How to Build up a Child’s Microbiome

The gut microbiome plays a crucial role in all aspects of human health.  One question that I get a lot from parents is how to build up their child’s microbiome.

During a child’s first 3 years, the microbiome is dynamic and its composition is shifting and evolving.  After that, it is more stable, and starts to resemble the microbiome that the child will carry into adulthood.  So the first 3 years are especially critical.

This begins with childbirth where vaginally delivered children generally start out with a more healthy and robust microbiome than those born by C-section. Then, breast-feeding for as long as feasible has been shown to lead to a stronger microbiome than in formula-fed children.  This is because breast milk contains a prebiotic (food for gut bacteria) known as GOS that is effective at stimulating the growth of Bifidobacterium and other beneficial bacterial species.

As children begin solid foods, encouraging them to consume a wide variety of fruits, vegetables, healthy whole grains, legumes, nuts and seeds is the best way to strengthen their microbiome.  The key is variety because every whole food feeds a different cluster of bacteria, so having a diverse diet helps to build a diverse, strong microbiome.  If children are willing to consume fermented foods like sauerkraut, kefir or yogurt, that is an additional bonus.

One important factor is to avoid unnecessary antibiotic usage. Recent research from Harvard found that repeated exposure to antibiotics lowers the diversity and robustness of children’s gut bacteria, and, concerningly, leads to an increase in antibiotic resistance genes.

In children with repeated exposure to antibiotics, the study found decreased numbers of some types of beneficial bacteria involved in training the immune system at an early age.  These include certain bacteria from the Clostridium species, which help promote T-regulatory cells that modulate the immune system and prevent autoimmune disease. We now know that disruptions in the microbiome are one of the first steps in the development of all autoimmune disease.

Limiting processed sugar is important because refined sugar supports the growth of harmful bacteria and can lead to bacterial overgrowth, thus crowding out the good bacteria in the microbiome.

Finally, environmental factors can make a difference.  Avoid excessive use of hand sanitizers or antibacterial soaps, as the FDA recently banned the use of these products. Also, exposure to animals like dogs or cats helps increase the diversity of bacteria the children are exposed to.  It is important not to overlook the effects of stress, which can have a harmful effect on the microbiome – ensuring adequate time for rest and play should not be overlooked.

While probiotics can be helpful in certain conditions, studies show that probiotics work more as immunomodulators and do not have long-term effects in changing the microbiome – for this reason I don’t recommend them unless there’s a specific reason. Ensuring regular physical activity, providing exposure to nature and the outdoors, and increasing quantity and variety of dietary fiber are other strategies that can help ensure the health of our children’s microbiome and give them the best possible start in life.


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