Long. gut metagenomes of mothers & children, Rhode Island

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sex differs between samples of the same subject id (14 subjects, 36 samples) — sex withheld; subject ids shared by samples of both sexes (14 ids, 36 samples) — ids withheld.

The sources disagree on 40 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–infantparent–child

275 of 735 people sampled more than once (626 samples; median 2, up to 4 per person) · follow-up median 3 mo (max 3.8 y) · median interval between samples 2 mo (time from collection dates). Schedule stated by the source: “Up to 12 numbered visits (BioSample timepoint 1-12); children with repeated C-prefixed samples; schedule not stated in description”.

Each row is one person (36 shown of 275); 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).

682 mother-child family ids (BioSample subject_id); 300 mothers (M) and 348 children (C) by library prefix; 67 families with both sampled; 789 FG samples role unknown · 441 families with 1,175 sampled people (67 with a parent and a child).

motherchildmember · 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 441 families (one per family structure, then more). 735 people in the project overall.

How longitudinal and relatedness information is derived

Genera, mean relative abundance over 1,614 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

• Comparative Analysis of 16S rRNA Gene and Metagenome Sequencing in Pediatric Gut Microbiomes. PMID 34335499 PMC8320171 curated
• Family SES Is Associated with the Gut Microbiome in Infants and Children. PMID 34442687 PMC8398307 curated
• Targeted High-Resolution Taxonomic Identification of Bifidobacterium longum subsp. infantis Using Human Milk Oligosaccharide Metabolizing Genes. PMID 34444993 PMC8401031 curated
• Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645 curated
• Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646 curated