Spanish mother-infant stool/milk metagenomes, cohort
155 samples from Spanish mothers (stool, milk) and infants (longitudinal stool, first year of age), in a cohort study comparing delivery mode (vaginal/cesarean), birth place (hospital/home), and breastfeeding duration. machine-written summary
182 samples · 182 runs · ES · Infant / toddler · 2024 · 3.53 Gbp / sample · cohort MAMI
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 394 sample values (collection date, country, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 337 sample values (location site, preterm status) · PMC11183301, PMC12222458, PMC13589485 |
| ✓ Supplementary tables | 2,221 sample values (age, antibiotic exposure, birth weight grams, bmi, delivery mode, family id, family role, feeding mode) |
| – 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 |
longitudinalfamiliesmother–infant
59 of 68 people sampled more than once (173 samples; median 3, up to 4 per person) · follow-up median 12 mo (max 37.9 y) · median interval between samples 6 mo (time from age at collection). Schedule stated by the source: “Infant stool at 1 week, 1 month, 6 months, 12 months; maternal stool and milk at 1 month postpartum” (time origin: birth); stated follow-up 12 mo.
Each row is one person (36 shown of 59); 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).
34 mother–infant dyads (MAMI, Spain); maternal stool/milk at 1 month, infant stool 1 wk–12 mo; no twins · 34 families with 68 sampled people (34 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 34 families (one per family structure, then more). 68 people in the project overall.
Families (25 of 34)
Genera, mean relative abundance over 141 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 | 182 | 100% | ||||
| country | 182 | 100% | 182 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 182 | 100% | 182 | |||
| age_at_collection_days | 182 | 100% | 182 | |||
| collection_date | 182 | 100% | 182 | |||
| detailed_location | 182 | 100% | ||||
| family_id | 182 | 100% | 182 | |||
| family_role | 182 | 100% | 182 | |||
| location_site | 182 | 100% | 182 | |||
| timepoint_label | 182 | 100% | 30 | 152 | ||
| birth_weight_grams | 155 | 85% | 155 | |||
| delivery_mode | 155 | 85% | 155 | |||
| feeding_mode | 155 | 85% | 155 | |||
| gestational_age_weeks | 155 | 85% | 155 | |||
| maternal_antibiotics | 155 | 85% | 155 | |||
| preterm_status | 155 | 85% | 155 | |||
| sex | 155 | 85% | 155 | |||
| antibiotic_exposure | 148 | 81% | 148 | |||
| bmi | 145 | 80% | 145 | |||
| probiotic_exposure | 118 | 65% | 118 |
- Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome. 2025 PMID 40603287 PMC12222458 cites_accession
- Maternal secretor status and human milk oligosaccharides influence the infant gut resistome. 2026 PMID 42679805 PMC13589485 cites_accession
- Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year. PMID 38870906 PMC11183301 curated
- Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome. PMID 40603287 PMC12222458 curated
- Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year. 2024 PMID 38870906 PMC11183301 own_data
Archive description
Cohort of spanish mother and infants across multiple delivery mode and perinatal conditions: place (hospital, home), mode of delivery (vaginal, cesarean), breastfeeding and its duration. For the mothers, stool and milk shotgun metagenomics samples are available. For the infant, longitidinal stool shotgun metagenomics samples are available across the first year of age (1 week, 1 month, 6 months, 12 months)
How this project entered the registry
Classified as human gut / stool / human milk / vaginal / urogenital 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.title · “infants metagenomes of stool and milk samples”
- body site study.description · “For the mothers, stool and milk shotgun”
- body site study.title · “of stool and milk samples”
- body site study.description · “mothers, stool and milk shotgun metagenomics samples”
- body site study.description · “of delivery ( vaginal , cesarean), breastfeeding”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Spanish mother and infants metagenomes of stool”
- life stage study.description · “duration. For the mothers , stool and”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA115454944 | age_at_collection_days | 30 | R2 | 0.85 | paper.supp.table | timepoint_months=1.0 |
| SAMEA115454944 | antibiotic_exposure | no | R2 | 0.85 | paper.supp.table | AB_BB=no |
| SAMEA115454944 | birth_weight_grams | 3950 | R2 | 0.85 | paper.supp.table | birth_weight (Kg)=3.95 |
| SAMEA115454944 | bmi | 15.01 | R2 | 0.85 | paper.supp.41467_2025_61154_MOESM8_ESM.xlsx[metadata_infants][BMI_BB] | 15.005 |
| SAMEA115454944 | collection_date | 2016 | R1 | 0.85 | biosample.attribute:collection_date | 2016 |
| SAMEA115454944 | country | ES | R1 | 0.90 | biosample_attr | Spain |
| SAMEA115454945 | country | ES | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Spain |
| SAMEA115454944 | delivery_mode | c_section | R2 | 0.85 | paper.supp.table | delivery=csection |
| SAMEA115454944 | family_id | 17 | R2 | 0.85 | paper.supp.mmc2.xlsx[Tab1!family] | MAMI_017B04H family=17 |
| SAMEA115454944 | family_role | child | R2 | 0.85 | paper.supp.mmc2.xlsx[Tab1!mother_infant] | MAMI_017B04H mother_infant=infant |
| SAMEA115454944 | feeding_mode | exclusive_breast | R2 | 0.85 | paper.supp.table | feeding_cat=Breastfeeding |
| SAMEA115454944 | gestational_age_weeks | 39.0 | R2 | 0.85 | paper.supp.table | gestational_age=39.0 |
| SAMEA115454944 | location_site | Hospital La Fe, Hospital Clinico Universitario, Parc de Salut MAR | R3 | 0.70 | paper.fulltext.methods | Hospital La Fe, Hospital Clinico Universitario, Parc de Salut MAR |
| SAMEA115454944 | maternal_antibiotics | yes | R2 | 0.85 | paper.supp.table | intrapartum_ATB=1.0 |
| SAMEA115454944 | preterm_status | term | R3 | 0.80 | paper.fulltext.methods | 66 of healthy, full-term mother-infant pairs |
| SAMEA115454944 | probiotic_exposure | no | R2 | 0.85 | paper.supp.table | Probiotic=no |
| SAMEA115454944 | sex | male | R2 | 0.85 | paper.supp.table | sex=Male |
| SAMEA115454944 | subject_id | 017B | R2 | 0.85 | paper.supp.mmc2.xlsx[Tab1][subject] | 017B |
| SAMEA115454966 | timepoint_label | 1 month | R1 | 0.70 | sample.name_rule:title | MAMI_518M04H |
| SAMEA115454944 | timepoint_label | 1month | R2 | 0.85 | paper.supp.table | Time=1month |
Sequencing
182 runs over 182 samples · mean 4.27 Gbp per run (median 3.53 Gbp, total 777.72 Gbp; 182 runs with a base count) · layout PAIRED 182 · platform ILLUMINA 182 · models Illumina HiSeq 2500 (182) · 81% of runs with a Sandpiper profile · first public 2024-04-01
Authors (18)
Selma-Royo M first · Dubois L · Manara S · Armanini F · Cabrera-Rubio R · Valles-Colomer M · González S · Parra-Llorca A · Escuriet R · Bode L · Martínez-Costa C · Segata N · Collado MC last · Samarra A first · Alcañiz AJ · Marina A · Comas I · Quijada NM
Downloads
PRJEB74322.csv.gz (8.7 KB) · parquet (82.3 KB) — all 182 samples, every field with route and confidence · PRJEB74322_determinations.csv.gz (34.4 KB) — 2,952 evidence rows