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Oral cavity oral

Saliva, plaque, tongue and other oral-cavity shotgun metagenomes (all ages).

Membership rule (config/scope.yaml): oral in body_sites. Memberships derive deterministically from host, body sites, life stages and assay; a study can belong to several scopes.

613

studies

140,572

runs

106,761

BioSamples

61,531

BioSamples with harvested attributes — site known 60 %, age 25 %, sex 29 %

43,001

runs with a Sandpiper profile (31 %)

613

classified · 0 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
oral	423	49,081
multi_site	80	61,036
gut_stool	76	22,177
respiratory_lower	9	1,757
blood_tissue	6	775
unknown_site	6	3,543
nasal_nasopharyngeal	5	633
skin	3	1,009
vaginal_urogenital	3	512
other_site	2	49

Primary life stage (life_stage_primary)

value	studies	runs
unknown_age	383	64,454
adult	135	38,655
child	41	4,487
infant	26	26,439
mixed_ages	12	1,993
elderly	8	3,605
adolescent	7	919
neonate	1	20

Assay (assay)

value	studies	runs
shotgun_dna	462	88,757
other	68	8,287
amplicon_misfiled	35	13,357
amplicon	22	11,152
mixed	15	18,308
isolate_genome	6	557
unknown	4	94
rna	1	60

Classification stage (classification_stage)

value	studies	runs
sonnet_x2	418	62,510
opus_adjudicated	119	58,629
deterministic_prior	70	14,653
owner_decision	4	3,619
curator_audit	1	1,118
deterministic_rule	1	43

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
PRJEB81814 ENA	The Swedish Maternal Microbiome project	7,510	8,243	vaginal_urogenital;gut_stool;oral	adult;infant	amplicon_misfiled	opus_adjudicated
PRJNA801882 ENA	The human oral microbiome and risk of multiple cancers: An analysis of three prospective cohort studies.	5,685	5,685	oral	unknown_age	amplicon	opus_adjudicated
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
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
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
PRJEB47383 ENA	Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance	2,018	2,018	gut_stool;oral	adult	shotgun_dna	opus_adjudicated
PRJEB83236 ENA	SEPSIS Human Microbiome Study	1,917	1,917	gut_stool;milk;oral;skin	infant;child;adult	shotgun_dna	deterministic_prior
PRJEB87865 ENA	Microbiome profile in Shallow and Deep Periodontal Pockets	1,633	1,633	oral	elderly	shotgun_dna	sonnet_x2
PRJNA699281 ENA	The microbiome of aging: instability, heterogeneity, and pathogenicity reservoirs in the skin, oral, and...	1,569	1,569	skin;oral;gut_stool	elderly;adult	shotgun_dna	opus_adjudicated
PRJEB83572 ENA	Oral bacterial community dynamics during induction of gingival inflammation.	1,137	2,274	oral	adult	shotgun_dna	sonnet_x2
PRJEB14941 ENA	The microbiota at multiple body sites during pregnancy in a rural Tanzanian population and the effects of...	1,118	1,118	gut_stool;oral;vaginal_urogenital;milk	adult;infant	amplicon	curator_audit
PRJNA296814 ENA	New Hampshire Birth Cohort Study microbiome: marker gene and shotgun metagenomic sequencing	1,063	1,082	gut_stool;oral	infant	shotgun_dna	deterministic_prior
PRJEB10914 ENA	Developmental Ecology of the Human Microbiome - Restoration Study of babies.	1,016	1,016	gut_stool;oral;skin;vaginal_urogenital	infant;adult	amplicon	owner_decision
PRJNA767189 ENA	The oral microbiome and breast cancer and non-malignant breast disease, and its relationship with the...	947	947	oral;gut_stool	unknown_age	amplicon	opus_adjudicated
PRJDB14987 ENA	SMVG analysis of human oral microbiome and oral pathogens	864	864	oral	unknown_age	other	sonnet_x2
PRJNA1267287 ENA	Integrated oral microbiome profiling from aligners identifies biosynthetic signatures of disease	860	860	oral	adult	shotgun_dna	sonnet_x2
PRJNA1395616 ENA	Development of ECC Prediction Models from Oral Microbiome Diversity and Functions in Early Infancy of...	852	852	oral	infant;child;adult	shotgun_dna	deterministic_prior
PRJEB77729 ENA	First-Year Dynamics of the Microbiome in Infants’ Oral and Gastrointestinal Systems	840	1,787	gut_stool;oral;milk	infant	amplicon_misfiled	owner_decision
PRJNA756701 ENA	Foregut Microbiome and Risk of Gastric Intestinal Metaplasia, and Gastric Cancer Risk	776	776	oral;other_site	adult	shotgun_dna	sonnet_x2
PRJEB14801 ENA	Puerto Rico and Plantanal	767	767	skin;gut_stool;oral;nasal_nasopharyngeal;multi_site	infant	amplicon	owner_decision
PRJNA984617 ENA	CCSORC004913 - Supragingival Plaque Microbiome	763	763	oral	adult	shotgun_dna	sonnet_x2
PRJNA957107 ENA	Imrabiome - Rheumatoid project	726	726	gut_stool;oral	adult;elderly	shotgun_dna	opus_adjudicated
PRJEB64861 ENA	Impact of dietary interventions on pre-diabetic oral and gut microbiome, metabolites and cytokines	706	706	gut_stool;oral	adult	shotgun_dna	sonnet_x2

Counts are computed from data/registry_studies.parquet at build time (release R2026.25).