Influence of Early Life Factors, including Breastmilk Composition, on the Microbiome of Infants Born to Mothers with and without Inflammatory Bowel Disease

J. Sabino, L. Tarassishin, C. Eisele, K. Hawkins, A. Barré, N Nair, A. Rendon, A. Debebe, M. Picker, M. Agrawal, J. Stone, J. George, Peter Legnani, Elana Maser, Ching-Lynn Chen, Anne Thjømøe, Einar Mørk, M. Dubinsky, J. Hu, J. F. ColombelI. Peter, J. Torres*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

2 Citations (Scopus)


Background and Aims: Herein we analysed the influence of early life factors, including breast milk composition, on the development of the intestinal microbiota of infants born to mothers with and without IBD. Methods: The MECONIUM [Exploring MEChanisms Of disease traNsmission In Utero through the Microbiome] study is a prospective cohort study consisting of pregnant women with or without IBD and their infants. Longitudinal stool samples were collected from babies and analysed using 16s rRNA sequencing and faecal calprotectin. Breast milk proteomics was profiled using Olink inflammation panel. Results: We analysed gut microbiota of 1034 faecal samples from 294 infants [80 born to mothers with and 214 to mothers without IBD]. Alpha diversity was driven by maternal IBD status and time point. The major influencers of the overall composition of the microbiota were mode of delivery, feeding, and maternal IBD status. Specific taxa were associated with these exposures, and maternal IBD was associated with a reduction in Bifidobacterium. In 312 breast milk samples [91 from mothers with IBD], mothers with IBD displayed lower abundance of proteins involved in immune regulation, such as thymic stromal lymphopoietin, interleukin-12 subunit beta, tumour necrosis factor-beta, and C-C motif chemokine 20, as compared with control mothers [adjusted p=0.0016, 0.049, 0.049, and 0.049, respectively], with negative correlations with babýs calprotectin, and microbiome at different time points. Conclusion: Maternal IBD diagnosis influences microbiota in their offspring during early life. The proteomic profile of breast milk of women with IBD differs from that of women without IBD, with distinct time-dependent associations with baby's gut microbiome and feacal calprotectin.

Original languageEnglish
Article numberjjad096
JournalJournal of Crohn's and Colitis
Issue number11
Pages (from-to)1723-1732
Number of pages10
Publication statusPublished - 24 Nov 2023

Bibliographical note

© The Author(s) 2023. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation. All rights reserved. For permissions, please email:


  • Feces/chemistry
  • Female
  • Humans
  • Infant
  • Inflammatory Bowel Diseases/metabolism
  • Leukocyte L1 Antigen Complex/analysis
  • Microbiota
  • Milk, Human/chemistry
  • Mothers
  • Pregnancy
  • Prospective Studies
  • Proteomics
  • RNA, Ribosomal, 16S/genetics
  • microbiota
  • breast milk
  • Early life
  • IBD


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