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“Work on healing the gut” is a common recommendation in integrative medicine. However, if you’re not a natural health professional, that advice is vague! You might be wondering: What exactly is the gut? How do I heal the gut? And how can I safely improve the gut health of my children?

This article will outline what organs are included in the gut and its importance to overall health, ways that gut health might be disrupted, symptoms of compromised gut health, and healing methods that are safe and effective for kids but applicable at any age. 

What Is The Gut? Why Is It Important?

The gut is a short way of saying the gastrointestinal tract. The gut includes the mouth, esophagus, stomach, small intestine, large intestine, rectum, and anus. Sometimes when people talk about the gut, they are only referring to the stomach, small intestine, and large intestine. However, the entire digestive tract is connected; so when I speak about the gut, I mean the whole thing. 

A healthy gut is free from inflammation and houses a healthy microbiome, which in turn supports a well-balanced immune system. A healthy gut secretes the enzymes needed to break down food into absorbable components. A healthy gut absorbs nutrients and eliminates waste. A healthy gut produces hormones and neurotransmitters that help to balance the body’s neuroendocrine system.

When the gut isn’t functioning well, one or more of the following problems may arise:

  1. Inflammatory conditions (eg eczema) and pain develop or worsen. 
  2. Allergic disease (eg asthma) develops or worsens.
  3. Autoimmune disease develops or worsens.
  4. Immune response is diminished resulting in increased susceptibility to infectious disease.
  5. Malabsorption and malnutrition may develop, which can lead to growth problems, anemia, hormonal problems, and in extreme cases, failure to thrive.
  6. Toxins can build up in the body. Liver health can be compromised.
  7. Hormonal imbalance can occur. Estrogen, cortisol, thyroid, are of concern.
  8. Mental health and nervous system health are impaired.
  9. Cognitive function and development may be compromised. 
  10. Circadian rhythm and sleep may be disrupted.

Ways That Gut Health Can Be DisruptedA forlorn child sits in bed hugging her knees to her chest.

In general the human body is resilient and can maintain good health through all kinds of challenges, including the ones below. However, sometimes these challenges add up or interact with underlying vulnerabilities and weaken the health of the gut. 

  1. Antibiotic use
  2. Stress 
  3. Food allergies/sensitivities
  4. Parasitic infection
  5. Food poisoning
  6. Stomach flu 
  7. Brain injury
  8. Being underweight or malnourished
  9. Side effect of some vaccines
  10. C-section birth
  11. Chronic NSAID use and other drugs that injure the gastrointestinal tract 
  12. Long term inflammatory diet 
  13. Autoimmune disease

Symptoms Of Compromised Gut Health

Most of the symptoms of compromised gut health are focused on the digestive system, but because of the interconnectedness of the human body, many other organ systems may be affected as well. This is an area of intense research, so I expect that this list will grow in the future.

  1. Mouth: foul breath, bleeding gums, sores in the mouth
  2. Esophagus: difficulty swallowing, frequent burping, reflux
  3. Stomach: indigestion, heartburn, pain after eating
  4. Small intestine: bloating, cramping, diarrhea, undigested food in poop
  5. Large intestine: constipation, foul smelling or odd colored poop
  6. Rectum and anus: gas, itchy anus, anal leakage or incontinence
  7. Skin: dry skin, eczema, acne, hidradenitis suppurativa, psoriasis
  8. Respiratory tract: frequent colds and flus, asthma
  9. Neurologic system: depression, anxiety, post-concussion syndrome, post-traumatic stress disorder, autism, Alzheimer’s disease, brain fog, developmental delay.
  10. Metabolic system and endocrine system: imbalances of cortisol, estrogen, thyroid, low vitamin D, circadian rhythm dysfunction
  11. Nutrient status: multiple nutrient deficiencies, unresponsive to supplemental nutrients, growth delays, failure to thrive, anemia
  12. Immune system: frequent infections, allergies, autoimmune conditions

Strategies For Healing The Gut

The following are the best strategies for healing the gut that I’ve used in my clinical practice. The tendency is to jump to supplementation, and it can definitely help. However, research has shown that lifestyle is very important when healing the gut. 

It is important to remember that stress is not good for gut health, so when speaking with kids about changes to lifestyle, diet or supplements, it is important to focus on the positives and on adding more healthy food into the diet. Avoid overly restrictive diets and aim for gradually improving healthy balance.

Gut repair happens over months and years rather than weeks. Patience, consistency, and sustainable changes to diet and lifestyle are key. 

Reduce Inflammation In The Gut

Reducing inflammation in the gut starts with an anti-inflammatory diet and lifestyle. Emphasize foods that are nutrient-dense, high in fiber, and minimally processed. Reduce foods that are high in sugar, salt, trans-fats, refined carbohydrates, and food additives. Many of the healing herbs and nutrients listed below also help reduce inflammation as can omega 3 fatty acids found in fish and fish oil. 

Mindful Eating

Mindful eating means focusing on eating and sharing food with the people you care about. To eat mindfully, clear a spot at the table, set aside screens and books, sit down as a family, and give thanks before eating. Encourage your children to notice the colors, smells, and tastes of the food that you’re eating. Connect meaning to mealtime by telling stories about other times that you’ve eaten similar meals and/or how it connects to your culture, heritage, community, or family. 

I 100% empathize with how difficult it is to find time to sit down as a family at every meal! It doesn’t happen every single day in our home. But starting with even one or two meals a week is a win!

Mindful eating also means being mindful of the words and messages that you’re sharing about food. Check in and notice if you are adding words like “good” and “bad” to foods. Compassionately tune in to your own emotional reaction to foods that you perceive to be unhealthy to start to uncover whether you’re potentially contributing to your children’s stress and anxiety around eating. 

Soothe & Repair Tissues

The essential foundation for healing involves: adequate sleep, hydration, nutrients, and calories.  

When sleep is impaired along with gut health, I often consider melatonin as a supplement because of its action on the gastrointestinal tract. Soothing herbal teas like chamomile and fennel also help to ready a child for bed while providing double duty as gut healers. 

If a child has been having digestive difficulties for a long term, I consider supplementing with vitamin A, vitamin D, free amino acids (including glutamine), and a multivitamin to ensure that all the nutrients needed to heal the gut are included. 

Low calorie diets are a problem for kids (and adults) trying to heal the gut. In kids this can result from picky eating, restrictive diets and/or anxiety that develops around food. 

When picky eaters won’t eat a healthy family meal, I recommend that parents have “safe food” that the child will eat as part of dinner. This ensures that kids are able to get the calories they need, even if it is just from white rice with butter. Multivitamins, fish oil, and smoothies at other meals can help supply other nutrients. 

There are many healing herbs that can be used to repair the gut. Some of my favorites for kids include: chamomile, dill, fennel, marshmallow, plantain, licorice, lemon balm, mint, goldenseal, ginger, turmeric, cinnamon, black cumin seed oil and slippery elm. 

Strengthen Digestion

Strengthening digestion means optimizing the production of enzymes, the movement of the digestive tract, and the connectivity of the nerves. 

Mindful eating helps to strengthen digestion by sending signals from the brain to the gut telling it that food is coming and it is time to get ready!

Sometimes mindful eating alone isn’t enough to stimulate the digestive system adequately. In those cases, I use either ¼-1 tsp of apple cider vinegar before a meal, or digestive bitters, or digestive enzymes

A walk around the neighborhood after dinner helps to improve digestion. When walking, the iliopsoas muscles, which attach your thighs to your torso, massage the intestines and help physically move food along the digestive tract. As a bonus, some fresh air before bed and gentle exercise also helps everyone sleep better. 

Rebalance The Gut Microbiome

An imbalanced microbiome causes havoc on the rest of the body. If a pathogenic bacterial, parasitic, or fungal infection is suspected, it is important to have it evaluated and treated. 

If the microbiome imbalance is mild and doesn’t require treatment, gentle antimicrobials found in vegetables and bitter tinctures help to clear away the unhelpful bacteria so that helpful bacteria can take their place. 

We originally got our probiotics from the dirt. Playing outside, gardening, and shopping for local food grown in real dirt are all ways to expose kids to wild probiotics. Supplemental probiotics are also helpful and vitamin A and vitamin D seem to help heal the gut and promote the population of healthy bacteria. 

Fermented foods like yogurt and sauerkraut are a good source of both probiotics and prebiotics. Ironically, when people don’t have digestive issues, they can eat as much as they like of these foods, however when people have compromised gut health, fermented foods may cause symptoms to worsen. Fermented foods should be considered on a case-by-case basis. 

In addition to fermented foods, prebiotics are found in many fiber-rich foods including fruits, vegetables, roots, grains, and legumes. They are also added to supplements. Inulin, larch arabinogalactans, and butyrate are the most common prebiotics in supplements. 

Probiotics are microbes like lactobacillus bacteria that promote health. Prebiotics are the food that they eat.

Finally, exercise is very important for gut health. Increasing exercise can improve the composition of the gut microbiome. 


Healing the gut is important for a foundation of good health. Compromised gut health can affect the digestive system, respiratory system, skin, immune system, nervous system, endocrine system, and metabolic system. Healing the gut involves: reducing inflammation, mindful eating, repairing tissues, strengthening digestion, and rebalancing the gut microbiome. Healing the gut takes time, therefore patience, consistency, and sustainability are important.



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Dr. Green Mom

Dr. Mayer is a naturopathic medical doctor and an expert in nutrition and wellness as it relates to pediatrics and families. Her passion for prevention of disease as cure fueled her desire to immerse herself into specializing in adult onset chronic conditions, as well as childhood chronic illness.

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