Delivery Mode Affects Stability of Early Infant Gut Microbiota

Caroline M. Mitchell, Chiara Mazzoni, Larson Hogstrom, Allison Bryant, Agnes Bergerat, Avital Cher, Shawna Pochan, Penelope Herman, Maureen Carrigan, Karen Sharp, Curtis Huttenhower, Eric S. Lander, Hera Vlamakis, Ramnik J. Xavier, Moran Yassour

Research output: Contribution to journalArticlepeer-review


Mode of delivery strongly influences the early infant gut microbiome. Children born by cesarean section (C-section) lack Bacteroides species until 6–18 months of age. One hypothesis is that these differences stem from lack of exposure to the maternal vaginal microbiome. Here, we re-evaluate this hypothesis by comparing the microbial profiles of 75 infants born vaginally or by planned versus emergent C-section. Multiple children born by C-section have a high abundance of Bacteroides in their first few days of life, but at 2 weeks, both C-section groups lack Bacteroides (primarily according to 16S sequencing), despite their difference in exposure to the birth canal. Finally, a comparison of microbial strain profiles between infants and maternal vaginal or rectal samples finds evidence for mother-to-child transmission of rectal rather than vaginal strains. These results suggest differences in colonization stability as an important factor in infant gut microbiome composition rather than birth canal exposure.

Original languageEnglish
Article number100156
JournalCell Reports Medicine
Issue number9
StatePublished - 22 Dec 2020


  • infant gut microbiota, caesarean delivery, Bacteroides, delivery mode, transmission of maternal strains

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)


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