Early gut microbiome colonization in mother-neonate pairs

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intervention — arms not resolved

Other administered intervention (see intervention_detail) design observational_with_procedure · population preterm_nicu · Delivery mode (vaginal vs caesarean section) cohort comparison

“born vaginally, by caesarean section and born by caesarean section” — bioproject.description (study level; per-sample arms are in the intervention column below)

age: supplementary table and curatedMetagenomicData disagree for 13 samples (e.g. 0 vs 14610.0) — withheld; country: sequence archive and microbeatlas disagree for 42 samples (e.g. LU vs FR) — withheld.

The sources disagree on 46 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).

longitudinalmother–infant

16 of 30 people sampled more than once (39 samples; median 2, up to 3 per person) · follow-up median 3 d (max 4 d) · median interval between samples 2 d (time from age at collection). Schedule stated by the source: “Neonate stool at first 24h, day 3, day 5 (shotgun); also days 28, 150, 1 year (16S/18S only)” (time origin: birth); stated follow-up 12 mo.

Each row is one person (16 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).

17 family C-numbers: 15 mother–neonate pairs (maternal stool/vaginal swab + neonate stool d1/d3/d5), 1 mother-only, 1 neonate-only · 15 families with 30 sampled people (15 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: 15 families. 30 people in the project overall.

How longitudinal and relatedness information is derived

Genera, mean relative abundance over 48 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

• Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential. PMID 30504906 PMC6269548 curated
• Metagenomic analysis of mother-infant gut microbiome reveals global distinct and shared microbial signatures. PMID 33960282 PMC8115609 curated
• Deterministic transition of enterotypes shapes the infant gut microbiome at an early age. PMID 34429130 PMC8383385 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
• Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645 curated