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

C-sections, Gut health, and Your Bub

Written by
Clare Carrick ANutr (BHSc Nutrition and Health Promotion)

Scientifically reviewed by
Dr Fathalla Ali, PhD (Paediatrics)


From the minute you see those two lines appear on the pregnancy test, many hours are spent discussing and planning out exactly how the birth will go…. ‘Have you got a playlist?’, ‘Will you consider a water birth?’, ‘What are your thoughts on epidurals and other drugs?’, ‘Have you heard of hypnobirthing?’. For some women, for a variety of reasons, a Caesarean section (C-section) is performed to bring the baby into this world.

C-sections Save Lives

C-sections are an absolutely critical procedure in some cases, saving many lives and protecting women and their babies from serious disability or illness (1). We are incredibly lucky to live in an age where these types of procedures are possible. As C-section rates continue to increase around the world, however, it is important to examine any potential downsides to C-sections, to help empower women and their healthcare teams to make the best choice for themselves, and their babies (1).

Gut Stuff

In recent years, the importance of the health of our gut microbiome, and its flow-on effect for so many other aspects of our health, has become clear (2). One of the major players in how our baby’s gut microbiome is established and continues to develop is whether they are born vaginally or via C-section (2).


Some fairly sizeable differences have been observed when comparing the gut microbiome of vaginally born babies to C-section babies (2). In vaginally born babies’ guts, one particular bacteria known for its health benefits, Bifidobacteria, has been found in larger quantities than in C-section babies (2). Even if C-section babies are breastfed, the Bifidobacterium levels seem to stay lower than in vaginally born babies, emphasising the impact of the delivery mode on the abundance of this bacteria (2). In fact, vaginally born, formula-fed babies commonly have more gut Bifidobacteria than breastfed C-section babies (2). In C-section babies, bacteria that are considered more pro-inflammatory, like Staphlococcus, Klebsiella and Enterococcus, are more likely to be abundant than in vaginally born bubs (2).

But What Does This Actually Mean for Baby?

An increased chance of allergies has been observed in C-section babies, which may have something to do with the increased Klebsiella:Bifidobacterium ratio being more common in C-section babies (2).

The risk of respiratory infections also seems to increase in the first year of life for C-section babies compared to vaginally born, and so too does the chance of bub needing to take an antibiotic before their first birthday (2). Greater amounts of the bacteria Klebsiella and Enterococcus has been linked to increased respiratory infections later in life, and are commonly over-represented in C-section babies. In contrast, having higher counts of the Bifidobacterium and Bacteroides bacteria, typically more abundant in vaginally born babies, seems to protect babies from these illnesses (2).

But I Had No Choice!

This article is definitely not intended to stress out anybody who had to have a C-section for medical reasons! Although present, the differences in health outcomes between vaginally born babies and C-section babies is still only modest, and there are a number of other factors that continue to play a part in the development of Bub’s microbiome after birth (2). It is, however, important to address the impact that a C-section may have on a baby’s future health, so that if women are lucky enough to be in the position where a choice is possible, they will feel empowered to make a well-informed choice with the facts available to them,

Keywords: Disease, Bifidobacteria, Allergy, Breastfeeding


  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. Reyman M, van Houten MA, van Baarle D, Bosch AA, Man WH, Chu ML, Arp K, Watson RL, Sanders EA, Fuentes S, Bogaert D. Impact of delivery mode-associated gut microbiota dynamics on health in the first year of life. Nature communications. 2019 Nov 1;10(1):1-2.
  3. Low JS, Soh SE, Lee YK, Kwek KY, Holbrook JD, Van der Beek EM, Shek LP, Goh AE, Teoh OH, Godfrey KM, Chong YS. Ratio of Klebsiella/Bifidobacterium in early life correlates with later development of paediatric allergy. Beneficial microbes. 2017 Oct 13;8(5):681-95.

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