Infant gut metagenomes in probiotic pregnancy trial
646 stool shotgun metagenome samples from neonates and infants (birth to 24 months) in a randomized trial testing probiotic (Bifidobacterium lactis HN019 or Lactobacillus rhamnosus HN001) versus placebo during pregnancy and early infancy, examining eczema risk at 2 years. machine-written summary
646 samples · 646 runs · NZ · Infant / toddler · 2019 · 3.37 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 4,522 sample values (age, health condition, health condition detail, intervention, probiotic exposure, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10092070, PMC10175488, PMC10769871, PMC10904392, PMC11019788, PMC11322291, PMC11494892, PMC12769767, PMC8518733, PMC9437082, PMC9512645, PMC9622858 |
| ✓ Supplementary tables | 1,731 sample values (antibiotic exposure, country, delivery mode, 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 |
intervention · arms resolved
Probiotic (live microorganisms; single strain or mixture) design randomized_controlled_trial · population pregnancy_postpartum · Bifidobacterium lactis HN019 or Lactobacillus rhamnosus HN001 vs placebo, pregnancy to infancy
“randomly assigned to receive a probiotic” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
199 of 210 people sampled more than once (635 samples; median 3, up to 5 per person) · follow-up median 2.0 y (max 2.0 y) · median interval between samples 9 mo (time from age at collection). Schedule stated by the source: “Stool collected shortly after birth, and at 3, 12, and 24 months of age” (time origin: birth).
Each row is one person (36 shown of 199); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 563 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 | 646 | 100% | ||||
| country | 646 | 100% | 646 | |||
| health_condition | 646 | 100% | 646 | |||
| subject_id | 646 | 100% | 646 | |||
| age_at_collection_days | 646 | 100% | 646 | |||
| health_condition_detail | 646 | 100% | 646 | |||
| intervention | 646 | 100% | 646 | |||
| probiotic_exposure | 646 | 100% | 646 | |||
| sex | 646 | 100% | 646 | |||
| timepoint_label | 531 | 82% | 531 | |||
| antibiotic_exposure | 333 | 52% | 333 | |||
| delivery_mode | 221 | 34% | 221 |
- 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
- Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645 curated
- Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium. PMID 36316342 PMC9622858 curated
7 more
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488
- BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. PMID 38172624 PMC10769871
- 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
- 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
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767
Archive description
In this study, pregnant women (from 35 weeks gestation until their infants were 6 months old) and their infants (from birth until 2 years of age) were randomly assigned to receive a probiotic (either Bifidobacterium animalis subsp lactis HN019, Lactobaciilus rhamnosus HN001, or placebo). Stool shotgun metagenomes were sequenced shortly after birth, and at 3, 12, and 24 months of age. This dataset allows examination of how early life probiotic intervention, mode of delivery, and other metadata contribute to risk of eczema at 2 years.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “HN001, or placebo). Stool shotgun metagenomes were”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “gestation until their infants were 6 months”
- life stage study.description · “In this study, pregnant women (from 35 weeks”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09278078 | age_at_collection_days | 730 | R1 | 0.90 | biosample_attr | 24_months |
| SAMN09278106 | antibiotic_exposure | no | R2 | 0.75 | paper.supp.table | Treatment=Probiotic |
| SAMN09278078 | country | NZ | R2 | 0.75 | paper.supp.table | Geographic location=New Zealand |
| SAMN09278078 | delivery_mode | vaginal | R2 | 0.75 | paper.supp.table | Delivery Mode=Vaginal |
| SAMN09278078 | health_condition | pregnancy_postpartum | R1 | 0.85 | biosample.attribute:studygroup | studygroup: placeb |
| SAMN09278078 | health_condition_detail | Probiotics in Pregnancy study: placebo arm, pregnant women and infants followed from 35wk gestation/birth for eczema risk at 2 years | R1 | 0.85 | biosample.attribute:studygroup | studygroup: placeb |
| SAMN09278078 | intervention | placebo | R1 | 0.85 | biosample.attribute:studygroup | studygroup: placeb |
| SAMN09278078 | probiotic_exposure | no | R1 | 0.60 | biosample_attr | placeb |
| SAMN09278078 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMN09278078 | subject_id | P006 | R1 | 0.85 | biosample_attr | P006 |
| SAMN09278080 | timepoint_label | 1 yr - 4 yr | R2 | 0.75 | paper.supp.table | AGE GROUP G12=1 yr - 4 yr |
Sequencing
646 runs over 646 samples · mean 3.64 Gbp per run (median 3.37 Gbp, total 2,351.02 Gbp; 646 runs with a base count) · layout PAIRED 646 · platform ILLUMINA 646 · models Illumina HiSeq 2500 (646) · 87% of runs with a Sandpiper profile · first public 2019-06-02
Authors (69)
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 · 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 · 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 · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Gennaioli E · Muscò A · Vitale SG · Angioni S
Downloads
PRJNA345144.csv.gz (20.3 KB) · parquet (99.2 KB) — all 646 samples, every field with route and confidence · PRJNA345144_determinations.csv.gz (46.2 KB) — 6,253 evidence rows