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Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer


Exposure of newborns to the maternal vaginal microbiota is interrupted with cesarean birthing. Babies delivered by cesarean section (C-section) acquire a microbiota that differs from that of vaginally delivered infants, and C-section delivery has been associated with increased risk for immune and metabolic disorders. Here we conducted a pilot study in which infants delivered by C-section were exposed to maternal vaginal fluids at birth. Similarly to vaginally delivered babies, the gut, oral and skin bacterial communities of these newborns during the first 30 d of life was enriched in vaginal bacteria—which were underrepresented in unexposed C-section–delivered infants—and the microbiome similarity to those of vaginally delivered infants was greater in oral and skin samples than in anal samples. Although the long-term health consequences of restoring the microbiota of C-section–delivered infants remain unclear, our results demonstrate that vaginal microbes can be partially restored at birth in C-section–delivered babies.

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Figure 1: Restoring the maternal microbiota in infants born by C-section.
Figure 2: Transmission of maternal vaginal microbes to the gauze.

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This work was partially supported by the C&D Research Fund (M.G.D.-B.), the US National Institutes of Health grant no. R01 DK090989 (M.G.D.-B), the Crohn's and Colitis Foundation of America grant no. 362048 (J.C.C.) and the Sinai Ulcerative Colitis: Clinical, Experimental & Systems Studies philanthropic grant (J.C.C.). Sequencing at the New York University Genome Technology Center was partially supported by the Cancer Center Support grant no. P30CA016087 at the Laura and Isaac Perlmutter Cancer Center. Computing was partially supported by the Department of Scientific Computing at the Icahn School of Medicine at Mount Sinai. We acknowledge the contribution of the students who participated in obtaining the samples and the metadata: S.M. Rodriguez, J.F. Ruiz, N. Garcia and J.L. Rivera-Correa. We also thank M.J. Blaser for discussions and critical comments, and three anonymous reviewers for their suggestions to improve this manuscript.

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Authors and Affiliations



M.G.D.-B. designed the study. M.G.D.-B., K.M.D.J.-L., J.I.R.-V. and K.M. collected and processed specimens. M.G.D.-B. sequenced and generated data. N.S., L.M.C., A.A., A.G., N.A.B., S.J.S., M.H. and J.C.C. performed experiments. M.G.D.-B., N.S., L.M.C., A.A., A.G., N.A.B., S.J.S., M.H., R.K. and J.C.C. analyzed data. M.G.D.-B. and J.C.C. drafted the manuscript. All authors reviewed the final manuscript.

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Correspondence to Maria G Dominguez-Bello or Jose C Clemente.

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Competing interests

New York University has filed a US patent application (number 62161549) related to methods for restoring the microbiota of newborns on behalf of M.G.D.-B.

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Dominguez-Bello, M., De Jesus-Laboy, K., Shen, N. et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat Med 22, 250–253 (2016).

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