Neonatal colonisation of bacteria affected by caesarean section

Published 30 September 2019

Findings from the largest ever study of the newborn microbiome offer the strongest evidence yet that children delivered vaginally carry different microbes from those delivered by caesarean section.

Previous studies have suggested that birth by caesarean section may be a risk factor for inflammatory conditions such asthma and other allergies by disrupting the neonatal colonisation of bacteria during the first days of life. The first study, which included only ten participants, was published in 2010 to conclude that four babies born vaginally acquired bacterial communities resembling their own mother's vaginal microbiota, in contrast to six babies born by caesarean section who harboured bacterial communities similar to those found on the skin surface.(1) A second study published in 2016 evaluated the microbial differences between vaginal birth and caesarean section in 700 babies to find significant differences in the first week of life, which would naturally normalise by the age of one year.(2)

Vaginal seeding was a novel idea introduced to restore the balance in the bacterial colonisation for babies born by caesarean section. The procedure involved incubating a sterile gauze in the vagina of mothers during the hour preceding the caesarean section followed by the swabbing of babies with the gauze, starting with the mouth, then face and finally the rest of the body within the first two minutes after birth. The first pilot study included four babies exposed to vaginal seeding and suggested that vaginal microbes could be partially restored at birth in babies delivered by caesarean section.(3) Despite the acknowledgement of unclear long-term health consequences of vaginal seeding, the procedure became so popular that over 90% of Danish obstetricians had already discussed vaginal seeding with their patients within the first year after the publication of the pilot study.

Consequently, a review of the evidence supporting vaginal seeding was published in BJOG and highlighted by the Royal College of Obstetricians and Gynaecologists (RCOG).(4,5) Experts concluded there was no robust evidence to suggest that vaginal seeding had any associated benefits and noted that some vaginal bacteria could be passed on to the baby, occasionally causing illness.

Now, the latest study in this evolving story has been published in Nature and analysed nearly 600 births in the United Kingdom. Authors sampled the stool from 314 babies born vaginally and 282 born by caesarean section to analyse the microbial DNA at 4, 7 and 21 days after birth.(6) Their findings demonstrate that the mode of delivery is indeed a significant factor affecting the composition of the gut microbiota throughout the neonatal period with babies born by caesarean section colonised by an abundance of opportunistic pathogens that are commonly associated with the hospital environment.

The enriched species identified in babies born by caesarean section included E. faecalis, E. faecium, E. cloacae, K. pneumoniae, K. oxytoca and C. perfringens, some of which are members of the ESKAPE (E. faecium, Staphylococcus aureus, K. pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) pathogens that are responsible for the majority of nosocomial infections.

The longer term follow up observed that microbiotas grew more similar in the months after birth, with the exception of Bacteroides, a genus known to influence the immune systems of their hosts and help to suppress inflammation, which were found absent or in very low levels following caesarean section. The study did not attempt to assess the health effects of these microbial differences later in life; however, the presence of disease-causing bacteria is a concern, according to Trevor Lawley, a microbiologist at the Wellcome Sanger Institute in Hinxton, UK, who led the study.

1. Dominguez-Bello MG, Costello EK, Contreras M, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A 2010; 107: 11971-11975.

2. Stokholm J, Thorsen J, Chawes BL, et al. Cesarean section changes neonatal gut colonization. J Allergy Clin Immunol 2016; 138: 881-889.

3. 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: 250-253.

4. Haahr T, Glavind J, Axelsson P, et al. Vaginal seeding or vaginal microbial transfer from the mother to the caesarean-born neonate: a commentary regarding clinical management. BJOG 2018; 125: 533-536.

5. RCOG press release:

6. Shao Y, Forster SC, Tsaliki E, et al. Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature 2019;

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