Building a Healthy Gut Microbiota in Babies

Sep 3, 2025

A healthy and balanced microbiota plays an important role in digestion, immunity, and overall health. The gut microbiota is the collection of microorganisms that live and interact within the digestive tract. It quickly begins developing at birth and continues to evolve in the first three years of life.

What Is the Gut Microbiota?

Gut microbiota refers to the diverse community of bacteria, and other microorganisms that live and interact throughout your digestive tract. These microorganisms help keep you healthy by supporting digestion and immune function. 

The composition of an infant’s gut microbiota is shaped early on and factors that have a big impact are baby’s delivery method, baby feeding choices, and environmental exposures.

How Do Babies Develop Their Gut Microbiota?

Several factors contribute to the development of a baby’s gut microbiota:

  • Delivery method: Babies born vaginally receive beneficial bacteria from their mother’s birth canal. Babies born by C-section aren’t exposed to bacteria in the birth canal, so the first bacteria they are exposed to is different.
  • Feeding practices:
    • Breastfeeding: Breast milk naturally contains probiotics and prebiotic HMOs that nourish beneficial bacteria in the gut microbiota.
    • Formula feeding: Baby formulas that contain added probiotics and/or HMOs (like 2’-FL) can help support the development of the baby’s gut microbiota.1
  • Environmental exposure: Many environmental factors including where you live, family members, and even pets introduce microbes that contribute to baby’s gut microbiota diversity.1

Why Is the Gut Microbiota Important for Baby’s Health?

A balanced gut microbiota is essential for supporting:

  • Digestion and nutrient absorption: Beneficial bacteria aid in breaking down certain complex carbohydrates and dietary fibres. They also help the body synthesize certain vitamins and nutrients.2
  • Immune system development: Up to 80% of the body’s immune cells are found in the digestive tract. The bacteria in the gut microbiota are constantly interacting with the immune system and contribute to its function and to overall health.3
  • Reducing digestive discomfort: Research suggests that promoting a healthy microbiota may increase digestive comfort, reduce crying time in colicky babies and promote softer stools.3

For more information or support, consult your healthcare provider about how feeding practices can support gut health and immune function.

References:

1.    Canadian Digestive Health Foundation. Microbiota in Early Years. November 2022. https://cdhf.ca/en/microbiota-in-early-years/ Accessed April 2025.
2.    Hesla H, et al. FEMS Microbiol Ecol. 2014;90(3):791-801.
3.    Saavedra J. Nutr Clin Pract. 2007;22(3):351-365.