The persistent effects of birth mode on gut microbiota composition, immune system development and antimicrobial resistance

Written by
Dr Fathalla Ali, PHD Paediatrics

Reviewed By
Dr Daniella Susic
FRANZCOG, BMed (Dist), Senior Lecturer UNSW


It is believed that mode of birth (Vaginal or Caesarean) has a significant effect on early gut microbiota acquisition and development. Globally, the rate of caesarean birth is consistently increasing as a result of multiple factors. Among these factors are the increase in the overall income and the easy access to health facilities. In 2015, around 29.7 million births happened by caesarean, accounting for about 18% of the births in 169 countries.

In recent study, Busi et al (2021) hypothesized that mode of birth elicits longer-term functional microbiome changes which may impact neonatal health and development. They investigated whether the difference in microbiota composition and it’s impacts on host physiology (specifically, immunogenic properties and their role in conferring antimicrobial resistance) persisted at 1 year. The study included 11 babies delivered by caesarean and 9 babies delivered vaginally. Babies were followed up during their first year of life at 1 month, 6 months and 1 year of age.


Results from this study showed that:

  • The structure of the microbiota community was influenced by mode of birth and babies’ age. Babies’ age was found contribute most to the variation in microbiota structure within and between both modes of birth.
  • A persistent difference in structural and functional of gut microbiota was identified in babies born by caesarean.
  • Colonization by a commensal microbiota generally associated with being a ‘healthy human’ such as Bifidobacterium and Faecalibacterium were increased in vaginal birth babies.
  • The alteration in the gut microbiota in caesarean born babies impacted the status of the immune system throughout the first year of life, which could explain the immunological association with the development of chronic diseases developed in children born by caesarean.
  • The immune activation potential of Lipopolysaccharides (LPS) was found to be significantly decreased in samples from babies born by caesarean.
  • Compared with vaginally born babies, caesarean born babies showed an increase in the abundance an Antimicrobial Resistant AMR genes at early days of life (5 days).
  • The early AMR resistance in caesarean born babies at day 5 was mainly attributed to Bacilli while Lachnospiraceae, BacteroidaceaeActinobacteriaand Oscillospirales were the main contributors to AMR at 1 year.
  • The number of AMR genes in caesarean born babies decreased significantly at 1 year compared with 5 days.
  • The enrichment biosynthesis of specific genes that are used clinically in fighting Gram-positive and Gram-negative pathogens was associated with vaginal birth. These genes are Carbapenem and Phenazine.
  • Caesarean birth is associated with resistant against semi- and synthetic antibiotics from early days of life.
  • In vaginal born babies, the AMR resistance at day 5 was attributed to the abundance of BacteroidalesLactobacillalesPropionibacteraceae and Enterobacteriaceae

Keywords: Microbiota, mode of birth, Caesarean section birth, Vaginal birth, immune system, antimicrobial resistant.


Busi, S.B., de Nies, L., Habier, J. et al. Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life. ISME COMMUN. 1, 8 (2021).


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