Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism

Tommi Vatanen, Karolina S. Jabbar, Terhi Ruohtula, Jarno Honkanen, Julian Avila-Pacheco, Heli Siljander, Martin Stražar, Sami Oikarinen, Heikki Hyöty, Jorma Ilonen, Caroline M. Mitchell, Moran Yassour, Suvi M. Virtanen, Clary B. Clish, Damian R. Plichta, Hera Vlamakis, Mikael Knip, Ramnik J. Xavier

Research output: Contribution to journalArticleScientificpeer-review


The perinatal period represents a critical window for cognitive and immune system development, promoted by maternal and infant gut microbiomes and their metabolites. Here, we tracked the co-development of microbiomes and metabolomes from late pregnancy to 1 year of age using longitudinal multi-omics data from a cohort of 70 mother-infant dyads. We discovered large-scale mother-to-infant interspecies transfer of mobile genetic elements, frequently involving genes associated with diet-related adaptations. Infant gut metabolomes were less diverse than maternal but featured hundreds of unique metabolites and microbe-metabolite associations not detected in mothers. Metabolomes and serum cytokine signatures of infants who received regular—but not extensively hydrolyzed—formula were distinct from those of exclusively breastfed infants. Taken together, our integrative analysis expands the concept of vertical transmission of the gut microbiome and provides original insights into the development of maternal and infant microbiomes and metabolomes during late pregnancy and early life.

Original languageEnglish
Pages (from-to)4921-4936.e15
Issue number26
Publication statusPublished - 22 Dec 2022
Publication typeA1 Journal article-refereed


  • gut metabolome
  • horizontal gene transfer
  • infant gut microbiome
  • mother-to-infant microbiome transmission

Publication forum classification

  • Publication forum level 3

ASJC Scopus subject areas

  • General Biochemistry,Genetics and Molecular Biology


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