TEDDY infant gut microbiome and type 1 diabetes risk
12,266 gut microbiome samples from a longitudinal cohort following genetically at-risk infants across multiple countries to study environmental factors linked to islet autoimmunity and type 1 diabetes. machine-written summary
12,266 samples · 13,245 runs · FI · Infant / toddler · 2018 · 1.29 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 24,532 sample values (sex, subject id) |
| ✓ Abstract / description | 12,266 sample values (country) |
| ○ Full text | read; no usable statement or table · PMC11445081, PMC9213500, PMC9403272 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
849 of 888 people sampled more than once (12,227 samples; median 12, up to 45 per person).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 12,266 | 100% | 12,266 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 12,266 | 100% | 12,266 | |||
| sex | 12,266 | 100% | 12,266 |
- Islet autoantibody seroconversion in type-1 diabetes is associated with metagenome-assembled genomes in infant gut microbiomes. PMID 35729161 PMC9213500 curated
- Genomic reconstruction of short-chain fatty acid production by the human gut microbiota. PMID 36032669 PMC9403272 curated
- Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly. PMID 39242817 PMC11445081 curated
Archive description
The Environmental Determinants of Diabetes in the Young (TEDDY) Study investigates genetic and genetic-environmental interactions, including gestational infection or other gestational events, childhood infections and other environmental factors after birth, in relation to the development of pre-diabetic islet autoimmunity and type 1 diabetes (T1D). Beginning in 2002, a consortium of six centers assembled to participate in the development and implementation of studies to identify environmental factors that trigger the development of islet autoimmunity and T1D in genetically susceptible individuals. The TEDDY study screened around 400,000 newborns and recruited 7,749 neonates from the general population with a pre-determined T1D risk of 3% and 919 neonates with first degree relatives who have T1D and who have a pre-determined T1D risk of 10%. Thus, TEDDY proposes to follow over 8,000 participants across six clinical centers worldwide (Finland, Germany, Sweden... (for more see dbGaP study page.)
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and neonate and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “screened around 400,000 newborns and recruited 7,749”
- life stage study.description · “other gestational events, childhood infections and other”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09408007 | country | FI | R4 | 0.40 | study.description | six clinical centers worldwide (Finland, Germany, Sweden |
| SAMN09408007 | sex | female | R1 | 0.90 | biosample_attr | female |
| SAMN09408007 | subject_id | 1406786 | R1 | 0.85 | biosample_attr | 1406786 |
Sequencing
13,245 runs over 12,266 samples · mean 1.26 Gbp per run (median 1.23 Gbp, total 16,738.52 Gbp; 13,245 runs with a base count) · layout PAIRED 13,245 · platform ILLUMINA 13,245 · models Illumina HiSeq 2000 (13,245) · 0% of runs with a Sandpiper profile · first public 2018-09-01
Authors (26)
Zhang L first · Jonscher KR · Zhang Z · Xiong Y · Mueller RS · Friedman JE · Pan C last · Frolova MS first · Suvorova IA · Iablokov SN · Petrov SN · Rodionov DA last · Shao Y first · Garcia-Mauriño C · Clare S · Dawson NJR · Mu A · Adoum A · Harcourt K · Liu J · Browne HP · Stares MD · Rodger A · Brocklehurst P · Field N · Lawley TD last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA400115.csv.gz (300.8 KB) · parquet (559.0 KB) — all 12,266 samples, every field with route and confidence · PRJNA400115_determinations.csv.gz (244.9 KB) — 36,798 evidence rows