One of the early-life factors that strongly influences newborns’ gut microbiota development is delivery type. Previous observational data have shown that newborns delivered by C-section tend to harbor in their gut disease-causing microbes commonly found in hospitals (e.g. Enterococcus and Klebsiella), whereas they lack strains of gut bacteria found in healthy children and adults (e.g. Bacteroides spp.).

The observation that C-section babies fail to acquire some of the microbes from their mothers compared to vaginally delivered children led Maria Gloria Domínguez-Bello and colleagues to swab infants born by C-section with vaginal fluids from their mothers in an attempt to restore the microbiome they had missed. However, although the protocol (also known as vaginal seeding or microbial bath) includes testing for some infectious pathogens such as B Streptococcus, the method’s safety and health effects remain unclear.

Now, researchers are showing that orally delivered fecal microbiota transplantation can make the neonatal microbiota more similar to that of a vaginally born baby, as reported in a pioneering study published in Cell.

Korpela and colleagues collected fresh fecal samples and blood samples from 17 mothers, 3 weeks prior to delivery. Blood samples were screened for infectious pathogens such as HIV, hepatitis, Clostridioides difficile, Helicobacter pylori, norovirus, drug-resistant bacteria and group B Streptococcus, among others. Seven women qualified for the second step of the research, with 10 classed as ineligible and 29% of samples from the original 17 screening positive for pathogenic microbes.

In a second step, all 7 newborns received a dose of maternal fecal microbiota transplant (FMT)—containing on average 7 x 106 viable bacterial cells—in their first milk feed via a bottle and their health outcomes were monitored two days after delivery, and subsequently at 4 weeks and 3 months of age. Samples from 29 vaginally born babies and 18 untreated C-section babies were used as controls.

A 16S ribosomal ribonucleic acid analysis of stool samples revealed that the maternal microbiota was different compared to the microbiota of transplanted C-section-born infants, with the meconial microbiota the most distinct in comparison with the other fecal samples.

After a week, the gut microbiota of FMT-treated C-section babies resembled that of vaginally born infants, whereas both were distinct from the gut microbiota of untreated C-section babies. While C-section-born babies showed a consistent lack of Bacteroidales and Bifidobacteriales, FMT-treated C-section-born newborns exhibited a rapid normalization of Bacteroidales abundance. In addition, the relative abundance of potential pathogens remained lower in FMT-treated C-section-born babies at 1 week and 12 weeks compared to the C-section group. A concomitant effect of maternal FMTs was the increase in fecal microbiota diversity as early as the age of 1 week.

It should be acknowledged that the gut microbiota of newborns born vaginally or via C-section and who received FMT was different to that of C-section infants who received vaginal swabs (the latter data are available in microbiota datasets). The findings show that maternal fecal microbiota transplants can restore the gut microbiota in C-section-born infants, while vaginal swabbing failed to do the same.

None of the infants showed adverse effects or changes in weight during the 3-month follow-up period.

To sum up, this is the first preliminary study showing the potential effectiveness of maternal feces administered in human milk as a delivery system for restoring the microbiota composition of babies born by C-section, a type of delivery previously associated with metabolic and immune-related diseases. However, as the authors acknowledge in the discussion, the science is not yet mature enough for parents to use the procedure as a “do-it-yourself” practice, due to the inherent risk of transmitting harmful microbes.



Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat Med. 2016; 22(3):250-253. doi: 10.1038/nm.4039.

ACOG Committee on Obstetric Practice. Committee opinion no. 725. Vaginal seeding. Obstet Gynecol. 2017; 130:e274. doi: 10.1097/AOG.0000000000002402.

Wald A. Vaginal seeding – unproven benefits, potential risks. 2017 Nov 12 [cited 5 October 2020]. In: NEJM Journal Watch [Internet]. San Francisco: NEJM. [about 1 screen]. Available from:

Korpela K, Helve O, Kolho KL, et al. Maternal fecal microbiota transplantation in cesarean-born infants rapidly restores normal gut microbial development: a proof-of-concept study. Cell. 2020. doi: 10.1016/j.cell.2020.08.047.