Infant gut microbiome cohort in Finland, Estonia, Russia
785 stool samples from infants (and some children) at risk for autoimmunity in Estonia, Finland, and Russian Karelia, mostly healthy with some infections noted, in a longitudinal cohort design. machine-written summary
785 samples · 785 runs · RU, FI, EE · Infant / toddler · 2016 · 1.85 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,355 sample values (age, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10092070, PMC10175488, PMC10187079, PMC10269646, PMC10292843, PMC10769871, PMC10846076, PMC10904392, PMC11019788, PMC11170968, PMC11322291, PMC11494892, PMC12677589, PMC12769767, PMC13081238, PMC6429046, PMC7391733, PMC8518733, PMC9437082, PMC9512645, PMC9622858 |
| ✓ Supplementary tables | 3,396 sample values (antibiotic exposure, delivery mode, feeding mode, gestational age weeks, sex, timepoint) |
| ✓ External resources | 1,577 sample values (antibiotic exposure, health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
antibiotic exposure: supplementary table and curatedMetagenomicData disagree for 219 samples (e.g. yes vs no) — withheld; sex: supplementary table and curatedMetagenomicData disagree for 4 samples (e.g. female vs male) — withheld.
The sources disagree on 219 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (40 of 223)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN05826492 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826496 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826498 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826499 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826504 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826505 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826510 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826514 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826519 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826524 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826525 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826527 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826532 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826539 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826540 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826543 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826548 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826551 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826559 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826568 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826572 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826574 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826575 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826578 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826583 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826588 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826589 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826590 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826592 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826598 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826599 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826601 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826602 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826605 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826609 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826611 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826612 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826615 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826617 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMN05826619 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
longitudinal
185 of 212 people sampled more than once (758 samples; median 3, up to 13 per person) · follow-up median 15 mo (max 2.9 y) · median interval between samples 3 mo (time from age at collection). Schedule stated by the source: “Repeated stool sampling of infants over infancy/childhood at multiple age-based timepoints (e.g. 3-6 months, 6 months-1yr, 1-4yr) through prospective follow-up.”.
Each row is one person (36 shown of 185); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 716 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 | 785 | 100% | ||||
| country | 785 | 100% | 785 | |||
| health_condition | 780 | 99% | 780 | |||
| subject_id | 785 | 100% | 785 | |||
| age_at_collection_days | 785 | 100% | 785 | |||
| delivery_mode | 785 | 100% | 785 | |||
| sex | 781 | 99% | 781 | |||
| health_condition_detail | 780 | 99% | 780 | |||
| gestational_age_weeks | 774 | 99% | 774 | |||
| antibiotic_exposure | 566 | 72% | 566 | |||
| timepoint_label | 490 | 62% | 490 | |||
| feeding_mode | 17 | 2% | 17 |
- Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population. PMID 30894435 PMC6429046 curated
- Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon. PMID 32728114 PMC7391733 curated
- Investigating the infant gut microbiota in developing countries: worldwide metagenomic meta-analysis involving infants living in sub-urban areas of Côte d'Ivoire. PMID 34152069 PMC8518733 curated
- A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. PMID 36050292 PMC9437082 curated
- Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach. PMID 36123315 PMC10092070 curated
16 more
- Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645
- Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium. PMID 36316342 PMC9622858
- Universal gut microbial relationships in the gut microbiome of wild baboons. PMID 37158607 PMC10292843
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488
- Characterization of Bifidobacterium kashiwanohense that utilizes both milk- and plant-derived oligosaccharides. PMID 37188713 PMC10187079
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646
- BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. PMID 38172624 PMC10769871
- Temporal development and potential interactions between the gut microbiome and resistome in early childhood. PMID 38193687 PMC10846076
- A metagenomic catalog of the early-life human gut virome. PMID 38424077 PMC10904392
- Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032 PMC11019788
- Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life. PMID 38882494 PMC11170968
- Insights into the ecology of the infant gut plasmidome. PMID 39138199 PMC11322291
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892
- The Gut Resistome Atlas in Preterm Infants Enables Prediction of Necrotizing Enterocolitis Onset. PMID 41025564 PMC12677589
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767
- An adaptive weight self-distillation deep learning framework for phenotype prediction from longitudinal gut microbiome data. PMID 41796297 PMC13081238
Archive description
This is a longitudinal collection of stool samples from infants at risk for disease. Approximately 1,000 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. Follow-up was completed in April 2013 in Estonia and Finland, and in October 2013 in Russia. The final number of children included in the present study was 74 from each country. Inclusion criteria included positive cord blood testing for HLA DR-DQ alleles conferring increased risk for autoimmunity. 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 / blood / tissue / internal fluids 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 · “of the developing gut microbiome in infants”
- body site study.description · “longitudinal collection of stool samples from infants”
- body site study.description · “included positive cord blood testing for HLA”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “gut microbiome in infants from Finland, Estonia,”
- life stage study.description · “disease. Approximately 1,000 newborns were recruited to”
- life stage study.description · “final number of children included in the”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN05826486 | age_at_collection_days | 686 | R1 | 0.75 | biosample_attr | host_age=686 (days; U2_unique_admissible_unit) |
| SAMN05826505 | age_at_collection_days | 1105 | R1 | 0.80 | sample.attr.host_age | 1105 |
| SAMN05826486 | antibiotic_exposure | no | R2 | 0.75 | paper.supp.table | Infant antibiotics=no |
| SAMN05826580 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN05826486 | country | RU | R1 | 0.90 | biosample_attr | Russia:Petrozavodsk |
| SAMN05826486 | delivery_mode | vaginal | R2 | 0.75 | paper.supp.table | Delivery mode=vaginal |
| SAMN05826523 | feeding_mode | exclusive_breast | R2 | 0.75 | paper.supp.table | Feeding type=Breast Milk |
| SAMN05826486 | gestational_age_weeks | 39.71 | R2 | 0.75 | paper.supp.table | Gestational age (weeks)=39.71 |
| SAMN05826486 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN05826486 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN05826486 | sex | female | R2 | 0.75 | paper.supp.table | Sex=female |
| SAMN05826486 | subject_id | P018832 | R1 | 0.85 | biosample_attr | P018832 |
| SAMN05826486 | timepoint_label | 1 yr - 4 yr | R2 | 0.75 | paper.supp.table | AGE GROUP G12=1 yr - 4 yr |
Sequencing
785 runs over 785 samples · mean 2.04 Gbp per run (median 1.85 Gbp, total 1,604.75 Gbp; 785 runs with a base count) · layout PAIRED 785 · platform ILLUMINA 785 · models Illumina HiSeq 2500 (785) · 91% of runs with a Sandpiper profile · first public 2016-10-07 – 2016-10-16
Authors (156)
Majta J first · Odrzywolek K · Milanovic B · Hubar V · Wrobel S · Strycharz-Angrecka E · Wojciechowski S · Milanowska K last · Sprockett DD first · Martin M · Costello EK · Burns AR · Holmes SP · Gurven MD · Relman DA last · Tisza MJ first · Buck CB last · Fontana F first · Mancabelli L · Lugli GA · Taracchini C · Alessandri G · Longhi G · Anzalone R · Viappiani A · Famo R · Brognan M · Micondo KH · Turroni F · Ventura M · D'Alfonso R · Milani C last · Zeng S first · Patangia D · Almeida A · Zhou Z · Mu D · Paul Ross R · Stanton C · Wang S last · Tarracchini C · Bianchi MG · Rizzo SM · Argentini C · Vergna LM · Taurino G · Chiu M · Bussolati O · van Sinderen D · Roche KE first · Bjork JR · Dasari MR · Grieneisen L · Jansen D · Gould TJ · Gesquiere LR · Barreiro LB · Alberts SC · Blekhman R · Gilbert JA · Tung J · Mukherjee S · Archie EA last · Orihara K first · Yahagi K · Saito Y · Watanabe Y · Sasai T · Hara T · Tsukuda N · Oki K · Fujimoto J · Matsuki T last · 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 · Zhao L first · Yang X · Liang Y · Zhang Z · Ding Y · Wang Y · Chen B · Wu J · Jin C · Zhao G · Li Z · Zhang L last · Li S · Ying J · Wang H · Qu Y · Niu X · De Biase R · Bocchio F · De Conto F · Nouvenne A · Ticinesi A · Meschi T · Cecchi R · Xu X first · Feng Q · Zhang T · Gao Y · Cheng Q · Zhang W · Wu Q · Xu K · Li Y · Nguyen N · Taft DH · Mills DA · Lemay DG · Zhu W · Mao S · Zhang A · Liu J last · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Yuan Y · Tian M · Zhou M · Hu Y · Huang J · Zou R · Zhao F · Su X · Liu Q · He Y · Feng J · Huang W · Luo Y · Shen W · Gennaioli E · Muscò A · Vitale SG · Angioni S · Shi K first · He Q · Guo J last
Downloads
PRJNA290380.csv.gz (30.7 KB) · parquet (110.9 KB) — all 785 samples, every field with route and confidence · PRJNA290380_determinations.csv.gz (77.5 KB) — 7,328 evidence rows