OFFER EXTENDED: The entire MothersBabies course is free for a Limited Time. Access now

Differences in the Fecal Microbiota of Neonates Born at Home or in the Hospital

Written by
Dr Fathalla Ali, PHD Paediatrics


Many factors have been identified that alter the process of human microbiota development in early life. The prenatal, antenatal and postnatal period have been found to be the most developmentally sensitive times. The importance is that microbiota imbalance during these periods could lead to immune dysregulation with the implication to later life health. On the other hand, these developmentally sensitive periods may also offer opportunities to modify microbiota development to enhance healthier and more robust microbiota communities, and therefore potentially prevent future disease. Standard hospital intervention during labour and delivery such as antibiotics administration to the mother and baby, separation of mother and baby, and early infant bathing could reduce the chance of early microbiota transmission to the newborn infant. The hospital environment provides both an antiseptic environment for labour and delivery, as well as possible exposure to antibiotic resistant bacteria. To investigate the neonatal microbiota development in the absence of standard hospital intervention, a group of researchers conducted a prospective cohort study on 35 vaginally-delivered infants, and their 34 mothers to compare the gut microbiota from vaginally delivered babies born at home (14 babies) with babies born at hospital (21 babies). Study investigators found that the maternal gut microbiota is significantly different between those delivered at home and the hospital without antibiotic exposure. Additionally, hospitalization was associated with alterations in the neonatal microbiota structure during the first month of life:

  • Mother who delivered in the hospital showed lower alpha diversity, lower colonization rate of Corynebacterium, Dialister, Veillonella, Finegoldia, and Peptoniphilus, and higher colonization rate of Lactobacillus compared with mothers who delivered at home.
  • Low fecal alpha diversity in infants born in the hospital compared with babies delivered at home.
  • Lower colonization rate of Bacteroides (day 2), Bifidobacterium (day 7, 21, 28), Streptococcus (day 14, 21, 28), Lactobacillus (day 21) in hospital-born babies.
  • This pattern of colonization resembles the pattern of colonization due to some of other early life influences such as cesarean section delivery, antibiotic exposure and formula feeding.
  • Babies born in the hospital had higher colonization rate of Clostridium (day 21), Enterobacteriaceae (day 28) and Citrobacter (day 21, 28) than home-born babies. Higher Clostridium colonization in early life has been associated with increased risk of eczema and asthma at age 6-7 years.
  • Babies born in water (home delivered babies) showed higher relative abundances of Erysipelotrichaceae and Comamonadaceae families in compared with babies born outside water bath (home delivered babies).
  • Babies delivered in hospital exhibited a distinct capacity to induce a greater degree of pro-inflammatory gene expression at 1 month of age.

In conclusion, this study showed that home versus hospital birth of exclusively breastfed, vaginally delivered babies is associated with the difference in gut microbiota composition. Additionally, increased capacity for hospital-delivered fecal microbiota associated products were found to induce pro-inflammatory epithelial gene expression.


Combellick, J. L., Shin, H., Shin, D., Cai, Y., Hagan, H., Lacher, C., Lin, D. L., McCauley, K., Lynch, S. V., & Dominguez-Bello, M. G. (2018). Differences in the fecal microbiota of neonates born at home or in the hospital. Scientific reports, 8(1), 15660. Click here.

Search MothersBabies

Looking for something in particular? Find it here using our search query function. Simply type in your keyword and click the icon.

Recent Articles

Join Us