Finnish infant/parental stool metagenomes, cohort
2664 stool WGS metagenome samples from a longitudinal cohort of healthy Finnish infants (birth to ~1 year) and their parents, collected in Finland; infant samples at 3, 6, and 12 months, parents sampled late in pregnancy. machine-written summary
2,664 samples · 2,664 runs · FI · Infant / toddler · 2024 · 12.87 Gbp / sample · cohort HELMi Helsinki infant/family microbiome cohort
One study deposited as 2 BioProjects (3,141 catalog samples together): PRJEB52774 · PRJEB70237 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 20,402 sample values (age, collection date, country, family role, health condition, health condition detail, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 5,329 sample values (collection date, location region, preterm status) · PMC11215963, PMC11299627 |
| ✓ Supplementary tables | 2,328 sample values (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 |
longitudinalmother–infant — not resolvedparent–child — not resolved
618 of 1,085 people sampled more than once (2,197 samples; median 4, up to 4 per person) · follow-up median 21 mo (max 21 mo) · median interval between samples 6 mo (time from age at collection). Schedule stated by the source: “Infant stool at 3, 6, and 12 months of age; parental stool in the last weeks of pregnancy” (time origin: birth).
Each row is one person (36 shown of 618); dots are samples at days since that person's first sample.
HELMi infants with pregnant mothers (305 samples) and fathers / non-pregnant partners (123); family links not deposited.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 2,663 | 100% | ||||
| country | 2,664 | 100% | 2,664 | |||
| health_condition | 2,210 | 83% | 2,210 | |||
| subject_id | 2,664 | 100% | 2,664 | |||
| collection_date | 2,664 | 100% | 2,663 | 1 | ||
| detailed_location | 2,664 | 100% | ||||
| family_role | 2,664 | 100% | 2,664 | |||
| location_region | 2,664 | 100% | 2,664 | |||
| preterm_status | 2,664 | 100% | 2,664 | |||
| sex | 2,664 | 100% | 2,664 | |||
| age_at_collection_days | 2,663 | 100% | 2,663 | |||
| timepoint_label | 2,328 | 87% | 2,328 | |||
| health_condition_detail | 2,210 | 83% | 2,210 |
- Human milk oligosaccharide composition is affected by season and parity and associates with infant gut microbiota in a birth mode dependent manner in a Finnish birth cohort. PMID 38838470 PMC11215963 curated
- A cohort study in family triads: impact of gut microbiota composition and early life exposures on intestinal resistome during the first two years of life. PMID 39092808 PMC11299627 curated
- (no title) curated
- (no title) curated
- (no title) curated
Archive description
The Health and Early-Life Microbiota (HELMi) is a cohort study of 1055 healthy Finnish infants who are currently followed from birth until 4 to 5 years of age. The HELMi infant-parents WGS dataset is composed of fecal samples from infants collected from 3 weeks of age to 1 year and parents’ (pregnant mother and father or non-pregnant partner) stool samples collected in the last weeks of pregnancy. Infant stool samples were collected at 3 months, 6 months, and 12 months of age. The samples were collected by the parents at home and samples were stored at home at -20°C until being brought to the lab in frozen form. Upon receival the samples were immediately stored at -80°C until processing. Fecal DNA was generated by repeated beat beating method and stool WGS metagenomes were generated through MGI sequencing technology. The study protocols have been approved by the ethical committee of The Hospital District of Helsinki and Uusimaa (263/13/03/03 2015 and HUS/2126/2020) and are performed in accordance with the principles of the Helsinki Declaration. The guardians have provided an informed, written consent. participation is voluntary and the participants can withdraw from the study at any point. The study does not include any invasive procedures for infants.
How this project entered the registry
Classified as human gut / stool 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 · “infant and parental stool WGS metagenomes”
- body site study.description · “is composed of fecal samples from infants”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “HELMi infant and parental stool”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114633094 | age_at_collection_days | 91 | R1 | 0.90 | biosample_attr | 13 |
| SAMEA115170002 | age_at_collection_days | 11323 | R1 | 0.90 | sample.attr.host_age | 31 |
| SAMEA114633094 | collection_date | 2016-07-02 | R1 | 0.85 | biosample.attribute:collection date | 2016-07-02 |
| SAMEA115170261 | collection_date | 2016/2018 | R3 | 0.70 | paper.fulltext.methods | mainly born in the Uusimaa region in 2016–18 |
| SAMEA114633094 | country | FI | R1 | 0.90 | biosample_attr | Finland |
| SAMEA114633094 | family_role | child | R1 | 0.85 | biosample.attribute:miscellaneous_parameter | infant born by Vaginal delivery with Intrapartum antibiotics |
| SAMEA114633095 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:miscellaneous parameter | infant born by Vaginal delivery |
| SAMEA114633095 | health_condition_detail | infant born by Vaginal delivery | R1 | 0.85 | biosample.attribute:miscellaneous parameter | infant born by Vaginal delivery |
| SAMEA114633094 | location_region | Uusimaa | R3 | 0.70 | paper.fulltext.methods | mainly born in the Uusimaa region in 2016–18 |
| SAMEA114633094 | preterm_status | term | R3 | 0.80 | paper.fulltext.results | born in Finland in hospital at term |
| SAMEA114633094 | sex | female | R1 | 0.90 | biosample_attr | female |
| SAMEA114633094 | subject_id | I53 | R1 | 0.85 | biosample_attr | I53 |
| SAMEA114703684 | timepoint_label | 3m | R2 | 0.85 | paper.supp.Supplementary_file_1_ENA_ID.xlsx[Supplementary_file_1_ENA_ID!Sampling_age] | ACCESSION=ERS17119729; Sampling_age=3m |
Sequencing
2,664 runs over 2,664 samples · mean 13.82 Gbp per run (median 12.87 Gbp, total 36,817.92 Gbp; 2,664 runs with a base count) · layout PAIRED 2,664 · platform DNBSEQ 2,664 · models DNBSEQ-T7 (2,664) · 0% of runs with a Sandpiper profile · first public 2024-03-31
Authors (39)
Matharu D first · Ponsero AJ · Lengyel M · Meszaros-Matwiejuk A · Kolho KL · de Vos WM · Molnar-Gabor D · Salonen A last · Jokela R first · Pärnänen KM · Lahti L · Galperina A first · Lugli GA · Milani C · Ventura M · Hurwitz B · Kiran S first · Cruz AR · Daniau A · Ma B · Marbouty M · Pipoli Da Fonseca J · Legrand A · Baudry L · Cokelaer T · Bensussan M · Moya-Nilges M · Garneau J · Monot M · Ochieng JB · Antonio M · Tamboura B · Hossain J · Omore R · Sow SO · Sansonetti PJ · Ravel J · Cerf-Bensussan N · Schnupf P last
Downloads
PRJEB70237.csv.gz (91.9 KB) · parquet (195.5 KB) — all 2,664 samples, every field with route and confidence · PRJEB70237_determinations.csv.gz (184.1 KB) — 28,059 evidence rows