Not Your Mothers Microbiome: Nature vs. Nurture

A vaginally delivered infant is directly inoculated and colonized by the mother's vaginal and gut microbiota, closely mirroring her microbial profile. In contrast, a baby born via cesarean section misses this exposure and is initially colonized by skin-associated microbes, leading to a different microbial starting point that shifts as the infant's microbiome gradually develops. 

A newborn’s first exposure to microbes is heavily influenced by how they enter the world—and this can have lasting effects on immune development. For babies born via C-section, breastfeeding becomes especially important—breastmilk provides beneficial oligosaccharides that help support the microbiome development they may have missed at birth.

In this study, researchers used advanced molecular techniques to analyze the gut microbiota of infants just three days after birth, comparing those born vaginally to those delivered via cesarean section. The findings showed a clear difference in microbial diversity: vaginally delivered babies had richer and more varied gut communities, including key species like Bifidobacterium longum and B. catenulatum, which  support gut and immune health by promoting regulatory T cells, strengthening the intestinal barrier, and reducing inflammation through both structural components and metabolic byproducts (Gavzy et al., 2023). In contrast, C-section babies showed reduced bacterial diversity and a noticeable absence of beneficial Bifidobacteria (Biasucci et al., 2008). These early microbial differences may influence the development of the immune system, showing the need for further research into how birth methods shape long-term health—and how we might support microbial colonization in C-section infants through targeted interventions.

From an immune standpoint, the first 3 years of development are critical. Researchers have discovered that although newborns start life with very different immune systems, they tend to follow a surprisingly similar developmental path in the first few months after birth. This convergence suggests that early environmental exposures—especially to microbes—play a powerful role in shaping the immune system. While the specific microbes or stimuli may differ from child to child, the sheer number and variety of exposures may drive a shared adaptive response. Some immune cells, like B cells (antibody cells), NK cells (natural killer cells), and dendritic cells (immune-processing cells), mature rapidly during this time, potentially locking in patterns that influence a person’s risk for immune-related diseases later in life. The immune system is highly responsive to its surroundings and critical early life is for setting the stage for long-term health (Olin et al., 2018).

A study analyzed microbiome and genotype data from 1,046 healthy individuals of diverse ancestral backgrounds living in similar environments to assess the influence of host genetics on gut microbiome composition. The findings revealed that genetic ancestry and host genetics have only a minor impact on shaping the gut microbiome. In contrast, individuals who share a household—regardless of genetic relatedness—had significantly more similar microbiome compositions. Over 20% of the variation in microbiome profiles was linked to lifestyle-related factors such as diet, medication use, and body measurements. Importantly, incorporating microbiome data improved the ability to predict complex traits like glucose levels and obesity compared to models based only on genetics and environment, highlighting the potential of microbiome-based interventions across genetically diverse populations (Rothschild et al., 2018).

This study explored how early gut microbiota colonization influences immune development in infants. Researchers followed 64 Swedish infants from birth to age 5, analyzing fecal samples for microbial composition and assessing immune responses via salivary secretory IgA (SIgA) and immune cell activity. They found that a higher number of Bifidobacterium species in early life was associated with increased SIgA levels at 6 months, suggesting enhanced mucosal immune development. In contrast, early colonization with Bacteroides fragilis was linked to reduced inflammatory responses to lipopolysaccharide (LPS) stimulation, indicating a potential immunomodulatory role (Sjögren et al, 2009). Specific early-life gut microbes may shape both mucosal and systemic immunity during infancy.

Breastfeeding plays a powerful role in shaping the infant microbiome and supporting healthy immune development, especially in the first year of life. Studies show that breastfed infants tend to have lower microbial diversity but higher levels of beneficial bacteria like Bifidobacterium, which thrive on the unique sugars found in human milk. As babies transition from breast milk to solid foods—a process called “weaning”—their gut microbiota shifts dramatically, influencing how the immune system matures. Research from the CHILD Cohort Study shows that breastfeeding doesn’t just impact the gut; it also affects the nasal microbiome, with breastfed infants showing healthier microbial patterns linked to lower risks of respiratory infections and asthma. In fact, scientists were able to predict asthma risk years later based on early microbiome data, revealing that the protective effects of breastfeeding may be driven, at least in part, by the microbes it helps establish (Shenhav et al., 2024).

Further supporting the importance of breast milk in immune system development, human breast milk provides a range of anti-infective components, including secretory IgA, anti-adhesive oligosaccharides and glycoproteins, and immunomodulatory cytokines. Breastfeeding has been linked to reduced risk of infections such as gastroenteritis, respiratory tract infections, otitis media, urinary tract infections, neonatal sepsis, and necrotizing enterocolitis. These protective effects may arise from altered mucosal colonization patterns in breastfed infants. The secretory IgA in breast milk coats intestinal bacteria, preventing their translocation across the gut barrier and potentially reducing the risk of systemic infections and gut inflammation. Even when exposed to diarrheal pathogens, breastfed infants may remain asymptomatic due to these protective and anti-inflammatory factors. Consequently, they experience less immune stimulation in the gut (Wold and Adlerberth, 2000). Another trial showed that adding two human milk oligosaccharides (HMOs) to infant formula helped shape the gut microbiome of formula-fed infants to more closely resemble that of breastfed babies. Infants who received the HMO-supplemented formula had higher levels of beneficial Bifidobacteriaceae and were less likely to need antibiotics in their first year (Berger et al., 2020)

It's clear that a mother’s impact on her child extends far beyond love and care. From the moment of birth, whether vaginally or by C-section, the microbes a baby encounters shape their gut health and immune system. This Mother’s Day, we celebrate not just the bond between mother and child, but the lasting effects a mother’s early contributions have on her child’s health.