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The Importance of Establishing A Healthy Gut Microbiome in Pediatrics

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The Importance of Establishing A Healthy Gut Microbiome in Pediatrics

It's said that 100 trillion microbes reside within the human body. The vast majority of those microbes are found within the gut, primarily in the small and large intestines. The colonization of gut microbiota has been a mainstream topic for years, with evidence showing that this process begins in utero. Establishing and maintaining a balanced and thriving gut flora can greatly contribute to health outcomes in childhood and throughout life.


What is The Gut Microbiome?

The gastrointestinal microbiota, also called the Gut Microbiome, consists of trillions of living microorganisms housed in the gastrointestinal tract. Our small and large intestines contain most of the microflora, including bacteria, viruses, fungi, and parasites. In a healthy functioning microbiome, these organisms are symbiotic with the human body and serve a purpose in the digestive system and beyond.

Evidence suggests that colonization of the microbiome begins in utero through amniotic fluid ingestion by the fetus. When the baby passes the vaginal birth canal, they pick up additional microbes that continue populating its microbiome. Within the first full year of an infant's life, exposure to their environment also aids in developing a diverse gut composition. Some research indicates that a child's microbiome can achieve adult-like status by age three. At the same time, other information concludes that the development of a diverse gut flora continues well into their teenage years.

Why is a Healthy Gut Microbiome So Important?

If an imbalance in the types and quantity of microorganisms occurs, the microbiome can become dysfunctional, leading to discomfort, gut disturbances, and negative influences on a vast spectrum of organ systems. The development of a healthy and diverse microbiome can aid in a child's overall health and wellness while also playing a key role in the prevention of chronic disease involving the gastrointestinal tract, immune system, metabolism, nervous system, respiratory tract, and cardiovascular system.

One study looked at correlations between gut microbiome in infancy and the development of children's fine motor skills, communication, and personal and social skills by 3 years old. Results showed that early gut microflora diversity is correlated to neurodevelopmental progress in children. At the same time, an overpopulation of pathogenic microbes such as Clostridial species can be detrimental to areas of communication skills. Data over the last decade has revealed that the development of a negatively impacted gut microbiota can also contribute to cardiovascular disease outcomes, Type 2 Diabetes, Inflammatory Bowel Disease (IBD), Irritable Bowel Syndrome (IBS), mental health, skin health, and autoimmune conditions to name a few.

Symptoms of an Unhealthy Gut Microbiome in Pediatrics

Variations in symptom presentation can occur depending on microbial imbalance and each individual's situation. The top common symptoms of an unhealthy gut microbiome include:

What Causes an Unhealthy Gut Microbiome in Pediatrics?

An unhealthy gut microbiome is not typically caused by one factor. Rather it's a combination of an imbalance of microbial colonization and impeded maturation. Some common detrimental influencing factors can negatively contribute to the downfall of a healthy gut microbiome, including maternal and perinatal health, mode of delivery at birth, antibiotic use, environmental factors, nutrition, and gut-brain interaction. One study examined fecal samples of preterm babies, their mothers, and then twenty full-term babies during the initial few days following birth. Gut microbiota was evaluated, and it revealed that there is a distinct difference between preterm and full-term gut microbiota. Infants born preterm, regardless of gestational age or mode of delivery, had less alpha gut microbiota and a distinct presence of beta microbiota.

In contrast, full-term infants predominantly presented the alpha set of microbial species. The microbiota variation (more beta than alpha) was also seen in the maternal microbiome samplings of the preterm infants. This altered preterm gut flora has clinical implications for adverse health outcomes, which is an area that warrants further investigation. While the mode of delivery was not a contributing factor in the preterm study, there is evidence that it can contribute to gut colonization variability. Vaginally born infants acquire the beneficial bacteria species-Bifidobacteriales and Bacteroidales while exiting their mother's birth canal. Cesarean-section delivered babies tend to acquire bacteria that are present in the mouth, skin, and hospital environment, which can negatively set up their microbiome. Much like vaginal delivery flora, breastmilk also contains Bifidobacteriales.

Antibiotic use is a hot topic, as early use in children and overuse throughout childhood can be detrimental to the healthy development of a child's microbiome. While antibiotics can kill off pathogenic bacteria, they are not discriminatory and can also rid the body of beneficial bacteria, decreasing gut microbial diversity. Studies have shown that antibiotics are major disruptors in gut microbiota which can lead to antibiotic-associated diarrhea and recurrent cases of Clostridioides difficile infections. Antibiotics used in early childhood years can disrupt gut health, leading to immunological, gastrointestinal, and neurocognitive conditions in kids.

Environmental factors can cause distress to the health of a child's gut by disrupting gut integrity. One prime example is glyphosate, the most ubiquitous herbicide used in agriculture and amongst the general public in the form of "Roundup." Its intended use is to eliminate weeds by inhibiting plant enzymes so they can not grow. This same inhibitory mechanism also inhibits certain beneficial bacteria when humans are constantly exposed to it. Pathogenic microbes like Clostridium and Salmonella are resistant to glyphosate's mechanism and, therefore, can take over, thus causing disruption in commensal gut flora and inducing dysbiosis in some cases. Other studies have shown more than 300 environmental contaminants or their byproducts have shown up in a variety of human samplings. These chemical compounds include phthalates, persistent organic pollutants (Example: PCBs), heavy metals, and bisphenols. Phthalates have also been found in newborns and are strongly associated with alterations in the gut microbiome and altered immune system response to vaccination.

The gut-brain connection is a bidirectional communication pathway in which they can influence one another's functionality. You may hear more about how gut health can impact other areas of one's health, but a child's brain function can also contribute to the composition of their gut. There are indirect ways in which the brain affects microbiota, including chemical messengers and nervous system stimulation for motility. There are also direct signals sent via neurons, immune cells, and enterochromaffin cells. The autonomic nervous system (ANS), which includes parasympathetic and sympathetic, can modulate motility and mucus secretion into the gut, contributing to microbial diversity. The ANS also controls stress. An increased stress response can negatively influence gut permeability and, therefore, the integrity of a healthy gut lining.

Last but not least is the implication that nutrition can have on gut health in kids. Science has shown that kids that eat primarily processed foods will have increased pathogenic bacteria. On the other hand, children whose second year of life includes high-fiber foods, good sources of proteins, and fresh produce have fewer pathogenic microbes. Other evidence suggests that artificial sweeteners may contribute to the rising cases of dysfunctional microbial flora.

Functional Medicine Labs to Test That Can Personalize Treatment Protocols for Establishing a Healthy Gut in Pediatrics

Gathering information about the status of your child's microbiome and potentially negative contributors can provide context to root cause issues and direct the path of patient care. Here are four key tests to utilize when gut health is in question:

Comprehensive Stool Test

The GI-MAP by Diagnostic Solutions and the GI Effects® Comprehensive Profile from Genova Diagnostics offers a comprehensive stool analysis that can asses gut microbiota. This test can also reveal if there is an imbalance in gut flora that is causing inflammation, digestion, and absorption issues manifesting as your child's symptoms. This quantitative test can guide patient care in creating an individualized and specific treatment protocol.

Organic Acids Test (OAT)

The OAT test by Mosaic Diagnostics will look at overall health, emphasizing pathogenic bacteria and yeast metabolites, vitamin and mineral levels, neurotransmitters present, and oxalates. It's helpful in cases of chronic stress and inflammation that are impacting gut health.

Heavy Metals

Evidence suggests that heavy metals can disrupt the gut microbiome. Toxic elements like heavy metals are 200 to 300 times more concentrated in the hair than other excretory samples. The Hair Element Test by Doctor's Data will provide insightful information on whether or not any toxic metal loads are impacting your child's gut health.


Nutrition Choices for Establishing A Healthy Gut in Pediatrics

Depending on functional laboratory testing and your child's symptoms, they may benefit from just optimizing their nutrition, or they may need full restoration of their gut microbiome. Nutrition that can support a healthy gut microbiome includes fiber-rich plants, probiotic-rich foods such as yogurt, and a variety of fruits and vegetables. Reducing processed foods as much as possible will also benefit a child's gut health. If your child has significant gut dysfunction, they may benefit from a Microbiome Diet, which may include utilizing the Four R's protocol. The four R's protocol is: removing gut offenders, repairing gut integrity, replacing necessary digestive aids, and reinoculating the gut flora with beneficial microbes. The dietary component includes eating a predominantly plant-based diet containing prebiotic and probiotic foods and avoiding inflammatory food categories. This diet can be challenging for anyone, but especially young kids. It's best to see an integrative health provider that can customize a practical option for your child's unique situation.

Supplements and Herbs That Can Help Establish A Healthy Gut in Pediatrics

Supporting gut health through botanicals and amino acids is a gentle yet effective way to assist a child's well-being. There are some key products to consider when looking to reduce inflammation, support mucosal lining, and re-establish an imbalanced gut flora. Here are several of the most effective considerations:

Slippery Elm

This botanical, also known as Ulmus rubra, is a wonderful botanical for supporting a child's gut health. It has a couple of primary functions when utilized in this capacity. One is that it provides a protective layer to the skin and GI tract, which can inhibit pathogens from entering the body. Secondly, its demulcent properties can soothe inflamed mucosal gut tissue. An additional benefit is that plant has inherent prebiotic properties, which can feed healthy bacteria in the gut. Slippery Elm comes in a variety of administrations, such as teas, powders, lozenges, and capsules. This botanical should be dosed based on weight, in which you can apply Clark's rule for dosing kids. Clark's rule is to take your kid's weight and divide it by 150. Then, you take that number and use it as the percentage of the adult dose that they should take. For example: if your child weighs 50 lbs, 50/150= .33. Your child would then take ⅓ of the recommended adult dose.

L-Glutamine for A Healthy Gut in Pediatrics

This amino acid is an excellent contributor to supporting gut integrity and permeability. It also contributes to three beneficial areas of gut health. It helps balance the gut microbiome, increases tight junctions of gut lining cells, and helps reduce inflammatory responses in cases of gut distress. The amino acid can also support healthy gut-brain communication by influencing the amount of GABA and Glutamate available, both of which play a vital role in depression and anxiety.

Curcumin for Leaky Gut

An active component of the turmeric plant is Curcumin. It's a great antioxidant and anti-inflammatory supplement, but it can also help assist in microbiota diversity. Evidence suggests that this polyphenol plant extract can help modulate gastrointestinal flora's abundance, diversity, and composition. An adult dosage of 500mg per day is commonly used. To calculate a child's dose, follow the above-mentioned Clark's rule.


Using the oil from the peppermint plant has been shown to support a child's gut health, especially in cases of IBS or abdominal pain. Peppermint is most effective in reducing pain, distention, and gas symptoms in kids with an IBS-like picture. Most trials on peppermint oil use enteric-coated encapsulated peppermint oil, but other forms are available such as topical peppermint oil or teas.

Probiotics for A Healthy Gut in Pediatrics

Supporting a healthy gut microbiome is important in establishing healthy gut flora early on. If kids have been given antibiotics, it is especially important to help re-establish gut health and repopulate the microbiota with beneficial microbes. Probiotic supplementation is great because it can not only help repopulate and balance the gut but also help support normal mucosal function while strengthening the integrity of a gut lining. Healthy gut integrity plays a vital role in preventing passage through tight junctions, protecting the child's body from foreign invaders reaching the bloodstream.



Establishing and maintaining a healthy gut microbiome can greatly impact your child's health. While the most obvious beneficiary is the gut itself, the brain, immune system, nervous system, and skin are just a few of the other areas that will also greatly benefit from a diverse and thriving microbiome. Over the last decade, this area has gained traction, which has geared us toward understanding the increased importance of supporting intestinal microflora. If your child suffers from chronic gut symptoms, it would be beneficial to investigate their microbiome through functional testing and utilization of integrative medicine support. Correcting this issue early on can set them up for a future of thriving gut health.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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