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Dysbiosis in infancy: c-section births and the gut health

8 mins


The gut microbiome is home to approximately 38 trillion microbes.1 While a healthy gut microbiome is difficult to define, since gut microbiota composition is highly variable amongst individuals, a hallmark feature of gut health is microbial diversity.2 This article explores the effects of delivery mode and nutrition, which are major determinants of the gut microbiome during infancy.3


What is Caesarean section?

A caesarean section (known as a c-section), is a surgical procedure performed when a vaginal delivery is not possible or carries risk to the health of the mother or infant. During the procedure, the infant is delivered through a surgical incision made in the abdomen and the uterus.4 In the UK, approximately one in four pregnant women has a c-section.4

The effects of dysbiosis on health

Dysbiosis can generally be defined as:5

  • An increase in potentially harmful microbiota

  • Reduced microbial diversity

  • Limited beneficial microbiota

There are many factors throughout the lifespan which can alter microbial composition and potentially drive dysbiosis, including mode of birth (caesarian delivery), age and antibiotic use.5

Research has shown that the gut microbiota of c-section infants is significantly different from that of vaginally delivered infants, partly due to the absence of exposure to the birth canal which contains beneficial microbiota including Lactobacillus reuteri and L. rhamnosus.3,6 Dysbiosis can be implicated in the pathophysiology of autoimmune and metabolic conditions including food allergy, asthma, diabetes and obesity.3

The role of breastfeeding in shaping the gut microbiome

Nutrition is a significant factor in shaping microbiota composition during infancy. Breastfeeding modulates the gut microbiome in early life, both directly by exposure of the infant to the milk microbiota and indirectly, via maternal milk factors that affect bacterial growth, including human milk oligosaccharides (HMOs).7

HMOs are the third largest solid component in breastmilk (BM) and have been shown to play an important role in the development of the gut microbiome in breastfed infants.8,9 A recent multicentre trial randomly assigned healthy infants between 7-21 days old to a standard cow's milk-based infant formula (CMF) or equivalent formula containing either 1.5 g/L or 2.5 g/L of five HMOs (2'-fucosyllactose, 2',3-di-fucosyllactose, lacto-N-tetraose, 3'-sialyllactose, and 6'-sialyllactose). Stool samples were analysed at baseline, three and six-years of age. Populations of ‘Bifidobacterium longum’ and ‘B. Infantis' were found to be higher in the microbiomes of infants given HMO formula in comparison to the CMF. Fewer pathogenic species e.g., ‘Clostridioides difficile’ were also found in infants fed with the HMO formula. Separated by delivery mode, a similar pattern was observed, particularly in the infants delivered by cesarean-section. Feeding a blend of 5 HMOs (2’FL, DFL, LNT, 3’SL,& 6’SL) can shift the gut microbiota of C-section born infants closer to breastfed and vaginally born infants by increasing beneficial Bifidobacterium. It was concluded that infant formula containing a specific blend of five HMOs, can support a shift in the gut microbiome towards that of breastfed infants.10

The risks of vaginal seeding

Other methods of increasing gut microbial diversity in infants includes “vaginal seeding”, which describes the transfer of maternal vaginal microbiota to an infant born by c-section.11 It’s proposed that vaginal seeding might restore the microbiota of infants born by caesarean section towards a state of infants born by vaginal birth and decrease the risk of disease.11 However, there is a risk that infants may develop severe infections from exposure to vaginal commensals and pathogens, including group B. streptococcus and herpes simplex virus. In the absence of evidence of benefit, or guidelines to ensure safe practice, many hospital trusts advise against vaginal seeding.12


Various factors including birth delivery can impact the gut microbiome.3 Breastfeeding has an important role in the establishing the gut microbiome during infancy. With increasing artificial HMOs* becoming available, it is possible to supplement formulas with blends of HMOs, providing complex oligosaccharides to formula-fed infants.13

HMO* - structurally identical Human Milk Oligosaccharides, not sourced from breastmilk

  1. Sender R, et al. 2016. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biology;14(8):e1002533.

  2. Berg G, et al. 2020. Microbiome definition re-visited: old concepts and new challenges. Microbiome;8:103.

  3. Zhang C, et al. 2021. The Effects of Delivery Mode on the Gut Microbiota and Health: State of Art. Frontiers in Microbiology;12:4084

  4. National Health Service (NHS). Caesarean section. [Internet]. 2019. [cited August 2022]. Available from:

  5. Petersen C, Round J. 2014. Defining dysbiosis and its influence on host immunity and disease. Cellular Microbiology;16(7):1024-33.

  6. Dominguez-Bello MG, et al. 2010. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences;107(26):11971-11975.

  7. van den Elsen L, et al. 2019. Shaping the gut microbiota by breastfeeding: The gateway to allergy prevention? Frontiers in Pediatrics;7(FEB):47.

  8. Sánchez C, et al. 2021. Human Milk Oligosaccharides (HMOs) and Infant Microbiota: A Scoping Review. Foods;10(6).

  9. Lewis Z, et al. 2015. Maternal fucosyltransferase 2 status affects the gut bifidobacterial communities of breastfed infants. Microbiome;3(1):1-21.

  10. Bosheva M, et al. 2022. 5 HMO Study Investigator Consortium. Infant Formula With a Specific Blend of Five Human Milk Oligosaccharides Drives the Gut Microbiota Development and Improves Gut Maturation Markers: A Randomized Controlled Trial. Frontiers in Nutrition;9:920362.

  11. Mueller N, et al. 2015. The infant microbiome development: mom matters. Trends in Molecular Medicine;21(2):109-117.

  12. Cunnington A, et al. 2016. ”Vaginal seeding” of infants born by caesarean section. British Medical Journal;352. doi:10.1136/BMJ.I227

  13. Bosheva M, et al. 2022. Infant Formula With a Specific Blend of Five Human Milk Oligosaccharides Drives the Gut Microbiota Development and Improves Gut Maturation Markers: A Randomized Controlled Trial. Frontiers in Nutrition;0:1315.


We believe that breastfeeding is the ideal nutritional start for babies, and we fully support the World Health Organization’s recommendation of exclusive breastfeeding for the first six months of life followed by the introduction of adequate nutritious complementary foods along with continued breastfeeding up to two years of age. We also recognise that breastfeeding is not always an option for parents. We recommend that healthcare professionals inform parents about the advantages of breastfeeding. If parents choose not to breastfeed, healthcare professionals should inform parents that such a decision can be difficult to reverse and that the introduction of partial bottle-feeding will reduce the supply of breast milk. Parents should consider the social and financial implications of the use of infant formula. As babies grow at different rates, healthcare professionals should advise on the appropriate time for a baby to begin eating complementary foods. Infant formula and complementary foods should always be prepared, used and stored as instructed on the label in order to avoid risks to a baby’s health.