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Kid’s Gut Microbiome Support: Tips from a Pediatric Naturopathic Doctor with Dr. Jordi Smith

Published October 01, 2023

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The health and integrity of the gut microbiome play a crucial role in overall pediatric wellness, especially during the childhood years where our little one’s bodies are still growing. Supporting a healthy gut microbiome in kids is important because it plays a foundational role in building a robust immune system, which can help prevent allergies, eczema, and other potential health issues [7]. As parents, understanding and supporting your kids’ gut health can pave the way for lifelong wellbeing. In my role as a Pediatric Naturopathic Doctor, I work with a variety of families to help their kiddos build healthy habits for life. Here are some of my insights along with the actionable steps you can take as a parent to maintain optimal gut health in your little ones.

Choosing Organic Produce

Organic fruits and vegetables are rich in fibers that are crucial for maintaining a healthy gut flora in our kiddos. By opting for organic produce over conventional, you avoid potential harmful pesticides that can disrupt the gut microbiome [5]. Families should choose organic options for their kids when possible because organic farming practices typically use fewer synthetic pesticides and herbicides, reducing exposure to harmful chemicals that can impact the microbiome. However, the specific vegetables that should be organic can change over time. To determine which vegetables are recommended as organic or non-organic, families can refer to the Environmental Working Group's (EWG) "Dirty Dozen" and "Clean Fifteen" lists, which are updated annually.

Eat Probiotic-Rich Foods Daily

Probiotic-rich foods are crucial for your kids to build a healthy gut. Probiotics contain beneficial bacteria that are essential for a balanced gut microbiome. Regular consumption of foods like yogurt, kefir, and sauerkraut can introduce and maintain a healthy gut flora, which has been linked to improved digestive and immune function [1]. The probiotic content of foods can vary significantly based on the type of food, its preparation method, and storage conditions. For more information regarding how much probiotics you can find in foods, check out our blog on Top Sources of Probiotic Foods for Kids.

Begin Health Expert Tip:For children over the age of 1 year old, incorporating probiotic-rich foods into at least one meal daily can foster a healthy gut microbiome.

Meanwhile, infants up to 12 months generally receive enough probiotics through breast milk, which naturally contains a beneficial mix of bacteria conducive to developing a healthy gut flora.

Incorporate Prebiotic-Rich Foods

While probiotics introduce beneficial bacteria to your kiddos’ microbiome, prebiotics act as healthy food for these bacteria to help their growth and activity. Natural sources of prebiotics include foods such as apples and asparagus. For our pickier eaters, a prebiotic supplement made specifically for kids like Begin Health’s Growing Up Prebiotic can also support a healthy digestion through softer and more frequent stooling [2].

Supplement with Probiotics As Necessary

While a balanced diet should ideally provide all the necessary probiotics from foods, there might be times when a kid’s probiotic supplement is beneficial. It’s particularly helpful for days when your kiddos haven’t consumed enough probiotic-rich foods and need extra support. When choosing a probiotic supplement, make sure it contains both the Lactobacillus and Bifidobacteria species - both are important strains of a healthy microbiome for infants and kids [7]. Pairing probiotics with prebiotic foods or prebiotic supplements can enhance their effectiveness by nourishing the gut microbiome [6].

Limit Processed Foods

Think of processed foods like the uninvited party crashers of your kiddo’s gut world. Processed foods can disrupt the balance of the gut microbiome. Reducing the intake of these foods can prevent the elimination of beneficial bacteria and promote a healthier gut environment [3]. Particularly, be vigilant about food additives such as emulsifiers, seed oils, and food dyes. To learn more about the preservatives you should consider avoiding in processed foods, check out our blog on Food Preservatives to Avoid.

Play in the Dirt

Exposing children to natural environments, such as gardens or playgrounds, can introduce them to diverse microbes that support the microbiome. What kids get by playing in nature that they don’t get from foods alone are the vast number of different types of microbes, including bacteria, fungi, and other microorganisms. Soil also contains minerals like zinc, magnesium, selenium, and iron. Exposure to these natural elements and microbes found in dirt can not only strengthen the immune system but also contribute to a balanced gut flora [4]. Plus, it’s the most fun option on this list!

Summary:Incorporating these simple yet important foundation choices into your family's routine can be a game-changer for your little one’s gut health and overall well-being. From choosing the right produce options to enriching their diets with probiotics and prebiotics, you have the power to help build a thriving gut microbiome in your kiddos. By limiting processed foods and encouraging outdoor adventures in the dirt, you're not just promoting a healthy gut; you're also fostering a stronger immune system and a lifetime of good health.


(1) Sanders, M. E. "Impact of probiotics on colonizing microbiota." Food Science & Technology Bulletin: Functional Foods 7.8 (2010): 59-64.

(2) Gibson, Glenn R., and Marcel B. Roberfroid. "Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics." The Journal of nutrition 125.6 (1995): 1401-1412.

(3) Suez, Jotham, et al. "Artificial sweeteners induce glucose intolerance by altering the gut microbiota." Nature 514.7521 (2014): 181-186.

(4) Lowry, Christopher A., et al. "Identification of an immune-responsive mesolimbocortical serotonergic system." Psychoneuroendocrinology 34.5 (2009): 693-711.

(5) Romagnolo, Donato F., and Ornella I. Selmin. "Mediterranean diet and prevention of chronic diseases." Nutrition today 52.5 (2017): 208.

(6) Hill, Colin, et al. "The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic." Nature reviews Gastroenterology & hepatology 11.8 (2014): 506-514.

(7) Stuivenberg, G. A., Burton, J. P., Bron, P. A., & Reid, G. (2022). Why are bifidobacteria important for infants? Microorganisms, 10(2), 278.

Dr. Jordi

Dr. Jordi Smith

I am a Pediatric Naturopathic Medical Doctor based in San Diego, CA, specializing in pediatric and preconception care with a proactive approach to prevent future diseases and ensure proper development. I firmly believe in establishing strong foundations for health, as they play a pivotal role in shaping a child's path towards a healthy future. Find more information on my website: