By Dr. Nicole Avena

Recent studies have brought to light the immense importance of the gut microbiome for immunity, metabolism, and overall human health. What is your gut microbiome? It is the colony of bacteria, fungi, and other microorganisms that inhabit your intestinal tract for the entirety of your life. It may seem bizarre to think about tiny living organisms making their home in your gut and feeding off the same food you ingest, but we actually have a complex and mutually beneficial symbiotic relationship with the microbes in our guts.

What does our microbiome do for us?

The bacteria in our guts are involved in many diverse and essential life functions. They help to regulate and strengthen the immune system by correcting T cell imbalances and reducing pro-inflammatory responses that cause the body distress. The gut microbiome also aids in metabolic functions, such as breaking down dietary sugars and turning them into fatty acids that can then be used to strengthen intestinal walls. Some gut bacteria even produce important vitamins and minerals like folate and vitamin K (1). Beyond these several key functions, there are other ways in which our microbiome can influence our health that have yet to be fully researched and understood. Nevertheless, it is well-established that gut health is imperative to overall health and well-being.

How does your child’s microbiome develop?

A child’s unique microbiome will develop based on whether or not they are breastfed, the makeup of their mother’s breastmilk and the types of foods they are fed for the first few years of life. This early establishment of the microbiome will actually determine the state of a child’s gut health for the rest of their lives, as gut bacteria tends not to change significantly after the first year or so of life (1). Breastmilk is thought to be more beneficial for the establishment of a healthy microbiome than formula due to the antibodies, oligosaccharides, and microbiota transferred from mother to baby during breastfeeding (2).

What happens if something is off?

When the gut microbiome is less diverse and low in certain beneficial strains of bacteria, there is increased likelihood to develop inflammatory diseases and be overweight. Studies have shown that children that are given large amounts of antibiotics during childhood (which reduce gut microbiome diversity) were more likely to be overweight or obese later in life. There are also relationships between low microbiome diversity and chronic inflammation, which is a result of immune system dysfunction and can even result in cardiometabolic disease (2).

What is the role of probiotics in children?

Probiotic supplements and probiotic-rich foods are meant to provide more good bacteria to the gut to strengthen and support the microbiome. Probiotics can help to regulate digestion and soothe symptoms of irritable bowel syndrome. Digestive issues are common in children and can be worsened by antibiotics, which probiotics can counteract the effects of (3). Probiotic-enhanced formula given to infants has also shown to result in a gut microbiome that is more similar to that of children that were breastfed, which can be beneficial to overall health (2). There have also been studies showing that probiotics may aid in preventing infection development in young, school-aged children. There have also been positive correlations between probiotic supplementation and decreased infection of the respiratory tract in children (4).

Ways to keep your child’s gut healthy

It is generally recommended that children eat probiotic foods like yogurt, kefir, and fermented foods like kimchi and sauerkraut. Unfortunately, many of the best sources of probiotics are foods that are unpalatable to many Western children. The Western diet in general is high in animal fat and simple carbohydrates, which perpetuates a lack of diversity in the gut microbiome and can be partially responsible for the high rates of obesity and obesity-related diseases in Western countries. Diets that are higher in plant foods and low in processed carbohydrates and saturated fat have been shown to promote diversity of the gut microbiota when adopted at a young age. Therefore, it is imperative to introduce high-fiber and nutrient-rich fruits and vegetables into your child’s diet as soon as possible to establish a diverse gut microbiome and to mold your child’s tastes to these kinds of foods (2). The best thing you can do for your child is to begin feeding them a whole foods-based diet that is high in fruits and vegetables and low in processed foods, this will set them up with a healthy gut and a sophisticated palate that will serve them well for the rest of their life! And if you feel that your child isn’t getting enough probiotic-rich foods in their diet, there is always the option to offer a probiotic in supplement form.


  1. Quigley EMM. Gut Bacteria in Health and Disease. Gastroenterology & Hepatology, 2013. 9(9): 560-569. Retrieved from:
  2. Mohammadkhah AI, Simpson EB, Ferguson JF. Development of the Gut Microbiome in Children, and Lifetime Implications for Obesity and Cardiometabolic Disease. Children, 2018. 5(12): 160. Retrieved from:
  3. Samonte M. Geisinger, 2018. The pros and cons of probiotics for kids. Retrieved from:

Hojsak I. Probiotics in Children: What Is the Evidence? Pediatric Gastroenterology, Hepatology & Nutrition, 2017. 20(3): 139-146. Retrieved from: