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*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

109 Scopus citations

Abstract

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 languageAmerican English
Article number100156
JournalCell Reports Medicine
Volume1
Issue number9
DOIs
StatePublished - 22 Dec 2020

Bibliographical note

Funding Information:
We thank T. Poon, L. Besse, S. Steelman, and C. Nusbaum (Broad Institute) for help in sequence production and sample and data management; V. Subramanian and T. Arthur for experimental methods support and helpful discussions; T. Reimels for valuable figure and text support; the nurses, midwives, and clinicians at the Labor and Delivery Department at Massachusetts General Hospital for their enthusiastic collaboration during enrollment; and the families that agreed to enroll and donate samples. C.M. was supported by the Vincent Memorial Research Funds; E.S.L. was supported by National Human Genome Research Institute grant 2U54HG003067-10; R.J.X. was supported by funding from JDRF, CCFA, and NIH grants R01 DK092405 and P30 DK043351; and M.Y. was supported by NIH grant DK113224-01, Israel Science Foundation grant 2660/18, an Azrieli Foundation Faculty Fellowship, and a BroadIgnite early career grant from the Broad Institute of MIT and Harvard. C.M.M. and M.Y. designed the study. C.M.M. A. Bryant, S.P. P.H. M.C. K.S. and M.Y. enrolled participants and conducted the study. A. Bergerat, A.C. and H.V. performed laboratory analyses. C.M.M. C.H. E.S.L. H.V. R.J.X. and M.Y. supervised the study. C.M.M. C.M. L.H. H.V. R.J.X. E.S.L. and M.Y. designed and conducted the analyses of data. All of the authors contributed to writing the manuscript and signed off on the final format. C.M.M. receives grant funding from Merck and has served as a consultant for Scynexis. C.H. is a member of the Seres Therapeutics, Empress Therapeutics, and ZOE Nutrition scientific advisory boards. E.S.L. serves on the board of directors for Codiak BioSciences and on the scientific advisory board of F-Prime Capital Partners and Third Rock Ventures; he is also affiliated with several non-profit organizations, including serving on the board of directors of the Innocence Project, Count Me In, and the Biden Cancer Initiative, and the board of trustees for the Parker Institute for Cancer Immunotherapy. He has served and continues to serve on various federal advisory committees. R.J.X. is a consultant to Nestl?.

Funding Information:
C.M.M. receives grant funding from Merck and has served as a consultant for Scynexis. C.H. is a member of the Seres Therapeutics, Empress Therapeutics, and ZOE Nutrition scientific advisory boards. E.S.L. serves on the board of directors for Codiak BioSciences and on the scientific advisory board of F-Prime Capital Partners and Third Rock Ventures; he is also affiliated with several non-profit organizations, including serving on the board of directors of the Innocence Project, Count Me In, and the Biden Cancer Initiative, and the board of trustees for the Parker Institute for Cancer Immunotherapy. He has served and continues to serve on various federal advisory committees. R.J.X. is a consultant to Nestlé.

Funding Information:
We thank T. Poon, L. Besse, S. Steelman, and C. Nusbaum (Broad Institute) for help in sequence production and sample and data management; V. Subramanian and T. Arthur for experimental methods support and helpful discussions; T. Reimels for valuable figure and text support; the nurses, midwives, and clinicians at the Labor and Delivery Department at Massachusetts General Hospital for their enthusiastic collaboration during enrollment; and the families that agreed to enroll and donate samples. C.M. was supported by the Vincent Memorial Research Funds ; E.S.L. was supported by National Human Genome Research Institute grant 2U54HG003067-10 ; R.J.X. was supported by funding from JDRF , CCFA , and NIH grants R01 DK092405 and P30 DK043351 ; and M.Y. was supported by NIH grant DK113224-01 , Israel Science Foundation grant 2660/18 , an Azrieli Foundation Faculty Fellowship , and a BroadIgnite early career grant from the Broad Institute of MIT and Harvard .

Publisher Copyright:
© 2020 The Author(s)

Keywords

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

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