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Microbiome Development and Its Early Influences

Your digestive microbiome is an ever-expanding area of medical research. Scientists are only beginning to understand its complexities.

The connection between the immune system and the microbiome is of particular interest. Both environmental and genetic factors contribute to the health of your microbiota, so it’s important to understand how (and when) the microbiome develops. Equally important is sourcing a healthcare team that can help you make research-based choices.


Where gut health begins

Prior to birth, the digestive system is a completely sterile environment. The introduction of bacteria to the gut starts during pregnancy. Research has shown that the mother’s microbiome undergoes profound changes during this time. These changes influence the infant’s microbiome at the moment of delivery. 

Both vaginal and caesarean deliveries will introduce bacteria to the infant. Each mode of delivery will introduce its own subset of bacteria, with vaginal delivery providing bacterial communities resembling their own mother’s vaginal microbiota, while c-section-delivered infants harbour bacterial communities similar to those found on the skin’s surface. 

Once born, the development of the microbiome is further influenced by several factors including:

  • exposure to the mother’s microbiota
  • geographic location
  • breastmilk or formula (or a combination of the two)
  • introduction of solid food (and its delivery method)

These factors can affect the development of the immune system and immune memory, with lasting effects.


First years of microbiome development

Gut microbiota undergoes various important changes in the first three years of life:

  • Following birth, the gut microbiota is predominantly colonized by bacteria that play a key role in preparing the gut for the colonization of necessary microbiota still to come.
  • During breastfeeding, new bacteria are introduced that help protect against infection and influence bacteria-host interactions.
  • At the time of weaning and the initiation of solids, another rapid and important shift in gut microbiota occurs. The introduction of a variety of nutrients, many of which are polysaccharides not digested by enzymes present in an infant, triggers a wave of new bacteria in the system and a reduction in the levels of those initially present.
  • By age three, the gut microbiota closely resembles that of the adult gut microbiota and is mostly colonized by bacteria involved with carbohydrate metabolism, the elimination of chemical substances that are foreign to the human body (such as food additives), and vitamin B synthesis.


Maternal diet and the immune system

The initial development is influenced by lifestyle factors such as diet during both pregnancy and lactation. The maternal diet has also been found to influence the gut microbiota and potentially the development of asthma. Research has identified specific microbial products that influence the regulatory immune cells associated with asthma. Based on this research, human trials have begun which administer live bacteria to newborn babies at high risk for asthma in order to modulate the immune response.

Further to this, a high-fat maternal diet during gestation is associated with lower levels of the important bacteria in the child’s gut. This decrease is linked with reduced production of short-chain fatty acids which are necessary for immune system development and function.


Infant nutrition

Current research indicates that breastfeeding is the most significant factor associated with the development of the microbiome. Breastfeeding introduces beneficial bacteria and metabolites that further provide protection against anti-infective agents. Breast milk is a source of probiotics and prebiotics which play a role in increasing the colonization of beneficial bacteria in an infant’s gut.

Not all infants can be breastfed for a variety of reasons, which is another factor that makes research into the microbiome so important. So far, such research has led to advancements in formula to closely mimic the probiotics and prebiotics of breastmilk and create optimal microbiota colonization. Further insights in this area can help determine how we can continue to improve digestive health for all infants.

Because the microbiome continues to develop beyond infancy, there is much that can positively influence its health, beyond the initial milk of choice. Selecting a healthcare team that is well informed on the latest research can help you navigate these choices, including the introduction of solid foods, the importance of fibre-rich diets and the use of antibiotics.


What you can do now

We have only begun to study the development of microbiota. Further research is needed to fully understand how healthy bacteria colonization is affected by the maternal diet during both pregnancy and lactation. Further knowledge of gut microbiota will aid our understanding of the connections to a healthy immune system as well as inflammatory and autoimmune conditions that develop later in life.

Generally speaking, research indicates the following may aid in microbiome repair:

  • Limit highly processed, carbohydrate-rich foods
  • Increase intake of fermented foods and vegetables
  • Leave enough time between eating to allow your gut to stimulate microbiome regrowth (12 hours at night, for example)
  • Add probiotic and prebiotic-rich, whole foods


You may be wondering what you can do now to repair your own gut health or that of your children. Your best first step is to speak with a healthcare team who is up to date on the latest microbiome research. As diet remains the most dominant factor in gut health, a Registered Dietitian at Harrison Healthcare is an ideal resource to support your Nurse Practitioner or Family Physician in microbiome restoration.


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