserotyping | 682 | 682 | gut_stool;nasal_nasopharyngeal | infant | shotgun_dna | deterministic_prior |
| PRJNA1277853 ENA | PediCAP metagenomics and metaserotyping | 682 | 682 | gut_stool;nasal_nasopharyngeal;multi_site | unknown_age | mixed | curator_audit |
| PRJNA1474087 ENA | Microbial and immune determinants of disease severity and death in pediatric pneumonia | 668 | 668 | nasal_nasopharyngeal;respiratory_lower | child;infant | shotgun_dna | sonnet_x2 |
| PRJEB30246 ENA | Metagenomic_analysis_nasopharyngeal_colonisation | 620 | 620 | nasal_nasopharyngeal | unknown_age | shotgun_dna | sonnet_x2 |
Counts are computed from data/registry_studies.parquet at build time (release R2026.25).