Optimizing the Pediatric Microbiome

The intestinal microbiome may evolve with the human host over its entire lifespan—from conception to death. Some scientists posit that early-life environmental exposures alter the development of the gut microbiome and that these changes may influence childhood development as well as the maturation of the immune system.^1-3 What factors influence a pediatric gut microbiome, and how might the health of the microbiome in early life impact the risk of chronic disease development as an adult?

Shaping the Early-Life Gut Microbiome & Chronic Disease

Continuing research on the microbiome suggests that a change to the composition of the pediatric intestinal microbiome known as dysbiosis may affect the development of inflammation⁴ and a variety of diseases —including, but not limited to, asthma and atopic disease, irritable bowel syndrome and inflammatory bowel disease, and obesity.^1,2,5 Researchers also speculate that caesarian delivery, formula feeding, and antibiotic use may alter the microbiome and promote the development of disease.⁶

Environmental factors like maternal diet, early-life stressors, and geographical location may influence the health of an infant’s intestinal microbiome.^1,5,6 A recent systematic review that investigated the composition of the pediatric gut microbiome found that study participants from non-Western locations reported higher levels of alpha-diversity (i.e., microbial richness and balance) and increased short-chain fatty acid concentrations compared to those from Western geographic locations.⁷ Researchers suggested that this may have been in part due to less exposure to Westernized dietary patterns in those areas.⁷

Research studies also suggest that delivery method, maternal mental and physical health, breastfeeding, and both maternal and pediatric antibiotic exposures may also shape a pediatric gut microbiome.^1,5,6,8-10 At the moment of a vaginal birth, neonates are exposed to the maternal vaginal microbiota, and the fecal microbiota of these neonates has been shown to have a dominating amount of Prevotella spp. and Lactobacillus.¹ Those born via cesarean section (CS) are more likely to have a microbiome dominated by microbes derived from maternal skin, the hospital environment, or hospital staff, such as Propionibacterium spp. and Staphylococcus.¹ Differences in the microbial population for vaginal versus CS-delivered infants also exists during the first week after birth; Bifidobacterium has been a primary microbe observed for vaginally delivered infants while Firmicutes has been the most prevalent for CS infants.¹ While this research continues, observational studies suggest that compared to vaginal delivery, CS delivery has been associated with increased risk of neurodevelopmental disorders in children.¹¹

BREASTFEEDING

Breastfeeding may influence the intestinal microbiota of neonates, through contact with maternal areolar and breast milk microbes.^1,2,5 Differences in intestinal microbes between exclusively breastfed vs. formula-fed infants have been well documented.¹ A 2024 systematic review compared the gut microbiota of breastfed and formula-fed infants and found those infants who were breastfed had higher levels of beneficial bacteria (i.e., Bifidobacterium and Lactobacillus) while those infants who were fed formula had a higher prevalence of  potentially pathogenic bacteria (i.e., Clostridium difficile and Enterobacteriaceae).¹² An additional 2024 observational study that included 55 mothers with infants reported that the gut microbiota diversity was the highest among those infants who were exclusively breastfed.¹³

In addition to a healthy microbiome, studies suggest that breastfeeding may support respiratory health in children and reduce the development of allergies and even the development of childhood obesity.^14-16 Results from a 2023 meta-analysis also suggested that breastfeeding in infancy was associated with lower risks of mortality in middle and late adulthood, including all-cause, cardiovascular, and respiratory mortalities.¹⁷

ANTIBIOTIC EXPOSURES

A significant early-life stressor on the pre- and postnatal microbiome is antibiotic exposure.¹⁸ Results from a 2021 systematic review indicated that maternal exposure to antibiotics during labor and delivery was associated with reduced microbial diversity in the infant’s intestinal microbiome.⁸ Some studies report that postnatal antibiotic courses given to the infant in the first three to nine months of life may alter abundances of Ruminococcus and Clostridiales.⁵ Antibiotic use in the first 6 to 12 months of life has also been associated with a decreased maturation of the infant microbiota.⁵ In addition, another 2021 systematic review of observational studies and randomized controlled trials found that antibiotic exposure was associated with reduced pediatric microbiome diversity, richness, and bacterial abundance, increasing the risk of gut dysbiosis.⁹

Functional Medicine Considerations

Research into the pediatric intestinal microbiome continues to expand.^19-22 While there is evidence that the makeup of the pediatric microbiome may have lasting consequences on health, it is important to note that there is individual variability among healthy microbiomes. Functional medicine is patient-centered rather than disease-centered, which is a particularly important distinction when it comes to microbiome research and application. All humans have unique microbiomes, and these communities may be shaped, in large part, by lifestyle factors. Clinicians who practice functional medicine seek to understand the antecedents, triggers, and mediators that underlie illness or dysfunction in each individual patient.

This approach requires a detailed examination of the patient’s timeline and facilitates the recognition of disturbances that are common in people with chronic illnesses, many of which may be traced back to the intestinal microbiome. From a patient perspective, altering one’s diet, nutrition, and exposure to environmental toxins comes at a very low risk. A deeper understanding of these factors and how they can be manipulated could alter the trajectory of disease, beginning as early as the preconception period. With deepening knowledge in this health area comes the hope of new approaches to improve wellness.