Infant gut microbiome development and type 1 diabetes risk
Longitudinal stool samples (N=124) from 33 infants in Finland and Estonia, recruited at birth based on HLA risk genotyping. Tracked monthly for three years to characterize microbiome changes preceding type 1 diabetes seroconversion and onset. machine-written summary
124 samples · 542 runs · FI, EE · Infant / toddler · 2015 · 2.01 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11322291, PMC11782615, PMC12764907, PMC6349461, PMC6358638, PMC9512645, PMC9589006 |
| ✓ Supplementary tables | 5 sample values (feeding mode) |
| ✓ External resources | 422 sample values (age, country, health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
Schedule stated by the source: “Stool collected at approximately monthly intervals from birth over a three-year follow-up window” (time origin: birth); stated follow-up 3.0 y.
Genera, mean relative abundance over 124 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 120 | 97% | ||||
| country | 120 | 97% | 120 | |||
| health_condition | 31 | 25% | 31 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 120 | 97% | 120 | |||
| sex | 120 | 97% | 120 | |||
| health_condition_detail | 31 | 25% | 31 | |||
| feeding_mode | 5 | 4% | 5 |
- Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. PMID 30661755 PMC6349461 curated
- Trait-based community assembly and succession of the infant gut microbiome. PMID 30710083 PMC6358638 curated
- Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645 curated
- Dysregulation of secondary bile acid metabolism precedes islet autoimmunity and type 1 diabetes. PMID 36195095 PMC9589006 curated
- Insights into the ecology of the infant gut plasmidome. PMID 39138199 PMC11322291 curated
2 more
- Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status. PMID 39885121 PMC11782615
- Microbiome-derived bile acid signatures in early life and their association with islet autoimmunity. PMID 41339624 PMC12764907
Archive description
This is a prospective, longitudinal collection of stool samples from infants at risk for disease. Infants from Finland and Estonia were recruited at birth based on HLA risk genotyping. Parents collected their infants’ stool at approximately monthly intervals and promptly stored the sample in the freezer prior to shipment for sample processing and sequencing. The cohort comprised of 33 infants, 11 of which seroconverted to serum autoantibody positivity and of those, four developed T1D within the three year time-frame of this study.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “of the developing gut microbiome in infants”
- body site study.description · “longitudinal collection of stool samples from infants”
- body site study.description · “which seroconverted to serum autoantibody positivity and”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “gut microbiome in infants en route to”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN03398637 | age_at_collection_days | 505.0 | R2 | 0.75 | external.cmd source | age: 505; age_unit: Day; age_group: Infant |
| SAMN03398637 | country | FI | R2 | 0.75 | external.cmd source | country: Finland |
| SAMN03398776 | feeding_mode | exclusive_breast | R2 | 0.75 | paper.supp.table | -=Breast milk |
| SAMN03398637 | health_condition | type1_diabetes | R2 | 0.75 | external.cmd source | disease: Type 1 Diabetes Mellitus |
| SAMN03398637 | health_condition_detail | Type 1 Diabetes Mellitus | R2 | 0.75 | external.cmd source | disease: Type 1 Diabetes Mellitus |
| SAMN03398637 | sex | female | R2 | 0.75 | external.cmd source | sex: Female |
Sequencing
542 runs over 124 samples · mean 0.51 Gbp per run (median 0.39 Gbp, total 277.89 Gbp; 542 runs with a base count) · layout PAIRED 542 · platform ILLUMINA 542 · models Illumina HiSeq 2000 (542) · 90% of runs with a Sandpiper profile · first public 2015-03-16 – 2015-04-20
Authors (82)
Pasolli E first · Asnicar F · Manara S · Zolfo M · Karcher N · Armanini F · Beghini F · Manghi P · Tett A · Ghensi P · Collado MC · Rice BL · DuLong C · Morgan XC · Golden CD · Quince C · Huttenhower C · Segata N last · Guittar J first · Shade A · Litchman E last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Lamichhane S first · Sen P · Dickens AM · Alves MA · Härkönen T · Honkanen J · Vatanen T · Xavier RJ · Hyötyläinen T · Knip M · Orešič M last · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Nooij S first · Plomp N · Sanders IMJG · Schout L · van der Meulen AE · Terveer EM · Norman JM · Larralde MF · Vossen RHAM · Kloet SL · Faber KN · Harmsen HJM · Zeller GF · Kuijper EJ · Smits WK · Ducarmon QR last · Buchacher T · Lou T · Charron-Lamoureux V · Kattelus R · Karmacharya P · da Silva LP · Kråkström M · Rasool O · Walker C · Patan A · Gentry EC · Zuffa S · Arzoomand A · Lakshmikanth T · Mikeš J · Mebrahtu A · Raffatellu M · Zengler K · Brodin P · Lahesmaa R · Dorrestein PC
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA231909.csv.gz (4.6 KB) · parquet (75.9 KB) — all 124 samples, every field with route and confidence · PRJNA231909_determinations.csv.gz (6.8 KB) — 427 evidence rows