Studies exploring the neonatal microbiome during early life have been performed mainly in the hospital setting, with both mode of delivery and antibiotics having the most profound impact on the microbiome. However, the development of the neonatal microbiome in the absence of routine hospital interventions during delivery has not yet been studied.

A new study, led by Prof. Maria Gloria Dominguez-Bello from the New York University School of Medicine and Rutgers University (USA), has found that hospital versus home delivery is linked with differences in the maternal vaginal microbiota and fecal microbiota of neonates that last until 1 month of age.

The researchers analyzed the structure of stool microbiota from vaginally-delivered babies born in hospital (n = 21) or at home in air or in water (n = 14), together with both the fecal and vaginal microbiota from their mothers. Babies born at home did not receive antibiotic treatment during the first month of life. Samples were collected at baseline, at birth and at different time points until 1 month of age.

Infant exposure to maternal peripartum antibiotics did not affect fecal microbiota diversity neither in hospital-born infants nor in home-born infants. Furthermore, home-born babies who were born in water (n = 4) showed higher relative abundances of Erysipelotrichaceae and Comamonadaceae families compared with air-born infants, with no differences in alpha diversity. However, these data should be considered with caution given the small sample size.

Hospitalization led to alterations in the fecal neonatal microbiota that were more apparent at day 2 of life. Specifically, hospital-born infants not exposed to perinatal maternal antibiotics or water birth showed lower proportions of Bacteroides, Bifidobacterium, Streptococcus and Lactobacillus and higher proportions of Clostridium, Enterobacteriaceae and Citrobacter when compared with home-born infants. These changes resembled the same effects of C-sections, antibiotics and formula feeding on the gut microbiome.

At birth, mothers who delivered in the hospital showed a higher alpha diversity of the vaginal microbiota—with an increase in Lactobacilluswhen compared with mothers who delivered at home.

When exploring the impact of neonates’ fecal microbiota on modulating epithelial gene expression, the researchers found that fecal microbiota from hospital-born infants at 1 month of age led to a higher pro-inflammatory gene expression—including microbial product sensing toll-like receptor 4, interleukin-8, occludin and tumor growth factor beta (TGFb)—in human colon epithelial cells. Furthermore, some correlations were found between Bacteroides genus and expressions of TGFb and occludin.

On the whole, the results of this study suggest that hospitalization may have an impact on maternal vaginal microbiota and neonate fecal microbiota, with effects that persist up to 1 month after birth. Due to its observational design and the short-term follow-up, the implications of these findings with regard to long-term infant health deserve further in vivo research.




Combellick JL, Shin H, Shin D, et al. Differences in the fecal microbiota of neonates born at home or in the hospital. Sci Rep. 2018; 8(1):15660. doi: 10.1038/s41598-018-33995-7.