A recent study published in Pediatric Allergy & Immunology (Nieto et al., 2025) looked at whether personalised support for the gut microbiome could help infants born via caesarean section (C-section) develop a healthier gut and reduce the risk of immune-related conditions. The trial included full-term C-section babies aged 0–3 months, who were randomly assigned to either an intervention group (n = 25) or a control group (n = 29).
Babies in the intervention group received two microbiome reports, tailored recommendations, educational resources, and six months of coaching for their parents. The researchers focused on how the babies’ gut microbiomes developed, specifically tracking the presence of beneficial bacteria like Bifidobacterium and genes that help break down nutrients in breast milk. They also measured how closely each baby’s microbiome resembled that of infants born vaginally.
At the end of the study, babies in the intervention group had higher levels of Bifidobacterium, more genes for digesting nutrients from breast milk, and a microbiome pattern similar to vaginally born infants. They also had a significantly lower rate of atopic dermatitis compared to the control group.
In short, giving C-section babies targeted support for their gut bacteria in the first months of life may help their microbiome develop more healthily and reduce early risks of allergies and immune issues.
Why Is This Important?
The early-life gut microbiome plays a foundational role in immune system development, metabolic programming, and even allergy and atopy risk. Delivery via C-section is associated with altered microbial colonisation in the newborn gut (for example, lower colonisation of bifidobacteria) and has been linked to higher risks of conditions such as eczema, food allergy, asthma, and other immune-related disorders (Catassi et al., 2025).
Addressing this early microbial difference is important because:
Research has clearly documented that the first 1000 days of life are a critical window for establishing positive long-term health outcomes.
If infants can be supported to develop a healthier gut microbiome, we might reduce their risk of immune dysfunction or atopic disease later in life.
C-section births are common, so any accessible or non-invasive intervention with benefits to the microbiome has wide-ranging potential.
The study shows how early microbiome intervention is emerging as a practical lever for health optimisation, and it is likely not just a theoretical concept.
Key Recommendations
Based on the trial findings and broader microbiome science, here are practical recommendations for health professionals and parents of infants (especially C-section born):
For infants born via C-section, consider early microbiome-support strategies, especially within the first three months of life.
Use or support interventions that include personalised assessment (microbiome testing or other markers where available), education, and ongoing support/coaching rather than simply prescribing a generic probiotic.
Encourage practices that promote colonisation of beneficial gut bacteria — for example, breastfeeding, which supports Bifidobacteria. Many studies document that breastfeeding is one of the most beneficial practices for a baby’s immune system (Patnode et al., 2025).
Limit unnecessary early antibiotic exposure and promote skin-to-skin contact.
Once solid food is introduced to the infant’s diet, include foods that promote the growth of beneficial gut bacteria, such as a wide variety of fibre-rich plant foods, colourful fruits and vegetables, and fermented options.
Monitor infant health for early signs of atopic disease (eczema, food allergy) — especially in higher-risk groups (C-section, family history) — and consider microbiome interventions as part of a holistic preventive approach.
Encourage environmental exposure to varied environments, including pets, soil, and natural settings. This supports the development of a diverse gut microbiome in infancy. Such exposure has been linked to increases in beneficial bacteria like Ruminococcus and Oscillospira and reductions in Streptococcus, potentially lowering risks of allergies and metabolic disease.
Communicate clearly to parents that microbiome intervention is only one piece of the puzzle. Good nutrition, minimising exposures harmful to microbial development (for example, excessive antibiotic use), and supporting healthy infant feeding/immune development remain critical.
Conclusion
This study highlights how personalised microbiome support in early life can help C-section-born infants develop a healthier gut and reduce the risk of conditions like eczema. Supporting the infant microbiome through breastfeeding, limiting unnecessary antibiotics, offering fibre-rich whole foods, and encouraging outside play with exposure to diverse environments can all make a difference.
With C-section births increasingly common, simple, evidence-based strategies that nurture the gut microbiome in the first months of life may help set the foundation for stronger immunity and better long-term health.
References
Nieto, P. A., Nakama, C., Trachsel, J., Goad, D., Soderborg, T. K., Tan, D. S., Orlandi, A., Yuan, Q., Song, E., & Mueller, N. T. (2025). Improving immune-related health outcomes post-cesarean birth with a gut microbiome-based program: A randomized controlled trial. Pediatric Allergy and Immunology, 36(9), e70182. https://doi.org/10.1111/pai.70182
Catassi, G., Garcia Mateo, S., Occhionero, A. S., Esposito, C., Giorgio, V., Aloi, M., Gasbarrini, A., Cammarota, G., & Ianiro, G. (2024). The importance of gut microbiome in the perinatal period. European Journal of Pediatrics, 183(10), 5085–5101. https://doi.org/10.1007/s00431-024-05795-x
Patnode, C. D., Henrikson, N. B., Webber, E. M., Blasi, P. R., Senger, C. A., & Guirguis-Blake, J. M. (2025). Breastfeeding and health outcomes for infants and children: A systematic review. Pediatrics, 156(1), e2025071516. https://doi.org/10.1542/peds.2025-071516
