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The way our babies are born affects their gut microbiome composition, their immune system development and their resistance to medicines, such as antibiotics, used to treat infections and diseases

Written by
Dr Daniella Susic
FRANZCOG, BMed (Dist), Senior Lecturer UNSW

Scientifically reviewed by
Dr Fathalla Ali, PhD Paediatrics


Caesareans can be a life saving necessity in the birth of a baby. Current scientific research into the development of a baby’s gut microbiome suggests that the way a baby is born, i.e. vaginally or by caesarean, can have a significant effect on the early development of the baby’s gut microbiome.


Since 1990, the global rate of caesarean section has increased steadily with greatest increases were noticed in Eastern Asia (44.9% point increase), Western Asia (34.7% point increase) and Northern Africa (31.5% point increase, respectively). The latest date obtained from 154 countries covering 94.5% of world live births between 2010-2018 shows that 21.1% of women gave birth by caesarean section worldwide and is anticipated to reach 28.5% by 2030 (2).


In Australia in 2019, of the 298,567 mothers who gave birth, 107,543 (36%) gave birth by caesarean section (3). This is consistent with an increase in caesarean section rate seen from 31% in 2008 to 35% in 2018 (4)


In a recent study (1) Busi and his colleagues sought to discover whether mode of birth, Vaginal Delivery or Caesarean, resulted in long term changes in the gut microbiome of the baby that may impact on the baby’s health and development. They specifically looked at the differences that mode of delivery made to the microbiota (the various microbes and bacteria) composition of the baby’s gut microbiome and how this impacted the immune system development of the baby and the baby’s resistance or otherwise to antibiotics at 1 year of age.


The study showed:

  • The structure of the microbiota in the gut microbiome of the baby was influenced by the mode of delivery as well as the number of weeks the baby was delivered at. The number of weeks the baby was delivered at had a high impact on the structure of the microbiota in the baby’s gut microbiome depending on which mode of birth was used.


  • After birth and as the baby grew, persistent differences in structural and functional gut microbiota were identified in babies born by caesarean.


  • Two beneficial bacteria associated with health, Bifidobacterium and Faecalibacterium were increased in babies born vaginally.


  • The difference in the gut microbiota in babies born by caesarean affects the status of the baby’s immune system throughout the first year of the baby’s life and this could explain the decreased ability of the baby’s immune system to prevent chronic diseases.


  • In the caesarean born babies there were more genes that were resistant to antibiotics at day 5 of life than in the babies delivered vaginally at day 5 of life but these decreased in the caesarean born babies by the time they were 1 year.


  • Caesarean birth is associated with resistance against semi- and synthetic antibiotics from early days of life in the baby.


Microbiota, Mode of Birth, Cesarean section birth, Vaginal birth, immune system, antimicrobial resistant.


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