Finnish infant & parent stool metagenomes, long. cohort
477 stool metagenome samples from Finnish infants (3 weeks to 1 year) and their parents, part of the HELMi longitudinal cohort study; no health condition or intervention specified. machine-written summary
477 samples · 486 runs · FI · Infant / toddler · 2022 · 5.53 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 | 2,529 sample values (age, collection date, country, health condition, health condition detail, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 810 sample values (feeding mode, preterm status) · PMC10508911, PMC9583133 |
| ✓ Supplementary tables | 951 sample values (delivery mode, maternal antibiotics, 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 |
longitudinalfamilies — not resolvedparent–child — not resolved
91 of 236 people sampled more than once (332 samples; median 4, up to 4 per person) · follow-up median 11 mo (max 11 mo) · median interval between samples 3 mo (time from age at collection). Schedule stated by the source: “Infant stool samples collected at 3 weeks, 3 months, 6 months, and 12 months of age” (time origin: birth); stated follow-up 12 mo.
Each row is one person (36 shown of 91); dots are samples at days since that person's first sample.
HELMi infants with pregnant mothers and fathers/partners; family linkage not published.
Genera, mean relative abundance over 425 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 | 477 | 100% | ||||
| country | 477 | 100% | 477 | |||
| health_condition | 72 | 15% | 72 | |||
| subject_id | 477 | 100% | 477 | |||
| age_at_collection_days | 477 | 100% | 477 | |||
| collection_date | 477 | 100% | 477 | |||
| sex | 477 | 100% | 477 | |||
| feeding_mode | 405 | 85% | 405 | |||
| preterm_status | 405 | 85% | 405 | |||
| timepoint_label | 373 | 78% | 373 | |||
| delivery_mode | 289 | 61% | 289 | |||
| maternal_antibiotics | 289 | 61% | 289 | |||
| health_condition_detail | 72 | 15% | 72 |
- Bacteroides abundance drives birth mode dependent infant gut microbiota developmental trajectories. PMID 36274732 PMC9583133 curated
- An extended catalog of integrated prophages in the infant and adult fecal microbiome shows high prevalence of lysogeny. PMID 37731926 PMC10508911 curated
- (no title) curated
- A metagenome-assembled genome inventory for children reveals early-life gut bacteriome and virome dynamics. PMID 39591974 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 weeks, 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 using Illumina Nextera Flex or iGenomX Riptide High Throughput Rapid Library Prep Kit and Illumina HiSeq and NovaSeq 6000 sequencing platforms respectively. 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 · “HELMi infant stool WGS metagenomes (3”
- 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 stool WGS metagenomes”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114191888 | age_at_collection_days | 364 | R1 | 0.90 | biosample_attr | 52 |
| SAMEA114192182 | age_at_collection_days | 13880 | R1 | 0.90 | sample.attr.host_age | 38 |
| SAMEA114191888 | collection_date | 2017-07-26 | R1 | 0.85 | biosample.attribute:collection_date | 2017-07-26 |
| SAMEA114191888 | country | FI | R1 | 0.90 | biosample_attr | Finland |
| SAMEA14382411 | delivery_mode | vaginal | R2 | 0.75 | paper.supp.table | Birth Mode=Vaginal |
| SAMEA114191888 | feeding_mode | exclusive_breast | R3 | 0.40 | paper.fulltext.results | All the children were breastfed during the first months |
| SAMEA14382824 | health_condition | pregnancy_postpartum | R1 | 0.85 | biosample.attribute:miscellaneous_parameter | pregnant mother |
| SAMEA14382824 | health_condition_detail | pregnant mother | R1 | 0.85 | biosample.attribute:miscellaneous_parameter | pregnant mother |
| SAMEA14382411 | maternal_antibiotics | no | R2 | 0.75 | paper.supp.table | Intrapartum antibiotics=False |
| SAMEA114191888 | preterm_status | term | R3 | 0.80 | paper.fulltext.abstract | study comprised 78 term infants sampled at 3 weeks |
| SAMEA114191888 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMEA114191888 | subject_id | I158 | R1 | 0.85 | biosample_attr | I158 |
| SAMEA14382411 | timepoint_label | Infant sample 3 weeks | R2 | 0.85 | paper.supp.Data_Sheet_4.XLSX[Supplemental_File4!Sample_type] | ERS11976565 | Sample_type: Infant sample 3 weeks |
Sequencing
486 runs over 477 samples · mean 5.07 Gbp per run (median 5.48 Gbp, total 2,463.50 Gbp; 486 runs with a base count) · layout PAIRED 486 · platform ILLUMINA 486 · models Illumina NovaSeq 6000 (480), Illumina HiSeq 4000 (6) · 88% of runs with a Sandpiper profile · first public 2022-05-31 – 2023-07-25
Authors (34)
Korpela K first · Dikareva E · Hanski E · Kolho KL · de Vos WM · Salonen A last · Matharu D first · Ponsero AJ · Lahtinen E · Miller M · Hurwitz BL last · Peng Y first · Zhu J · Wang S · Liu Y · Liu X · DeLeon O · Zhu W · Xu Z · Zhang X · Zhao S · Liang S · Li H · Ho B · Ching JY · Cheung CP · Leung TF · Tam WH · Leung TY · Chang EB · Chan FKL · Zhang L · Ng SC · Tun HM last
Downloads
PRJEB52774.csv.gz (17.9 KB) · parquet (94.0 KB) — all 477 samples, every field with route and confidence · PRJEB52774_determinations.csv.gz (32.0 KB) — 4,290 evidence rows