Anton Simeonov Ph.D. National Institute of Health

Establishment of Complete Microbiota Helps Drive Immune Development and Metabolic Programming of Newborn Babies


Figure A. Infants born by C-section were swabbed with a gauze that was incubated in the maternal vagina 60 min before the C-section. All mothers delivering by C-section received antibiotics (ABX) as part of standard-of-care treatment (top). The gauze was extracted before the procedure, kept in a sterile (middle) container and used to swab the newborn within the first 1–3 min after birth, starting with the mouth, then the face and the rest of the body (bottom).

By now, it is well established that newborn babies stand to benefit long term from exposure to commensal microorganisms during the birth process, as establishment of complete microbiota helps drive immune development and metabolic programming. Conversely, incomplete or skewed microbial colonization at birth has been associated with long-term effects on human metabolism or impaired immune development. Further, the lack of complete microbiota in babies born through a cesarean section, relative to vaginally delivered babies, has been documented. In an effort to correct for this deficiency, Dominguez-Bello and colleagues evaluated a microbiota restoration procedure, called vaginal microbial transfer, which involved incubating sterile gauze in the vagina of healthy mothers prior to them giving birth through a cesarean section and, within the first 2 min of birth, swabbing the newborns with the gauze, covering their mouth, face, and the rest of their bodies (Figure a). The study included a total of 18 babies, of whom 7 were born vaginally and the remaining 11 through scheduled C-section, with 4 of the 11 receiving the above maternal vaginal fluid treatment. The team noted that microbial colonization of the various vaginal fluid application sites in the newborns occurred quickly, within days. The authors further noted that bacterial source tracking of the infant microbiome revealed that the microbiomes of the four C-section–delivered infants exposed to vaginal fluids resembled those of vaginally delivered infants, and that Lactobacillus species were detected in anal samples from exposed infants, matching their vaginally delivered counterparts, while those newborns that were not exposed to vaginal fluids lacked this key component of human gut microbiota. There were no reports of negative reactions associated with the procedure. The present study provides an excellent proof of principle for this extremely simple procedure. However, a much larger study size combined with monitoring the cohort for a longer period will likely be needed in order to ascertain benefit.

Figure B. Restoring the maternal microbiota in infants born by C-section.

* Abstract from Nat Med 2016;22:250–253

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.

Figure C.


Figure D. Representative bacterial taxa enriched in infants with perinatal exposure to vaginal fluids during the first month of life. S24, Bacteroidales family S24-7 members. Error bars indicate mean ± s.d.

Anton Simeonov, Ph.D., works at the NIH.

ASSAY & Drug Development Technologies, published by Mary Ann Liebert, Inc., offers a unique combination of original research and reports on the techniques and tools being used in cutting-edge drug development. The journal includes a "Literature Search and Review" column that identifies published papers of note and discusses their importance. GEN presents here one article that was analyzed in the "Literature Search and Review" column, a paper published in Nature Medicine titled "Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer." Authors of the paper are Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, Bokulich NA, Song SJ, Hoashi M, Rivera-Vinas JI, Mendez K, Knight R, Clemente JC.

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