Long. gut microbiome in infants at risk for autoimmunity
1154 longitudinal stool samples from children in Finland, Russia, and Estonia at HLA-conferred risk for autoimmune disease, monitored prospectively for infections and drug use including antibiotics. machine-written summary
1,154 samples · 1,154 runs · FI, RU, EE · Infant / toddler · 2018 · 1.11 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,462 sample values (age, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 1,154 sample values (collection date) · PMC11834438, PMC6384140 |
| ✓ Supplementary tables | 5,094 sample values (delivery mode, feeding mode, maternal antibiotics, sex, timepoint) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
242 of 269 people sampled more than once (1,127 samples; median 4, up to 15 per person) · follow-up median 18 mo (max 2.9 y) · median interval between samples 3 mo (time from age at collection). Schedule stated by the source: “Repeated stool sampling across infancy/childhood timepoints: pre-weaning, post-weaning, 1-6 months, 6 months-1yr, 1yr-4yr” (time origin: birth).
Each row is one person (36 shown of 242); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 1,048 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 | 1,154 | 100% | ||||
| country | 1,154 | 100% | 1,154 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 1,154 | 100% | 1,154 | |||
| age_at_collection_days | 1,154 | 100% | 1,154 | |||
| collection_date | 1,154 | 100% | 1,154 | |||
| delivery_mode | 1,154 | 100% | 1,154 | |||
| sex | 1,154 | 100% | 1,154 | |||
| timepoint_label | 1,103 | 96% | 1,103 | |||
| feeding_mode | 883 | 77% | 883 | |||
| maternal_antibiotics | 800 | 69% | 800 |
- Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. PMID 30559407 PMC6384140 curated
- Deterministic transition of enterotypes shapes the infant gut microbiome at an early age. PMID 34429130 PMC8383385 curated
- Temporal changes in gastrointestinal fungi and the risk of autoimmunity during early childhood: the TEDDY study. PMID 35672407 PMC9174155 curated
- Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645 curated
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646 curated
7 more
- BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. PMID 38172624 PMC10769871
- Longitudinal quantification of Bifidobacterium longum subsp. infantis reveals late colonization in the infant gut independent of maternal milk HMO composition. PMID 38291346 PMC10827747
- Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032 PMC11019788
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892
- A novel robust network construction and analysis workflow for mining infant microbiota relationships. PMID 39745374 PMC11834438
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767
- Global analysis of infant gut microbiota revealed distinctive maturation dynamics across lifestyles. PMID 42618579 PMC13490558
Archive description
This is a longitudinal collection of stool samples from young children at HLA conferred risk for autoimmune diseases. Nearly 700 newborns were recruited to the birth cohort as part of the international DIABIMMUNE Study (http://www.diabimmune.org/) for which the consent rate was 80% in Tartu, Estonia, 59% in Espoo, Finland, and 24% in Petrozavodsk, Russia. Recruitment took place between September 2008 and May 2010 in Estonia and Finland, and between September 2008 and July 2011 in Russia. This data set consists of samples from three previously published diabimmune studies with PMIDs 25662751, 27306663, 27133167. The participating children were monitored prospectively for infections, use of drugs including antibiotics, and other life events.
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 study.title · “Longitudinal gut microbiome sequence data”
- body site study.description · “longitudinal collection of stool samples from young”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “diseases. Nearly 700 newborns were recruited to”
- life stage study.description · “samples from young children at HLA conferred”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN10265433 | age_at_collection_days | 1064 | R1 | 0.75 | biosample_attr | host_age=1064 (days; U2_unique_admissible_unit) |
| SAMN10267803 | age_at_collection_days | 1109 | R1 | 0.80 | sample.attr.host_age | 1109 |
| SAMN10265433 | collection_date | 2008-09/2011-07 | R3 | 0.70 | paper.fulltext.methods | recruitment took place between September 2008 and July 2011 |
| SAMN10265433 | country | FI | R1 | 0.90 | biosample_attr | Finland |
| SAMN10265433 | delivery_mode | vaginal | R2 | 0.75 | paper.supp.table | csection=False |
| SAMN10265433 | feeding_mode | exclusive_breast | R2 | 0.75 | paper.supp.table | Feeding type=Breast Milk |
| SAMN10265433 | maternal_antibiotics | no | R2 | 0.75 | paper.supp.table | abx_while_pregnant=False |
| SAMN10265433 | sex | male | R2 | 0.75 | paper.supp.table | gender=Male |
| SAMN10265433 | subject_id | E000823 | R1 | 0.85 | biosample_attr | E000823 |
| SAMN10265433 | timepoint_label | post-weaning | R2 | 0.75 | paper.supp.table | Time Group=post-weaning |
Sequencing
1,154 runs over 1,154 samples · mean 1.19 Gbp per run (median 1.11 Gbp, total 1,378.30 Gbp; 1,154 runs with a base count) · layout PAIRED 1,154 · platform ILLUMINA 1,154 · models Illumina HiSeq 2500 (1,154) · 91% of runs with a Sandpiper profile · first public 2018-10-22 – 2018-10-24
Authors (105)
Vatanen T first · Plichta DR · Somani J · Münch PC · Arthur TD · Hall AB · Rudolf S · Oakeley EJ · Ke X · Young RA · Haiser HJ · Kolde R · Yassour M · Luopajärvi K · Siljander H · Virtanen SM · Ilonen J · Uibo R · Tillmann V · Mokurov S · Dorshakova N · Porter JA · McHardy AC · Lähdesmäki H · Vlamakis H · Huttenhower C · Knip M · Xavier RJ last · Xiao L first · Wang J · Zheng J · Li X · Zhao F last · Auchtung TA first · Stewart CJ · Smith DP · Triplett EW · Agardh D · Hagopian WA · Ziegler AG · Rewers MJ · She JX · Toppari J · Lernmark Å · Akolkar B · Krischer JP · Vehik K · Auchtung JM · Ajami NJ · Petrosino JF last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Rizzo SM first · Viappiani A · Bianchi MG · Bussolati O · van Sinderen D · Hall B first · Levy S · Dufault-Thompson K · Arp G · Zhong A · Ndjite GM · Weiss A · Braccia D · Jenkins C · Grant MR · Abeysinghe S · Yang Y · Jermain MD · Wu CH · Ma B · Jiang X last · Ennis D first · Shmorak S · Jantscher-Krenn E · De Biase R · Bocchio F · De Conto F · Nouvenne A · Ticinesi A · Meschi T · Cecchi R · Jiang W first · Zhai Y · Chen D · Yu Q last · Longhi G · Gennaioli E · Muscò A · Vitale SG · Angioni S · Bücking R first · Pasquali G · Löber U · Buss C · Viemann D · Jarquín-Díaz VH · Forslund-Startceva SK last
Downloads
PRJNA497734.csv.gz (39.2 KB) · parquet (126.2 KB) — all 1,154 samples, every field with route and confidence · PRJNA497734_determinations.csv.gz (64.3 KB) — 9,710 evidence rows