TEDDY Infant Gut Phage-Bacteria Dynamics and Type 1 Diabetes
Longitudinal shotgun metagenomic study of 8743 samples from children in four countries, examining gut phage and bacterial community dynamics over the first four years of life in relation to type 1 diabetes. machine-written summary
8,747 samples · 43,327 runs · Mixed ages · 2019 · 74.5 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 17,494 sample values (sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 8,747 sample values (collection date) · PMC11790489 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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
115 of 275 people sampled more than once (625 samples; median 3, up to 40 per person). Schedule stated by the source: “Monthly stool samples from age 3 to 48 months, then every 3 months until age 10 years; prospective longitudinal cohort.”.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 8,747 | 100% | 8,747 | |||
| collection_date | 8,747 | 100% | 8,747 | |||
| sex | 8,747 | 100% | 8,747 |
- Longitudinal phage-bacteria dynamics in the early life gut microbiome. 2025 PMID 39856391 PMC11790489 own_data
Archive description
Study Overview The Environmental Determinants of Diabetes in the Young (TEDDY) Study is a longitudinal study that investigates genetic and genetic-environmental interactions, including gestational events, childhood infections, dietary exposures, and other environmental factors after birth, in relation to the development of islet autoimmunity and type 1 diabetes (T1D). A consortium of six clinical centers assembled to participate in the development and implementation of the study to identify environmental triggers for the development of islet autoimmunity and T1D in genetically susceptible individuals. Beginning in 2004, the TEDDY study screened over 400,000 newborns for high-risk HLA-DR, DQ genotypes from both the general population and families already affected by T1D. The TEDDY study... (for more see dbGaP study page.)
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of neonate and infant / toddler and child by sonnet_x2 with confidence 0.55. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- host study.description · “screened over 400,000 newborns for high-risk HLA-DR”
- body site sample.attr.body_site · “Stool (n=13047/21009)”
- body site sample.attr.body_site · “Plasma (n=6229/21009)”
- life stage study.description · “screened over 400,000 newborns for high-risk HLA-DR”
- life stage study.title · “Diabetes in the Young (TEDDY)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09408024 | collection_date | 2012-05 | R3 | 0.70 | paper.fulltext.methods | began on 31 May 2012 |
| SAMN09408024 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN09408024 | subject_id | 1409702 | R1 | 0.85 | sample.attr.gap_subject_id | 1409702 |
| SAMN13457738 | subject_id | 1409032 | R1 | 0.85 | biosample.attribute:gap_subject_id | 1409032 |
Sequencing
43,327 runs over 21,012 samples · mean 0.22 Gbp per run (median 7.0 Mbp, total 9,573.18 Gbp; 43,327 runs with a base count) · layout PAIRED 43,327 · platform ILLUMINA 43,327 · models Illumina HiSeq 2000 (43,327) · 0% of runs with a Sandpiper profile · first public 2019-12-22 – 2021-01-10
Authors (7)
Tisza MJ first · Lloyd RE · Hoffman K · Smith DP · Rewers M · Javornik Cregeen SJ · Petrosino JF last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, country, health_condition. Share metadata
Downloads
PRJNA416160.csv.gz (180.3 KB) · parquet (366.3 KB) — all 8,747 samples, every field with route and confidence · PRJNA416160_determinations.csv.gz (176.1 KB) — 26,241 evidence rows