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The Gut Microbiome-Part 2: The Infant Microbiome


In my last blog, I provided an overview of the gut microbiome and how important it is to our everyday functioning. This week, I want to focus in on how our microbiome develops as an infant, what can cause dysbiosis, and how that can affect children later in life.


A baby's intestinal flora is much different than an adult's. However, it reaches a stable state similar to an adult's by the age of three. Beginning at birth, the gut microbes have many important roles:

  • digestion

  • metabolism of food

  • activation of the immune system

  • production of neurotransmitters that affect behavior and cognitive function

  • development of the epithelial cells lining the intestinal tract


Researchers have found that there are four main factors that can have an impact on an infant's developing microbiome. These include maternal stress and medication use during pregnancy; vaginal versus surgical delivery; post-birth antibiotic exposure; and infant feeding patterns (Yang et al, 2016)


During pregnancy, a baby's intestinal microbiota (the bacteria that live in our gut) is already developing. Mom's diet, stress, levels, and medications can have an impact on how and what develops in the tiny intestinal tract. Research stress during pregnancy and/or antibiotic use can have a significant effect on the developing infant's microbiome.


When a baby is born vaginally, it is coated in the mother's bodily fluids as it travels through the birth canal. These bodily fluids are high in beneficial microbes needed to build a healthy gut. Babies born surgically via C-section, receive more from the mother's and doctor's skin and surfaces in the hospital. These are higher in pathogenic bacteria. C-sections after attempted labor, however, provide better benefits than elective C-sections as the baby does come in some contact with the mother's bodily fluids. It is still common practice for babies born pre-term or via C-section to receive a prophylactic dose or multiple doses of antibiotics to prevent possible infection. So, not only do these babies not receive the needed microbiota from their mother, but antibiotics further alter their fragile microbiome (Flannery & Pupolo, 2022). According to researchers at the University School of Medicine in St. Louis, nearly all premature babies receive antibiotics in their first weeks of life to ward off or treat potentially deadly bacterial infections. Not only did they find this is not necessary in most cases, but the practice can cause long-term collateral damage to the developing microbiome (Garparrini et al, 2022).


Finally, infant feeding patterns can have a significant impact on the baby's microbiome. For the first 2-5 days after giving birth, a mother produces only colostrum. This rich, thick fluid "has more protein and fewer carbohydrates and fat than mature breast milk. Colostrum is rich in secretory immunoglobulin A (IgA), which helps to protect the infant from infection" (Jozsa & Thistle, 2023). Between days 3-5, milk production begins. Breast milk, unlike formula, contains an indigestible substance that acts as a prebiotic that stimulates the growth of bifidobacterium and bacteroides which are vital to the infant microbiome. Researchers found that formula-fed babies had higher levels of clostridium, specifically C. difficile which is correlated with a higher risk of eczema, wheezing, allergies, and dermatitis (Yang et al, 2016). In addition, high levels of C. difficile and other pathogenic bacteria were correlated with higher levels of anxiety, poor cognition, mood dysregulation, poor working memory, and lower sociability (Yang et al, 2016).


Early-life dysbiosis may impact the developing immune system and increase the tendency toward inflammatory disease. Once stimulated, systemic inflammatory cytokines impact the central nervous system, shaping mood, stress responses, and "sick behaviors" such as fatigue, insomnia, lack of appetite, and depression (Yang et al, 2016). Gut dysbiosis also influences cortisol levels, increasing circulating levels which in turn increases gut permability. Gut permeability, known as leaky gut, has widespread health implications.


About 90% of the children I work with in my private practice had some challenges at birth such as those described above. I refer all of them out to knowledgeable naturopathic physicians who can test their microbiome. 100% of the time there is significant dysbiosis, including the presence of pathogenic bacteria, candida (yeast), parasites, mold, and/or heavy metals. This dysbiosis can cause a constant firing of the sympathetic nervous system and keep a child's primitive reflexes from integrating correctly as well as causing challenges with anxiety, working memory, processing speed, and sensory processing. The microbiome must be addressed for a child (or adult) to gain or regain optimal health and cognition.




Flannery, D. D., & Puopolo, K. M. (2022). Neonatal early-onset sepsis. Neoreviews, 23(11), 756-770.


Gasparrini, A.J., Wang, B., Sun, X. et al. Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome. Nat Microbiol4, 2285–2297 (2019). https://doi.org/10.1038/s41564-019-0550-2


Jozsa F and Thistle J. Anatomy, Colostrum. [Updated 2023 Feb 5]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2023 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK513256/


Yang, I., Corwin, E. J., Brennan, P. A., Jordan, S., Murphy, J. R., & Dunlop, A. (2016). The Infant Microbiome: Implications for Infant Health and Neurocognitive Development. Nursing research, 65(1), 76–88. https://doi.org/10.1097/NNR.0000000000000133

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