Longitudinal gut metagenomes, mothers and infants, Finland
Longitudinal gut metagenomes from mothers and their infants in the EDIA study
918 fecal metagenome samples from mother-infant dyads in Tampere, Finland, collected longitudinally from late pregnancy through infancy/neonatal stages to study vertical and lateral transmission of gut microbiome genes, strains, and species. machine-written summary
Sequencing depth per sample · this project all projects
Sampling design and relatedness
longitudinalfamiliesmother–infant
196 of 238 people sampled more than once (873 samples; median 3, up to 14 per person) · follow-up median 6 mo (max 18 mo) · median interval between samples 30 d(time from age at collection).
Schedule stated by the source: “third trimester of pregnancy; birth; 0.5, 1, 2, 3, 4, 5, 6, 7, 12, 18 months postpartum” (time origin: birth).
Each row is one person (36 shown of 196); 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).
76 families with mother and infant sampled (141 family IDs; 137 mothers, 80 infants); 23 control-woman samples · 76 families with 152 sampled people (76 with a parent and a child).
76 × mother + 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 76 families (one per family structure, then more). 238 people in the project overall.
Bacteroides 16.0%Bifidobacterium 14.3%Phocaeicola 7.2%Escherichia 5.1%Alistipes 3.2%Klebsiella 2.7%Blautia_A 2.6%Roseburia 2.6%Faecalibacterium 2.4%Parabacteroides 2.3%Veillonella 2.1%Mediterraneibacter 1.9%not assigned to a genus 7.9%other genera 29.7%
Genera, mean relative abundance over 847 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Associations between dietary fibers and gut microbiome composition in the EDIA longitudinal infant cohort. PMID 39551356PMC11747200curated
Protein language models uncover carbohydrate-active enzyme function in metagenomics. PMID 41299229PMC12659350curated
Details
Archive description
In a cohort consisting of 70 mother-infant dyads, we profiled the fecal microbiome and in late pregnancy and different stages of infancy. We used longitudinal sampling to investigate the vertical transmission of species, strains, and individual genes. We discovered hundreds of mother-to-infant gene transmission events in the absence of maternal carrier strains in the infant gut. Key maternal donor species in these events belonged to the Bacteroidales order. Although these species were rarely transmitted to infants, their relative abundance in maternal samples exerted a significant influence on infant gut microbial structure and functional potential, including HMO utilization capacity. Hence, apart from classical vertical transmission of strains and species, the maternal microbiome may also shape the infant gut microbiome through lateral gene transfer events.
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.
body sitestudy.title · “Longitudinal gut metagenomes from mothers”
body sitestudy.description · “we profiled the fecal microbiome and in”
life stageexternal_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
life stagestudy.title · “mothers and their infants in the EDIA”
life stagestudy.title · “gut metagenomes from mothers and their infants”
life stagestudy.description · “the absence of maternal carrier strains in”
Evidence examples (one per field × route)
sample
field
value
route
conf.
source
quote
SAMN27113187
age_at_collection_days
548
R1
0.90
biosample_attr
infant age 18 months
SAMN27113187
collection_date
2013-01/2016-07
R3
0.70
paper.fulltext.methods
Data collection concluded on July 26, 2016
SAMN27113187
country
FI
R1
0.90
biosample_attr
Finland: Tampere
SAMN27113187
family_id
M1409
R1
0.85
biosample.attribute:misc_param
family ID: M1409
SAMN27113187
family_role
mother
R1
0.85
biosample.attribute:TITLE
Stool sample collected 18 months postpartum from the mother in family M1409
SAMN27113836
health_condition
healthy_control
R1
0.70
sample.name_rule:title
Stool sample collected from a non-pregnant control woman M0004E
SAMN27113836
health_condition_detail
non-pregnant control woman
R1
0.70
sample.name_rule:title
Stool sample collected from a non-pregnant control woman M0004E
SAMN27113187
location_locality
Tampere
R3
0.70
paper.fulltext.methods
EDIA) cohort study in Tampere, Finland
SAMN27113187
location_region
Pirkanmaa
R3
0.70
paper.fulltext.methods
Pirkanmaa Hospital District
SAMN27113187
subject_id
M1409_mother
R1
0.70
sample.name_rule:title
Stool sample collected 18 months postpartum from the mother in family M1409
SAMN27113187
timepoint_label
18 months
R1
0.70
sample.title
Stool sample collected 18 months postpartum from the mother in family M1409
SAMN27113204
timepoint_label
0.5 months
R1
0.85
biosample.attribute:host_age
0.5 months
Sequencing
918 runs over 918 samples · mean 2.03 Gbp per run (median 1.84 Gbp, total 1,863.90 Gbp; 918 runs with a base count) · layout PAIRED 918 · platform ILLUMINA 918 · models Illumina HiSeq 2500 (918) · 92% of runs with a Sandpiper profile · first public 2022-12-06