Mother-to-infant gut strain transmission, long. cohort
286 gut microbiome samples from a longitudinal birth cohort of 44 mothers and infants, mostly healthy, profiling strain-level bacterial transmission and antibiotic resistance genes during the first months of life. machine-written summary
286 samples · 286 runs · FI · Infant / toddler · 2018 · 3.56 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,921 sample values (age, family id, family role, health condition detail, sex, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10092070, PMC12769767, PMC8115609 |
| ✓ Supplementary tables | 1,580 sample values (age, birth weight grams, country, delivery mode, diet, feeding mode, gestational age weeks, preterm status) |
| ✓ External resources | 271 sample values (health condition) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinalmother–infant
33 of 43 people sampled more than once (160 samples; median 5, up to 5 per person) · follow-up median 3 mo (max 3 mo) · median interval between samples 30 d (time from age at collection). Schedule stated by the source: “Birth, 14 days, 1 month, 2 months, 3 months (child); Gestation, Birth, 3 months (mother)” (time origin: birth); stated follow-up 3 mo.
Each row is one person (33 shown); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother, father, child, twin).
44 mother–infant families: 116 maternal and 170 infant stool samples (42 families with both sampled); strain transmission study · 42 families with 84 sampled people (42 with a parent and a child).
motherchild · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 24 of 42 families (one per family structure, then more). 43 people in the project overall.
Families (25 of 42)
Genera, mean relative abundance over 123 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 | 281 | 98% | ||||
| country | 286 | 100% | 286 | |||
| health_condition | 271 | 95% | 271 | |||
| subject_id | 286 | 100% | 286 | |||
| family_id | 286 | 100% | 286 | |||
| family_role | 286 | 100% | 286 | |||
| health_condition_detail | 286 | 100% | 286 | |||
| sex | 286 | 100% | 286 | |||
| timepoint_label | 286 | 100% | 247 | 39 | ||
| age_at_collection_days | 281 | 98% | 244 | 37 | ||
| delivery_mode | 280 | 98% | 280 | |||
| preterm_status | 268 | 94% | 268 | |||
| feeding_mode | 184 | 64% | 184 | |||
| birth_weight_grams | 166 | 58% | 166 | |||
| diet | 164 | 57% | 164 | |||
| gestational_age_weeks | 156 | 55% | 156 |
- Metagenomic analysis of mother-infant gut microbiome reveals global distinct and shared microbial signatures. PMID 33960282 PMC8115609 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
- Rapid evolution and strain turnover in the infant gut microbiome. PMID 35545448 PMC9248880 curated
- Impact of Extensively Hydrolyzed Infant Formula on Circulating Lipids During Early Life. PMID 35685890 PMC9171511 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
17 more
- Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach. PMID 36123315 PMC10092070
- 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
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488
- 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
- Longitudinal quantification of Bifidobacterium longum subsp. infantis reveals late colonization in the infant gut independent of maternal milk HMO composition. PMID 38291346 PMC10827747
- 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
- Inspecting mother-to-infant microbiota transmission: disturbance of strain inheritance by cesarian section. PMID 38486699 PMC10937581
- 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
- Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy. PMID 39428758 PMC11497992
- Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome. PMID 39866568 PMC11758915
- 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
Archive description
Bacterial community acquisition in the infant gut impacts immune education and disease susceptibility. We compared bacterial strains across and within families in a prospective birth cohort of 44 infants and their mothers, sampled longitudinally in the first months of each child’s life. We identified mother-to-child microbial transmission events and describe the incidence of family-specific antibiotic resistance genes. Across multiple species, we identified two inheritance patterns, where often the mother’s dominant strain is transmitted to the child, but occasionally her minor strains colonize the infant gut. We observed both inheritance patterns for Bacteroides uniformis strains. In families where the minor strain was inherited, we identified a starch utilization gene cluster that was absent in the mother’s dominant strain, suggesting the selective advantage of her minor strain in the infant gut. Our findings reveal mother-to-child bacterial transmission events at high-resolution and give insights into early colonization of the infant gut.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child 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 · “in the infant gut impacts immune education”
- 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 · “acquisition in the infant gut impacts immune”
- life stage study.title · “identification of mother-to- child bacterial transmission during”
- life stage study.description · “months of each child ’s life. We”
- life stage study.description · “infants and their mothers , sampled longitudinally”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09382449 | age_at_collection_days | 0 | R1 | 0.90 | biosample_attr | Birth |
| SAMN09382454 | age_at_collection_days | 189 | R2 | 0.85 | paper.supp.table | Sampling, day=189 |
| SAMN09382449 | birth_weight_grams | 3640 | R2 | 0.85 | paper.supp.table | Birth weight=3640 |
| SAMN09382449 | country | FI | R2 | 0.75 | paper.supp.table | Country=Finland |
| SAMN09382449 | delivery_mode | vaginal | R2 | 0.85 | paper.supp.table | Mode of delivery=vaginal |
| SAMN09382450 | diet | exclusive_breast_milk | R2 | 0.85 | paper.supp.41522_2025_868_MOESM2_ESM.xlsx[Data S1!Feeding type] | Breast Milk |
| SAMN09382449 | family_id | M0018 | R1 | 0.70 | sample.name_rule:title | M0018-Child:Birth |
| SAMN09382449 | family_role | child | R1 | 0.85 | biosample.attribute:title | M0018-Child:Birth |
| SAMN09382450 | feeding_mode | exclusive_breast | R2 | 0.85 | paper.supp.table | Feeding regimen=breast |
| SAMN09382449 | gestational_age_weeks | 39.1 | R2 | 0.75 | paper.supp.table | Gestational age (weeks)=39.1 |
| SAMN09382449 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN09382449 | health_condition_detail | birth-delivery-mode:Vaginal | R1 | 0.90 | biosample.attribute:health_state | health_state: birth-delivery-mode:Vaginal |
| SAMN09382449 | preterm_status | term | R2 | 0.85 | paper.supp.table | Gestational age=full-term |
| SAMN09382449 | sex | female | R1 | 0.90 | biosample_attr | female |
| SAMN09382449 | subject_id | M0018C | R1 | 0.50 | biosample_attr | M0018C |
| SAMN09382449 | timepoint_label | Birth | R1 | 0.70 | sample.title | M0018-Child:Birth |
| SAMN09382454 | timepoint_label | Gest | R1 | 0.70 | sample.name_rule:title | M0018-Mother:Gest |
| SAMN09382455 | timepoint_label | Neonatal | R2 | 0.75 | paper.supp.table | Time Group=Neonatal |
Sequencing
286 runs over 286 samples · mean 3.16 Gbp per run (median 3.56 Gbp, total 902.88 Gbp; 286 runs with a base count) · layout PAIRED 286 · platform ILLUMINA 286 · models Illumina HiSeq 2500 (286) · 80% of runs with a Sandpiper profile · first public 2018-06-09
Authors (150)
Wang S first · Zeng S · Egan M · Cherry P · Strain C · Morais E · Boyaval P · Ryan CA · M Dempsey E · Ross RP · Stanton C 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 · Chen DW first · Garud NR last · Lamichhane S first · Siljander H · Salonen M · Ruohtula T · Virtanen SM · Ilonen J · Hyötyläinen T · Knip M · Orešič M last · Patangia D · Almeida A · Zhou Z · Mu D · Paul Ross R · 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 · Ennis D first · Shmorak S · Jantscher-Krenn E · Yassour M 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 · Yang R first · Wang Y · Ying Z · Shi Z · Song Y · Yan J · Hou S · Zhao Z · Hu Y · Chen Q · Peng W · Li X last · 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 · Minot SS first · Mayer-Blackwell K · Fiore-Gartland A · Johnson A · Self S · Bhatti P · Yao L · Liu L · Sun X · Jinfa Y · Kublin J last · Pucci N first · Ujčič-Voortman J · Verhoeff AP · Mende DR last · Zhang L · Yuan Y · Tian M · Zhou M · 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
Downloads
PRJNA475246.csv.gz (11.6 KB) · parquet (84.9 KB) — all 286 samples, every field with route and confidence · PRJNA475246_determinations.csv.gz (34.5 KB) — 3,772 evidence rows