The Lingering Impact of Birth Mode

Written by Clare Carrick ANutr (BHSc)

Scientifically reviewed by Dr Fathalla Ali, PHD Paediatrics


No woman should ever feel any guilt or judgment surrounding the way her baby was born. Every birth is an act of heroism in its own special way.

Comparisons between C-sections and ‘natural births’ are loaded. It’s a huge topic, and it requires an equally huge level of sensitivity – but, it is also of vital importance that the science highlighting the differences between the gut microbiome of a C-section baby compared to a vaginally born baby is getting out there, and that it’s not pushed awkwardly to the side, for fear of offending people. 

C-sections are life savers, and we are so lucky they exist, however, their usage is increasing (not necessarily by choice!), and not everyone is made aware of the potential impact that this may have on the future health of their baby (1). If you are lucky enough to have a choice of birth mode for your baby, it’s powerful to know the facts.

This article will highlight some of the main differences seen between the gut microbiome of vaginally born babies, compared to the gut microbiome of C-section babies, in the first year of life (2).


What Do We Know So Far?

The baby’s first year of life offers a ‘critical window’ for physical growth and the healthy development of the immune system (2). We know that the baby’s gut microbiome, how well it functions, and the types of bugs it houses, plays a huge role in this development (2). We also know that whether a baby is born vaginally or via C-section, whether they’re breast or formula-fed, and any medications they may be given, all have a pretty dramatic impact on the composition of a baby’s gut microbiome in those early days (2). 

One study comparing the gut microbiome of vaginally born babies to c-section born babies at 1 month of age, 6 months of age, and then 1 year of age found some fascinating differences between the two (2). Here are five interesting takeaways from the study (2)*.


  1. The gut microbiome of C-section babies remained persistently different from vaginally-born babies in their 1st year of life.
  2. Babies born vaginally had more of the ‘beneficial’ gut bugs, like Bifidobacterium and Faecalibacterium. Generally speaking, people with more of these gut bugs tend to be considered ‘healthy people’.
  3. The gut microbiome in C-section babies affected their immune system status during that first year of life, which may be one of the reasons why C-section babies often end up with more chronic diseases, like metabolic disorders and allergy. At one year, C section babies had higher pro-inflammatory immune responses than vaginally born babies.
  4. A gut bug species known as Faecalibacterium prausnitzii (what a mouthful!) was found to be more abundant in vaginally born babies at one year of age. This particular species is associated with more richness and diversity of the gut microbiome, which we know is a good thing for overall health.
  5. The gut microbiome alterations associated with C-sections might allow the less beneficial gut bugs to ‘hold more ground’ in the baby’s gut, including some that may trigger antibiotic resistance. C-section babies showed signs of antibiotic resistance as early as 5 days of age.  


How Is This Knowledge Helpful?

This information is critical for parents-to-be, those who’ve already had babies, and healthcare professionals everywhere. 


For parents-to-be, understanding the impact that birth mode has on your baby’s gut and future health can help you to weigh up pros and cons if you are presented with a choice of birth mode. If you’ve had to undergo a C-section, or you’ve decided a C-section is the best option for your situation, this knowledge can still empower you to explore other known ‘gut-microbiome-supporting’ options that can positively impact your newborn’s gut, such as breastfeeding or owning a pet (3)!


On top of all this, information like this paves the way for more research into interventions that may help resolve imbalances in a C-section baby’s gut microbiome (1). Current research on interventions like vaginal seeding (where vaginal bacteria is transferred to a newborn – do not try at home!), and the use of probiotic supplements for newborns are promising, and may help to restore a C-section bub’s gut microbiome with all the beneficial bacteria they need for a strong start to life (4, 5). 


  1. Betran AP, Ye J, Moller AB, Souza JP, Zhang J. Trends and projections of caesarean section rates: global and regional estimates. BMJ Global Health. 2021 Jun 1;6(6):e005671. 
  2. Busi SB, de Nies L, Habier J, Wampach L, Fritz JV, Heintz-Buschart A, May P, Halder R, de Beaufort C, Wilmes P. Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life. ISME Communications. 2021 Mar 26;1(1):1-2. 
  3. Stewart CJ, Ajami NJ, OBrien JL, Hutchinson DS, Smith DP, Wong MC, Ross MC, Lloyd RE, Doddapaneni H, Metcalf GA, Muzny D. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature. 2018 Oct;562(7728):583-8. 
  4. Song SJ, Wang J, Martino C, Jiang L, Thompson WK, Shenhav L, McDonald D, Marotz C, Harris PR, Hernandez CD, Henderson N. Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding. Med. 2021 Aug 13;2(8):951-64.
  5. Duar RM, Kyle D, Tribe RM. Reintroducing B. infantis to the cesarean‐born neonate: an ecologically sound alternative to “vaginal seeding”. FEMS Microbiology Letters. 2020 Mar;367(6):fnaa032.

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