10 Signs Your Child’s Gut Flora Imbalanced |

10 Signs Your Child’s Gut Flora Imbalanced

Dee February 2, 2016

By Dee and Rustina, Contributing Writers

Some things in life you learn the painful way. My first son had 7 ear infections and antibiotics in his first 11 months of life. It was long before I had started my natural health journey. Since then I have learned a lot and am thankful for the rough path that led us here. Here is some of what we’ve learned about gut flora.

Due to the antibiotics, his gut flora became all messed up… all those good bacteria that live in you to make up 70-80% of your immune system. We have been working on the side effects of that ever since.

To save you some trouble-shooting, here are 10 signs your child’s gut flora is messed up.

10 Signs Your Child’s Gut Flora is Messed Up

By Dee, Contributing Writer

1. They are Excessively Gassy

With the flora out of balance, excessive gas is produced. Your son/daughter may seem to be gassy all of the time! I know my son was.

2. They are Frequently Constipated

My son had chronic constipation. Pooping was a horrible thing in our house until we started healing his leaky gut from all the antibiotics.

3. They have Constant Diarrhea

On the flip side he could have had diarrhea, but we experienced the opposite. When your gut flora is out of balance, your poop isn’t what it should be.

4. They have Dairy (or Other Food) Allergies/Intolerances

We had three food intolerances until we healed his leaky gut over a several year process. Dairy caused a quick case of diarrhea. Soy caused extremely painful gas and diarrhea. Gluten caused severe stomach cramping.

5. Constant Bad Breath

Not much to explain here other than your breath is reflecting what’s going on inside you. I’m sure you’ve noticed how sweet a newborn baby’s breath is…their gut flora is intact. Then, life happens!

6. Frequent Yeast Infections (Thrush)

They could have frequent diaper rashes or thrush while nursing. If they are a little girl, they could develop frequent yeast infections. Little boys can as well, but this is a more common symptom in females.

7. Chronic Respiratory Problems

Without their immune system working properly, more frequent respiratory issues seem to pop up.

8. Vitamin Deficiencies (Especially B) Despite a Healthy Diet

Without a properly functioning gut, your body can’t absorb all the nutrients needed leading to vitamin deficiencies.

9. Weight Loss (or Failure to Gain)

With a leaky gut, food could just be passing right through frequently undigested, so healthy weight gain can be a problem in little ones. 

(Note: Alternately, weight gain can be a problem for many also if the lymphatic system and/or liver are congested)

10. Frequent stomach pain and bloating.

I was up for 14 months with my son as he struggled through many of the above issues. Sleep and napping was never more than 3-4 hours at night. With extreme stomach pain and bloating, my son was miserable, and I was exhausted!

Notes from Dee: 

I have cited some websites below to give you more information. However, all of the information above I gained by living through it with my son and researching over the past 7 years of his life along with visiting numerous traditional and holistic minded doctors. I hope this can save you some of the problem solving that I had to go through.


  1. Dukowicz AC, Lacy BE, Levine GM. Small Intestinal Bacterial Overgrowth. Gastroenterol Hepatol (N Y). 2007;3(2):112–122.
  2. Williams, David D.C., Signs you have Too Much Bad Gut Bacteria
  3. Myers, Amy M.D., Signs You Have Small Intestinal Bacterial Overgrowth

How to help these concerns and restore gut flora

By Rustina, Contributing Writer

The ultimate goal is to improve gut health, which comes down to 3 basic steps.

  1. Remove pro-inflammatory foods. 
  2. Add anti-inflammatory foods.
  3. Add gut supporting supplements and habits.

#1 Remove pro-inflammatory foods (from mama’s diet too if nursing). 

That means eliminate processed foods, sugars, refined grains, and food toxins. These things are not meant to be in our diets. You can also keep a food journal to determine if there are natural foods that are also triggering inflammation in your little one’s gut (for some tomatoes, broccoli, dairy, all grains, etc may cause a reaction).

#2 Add anti-inflammatory foods 

Healthy fruits, herbs, and vegetables, healthy fats and proteins (read about the importance of protein here), small snacks, and lots of fresh, filtered water. We need real, whole food for a healthy diet and life. If you need more recipes to try, check out our many MAM recipes and Kate’s physical cookbook: Wholesome Real Food Favorites Cookbook.  

#3 Add gut supporting supplements and habits 

Helping get digestion moving again is very important. Everything ties back to digestive health. Sometimes, we are losing nutrients through a leaky gut or unable to process them properly because of imbalanced flora. In the blog linked above, 4 Simple and Natural Ways to Improve Digestion, we go over how our gut works and what we can do to improve digestion. 

When my youngest was gassy, I used an herbal glycerin extract of ginger, fennel seed, and catnip called Infant Tummy Relief. This gently eases the tummy with the ginger while the fennel seed breaks up gas and gastric mucus (S). The catnip, like ginger and fennel, is anti-inflammatory, i. It is also known to soothe indigestion and cramps. This herbal extract is safe for all ages.

Other helpful supplements:

Earthley’s Ginger Root Capsules 

Digestive bitters — Earthley’s Digest-Support

Earthley’s Turmeric Capsules (with Black Pepper)

Magnesium — Earthley’s Good Night Lotion

Earthley’s Liver Love with milk thistle, dandelion, and more herbs

Earthley’s Digest-Ease with marshmallow root, blackberry leaf, and more herbs

Earthley’s Candida Cleanse 

Gut Health Oil with pumpkin seed oil, calendula, whole cloves, and coconut oil.

You can read about these steps more in depth in Kate’s blog post: How to Heal Your Gut (Research + a Plan)

Help replenish your gut flora

We know that the gut’s microbiome is very important in reducing the risks of a “bad” bacteria overgrowth so adding “good” probiotics makes sense. The wall of our intestines is actually made with layers of these “good guys.” You can get a great activity guide to learn (and teach kiddos) all about gut flora here.

Studies show that oral consumption of probiotics is helpful to restoring the microbiome. 

Ways to add Probiotics to your diet:

  • Yogurt 
  • Kefir
  • Sauerkraut
  • Fermented vegetables
  • Kimchi
  • Sourdough bread
  • Kombucha 

More than just add probiotics, we also need to add prebiotics. These are foods that feed the “good bacteria”:

  • Dandelion greens
  • Almond
  • Chicory root
  • Banana
  • Garlic
  • Onion
  • Burdock root
  • Flaxseeds
  • Chia seeds
  • Apples 

Avoiding things that feed the “bad bacteria” are also important:

  • Soda
  • Processed sugars and corn syrup (high fructose syrup)
  • Processed foods

Further Reading Recommendations:

Kids Gut Healthy Activity Guide

4 Simple and Natural Ways to Improve Digestion

The Gut Health Support Guide

Fearless Healthy Living Guide 

How I Healed My Gut and Balanced My Hormones Naturally

The Natural Baby: 5 Tips for Establishing Healthy Gut Flora

5 Tips for Improving Your Toddler’s Gut Health

5 Ways to Help Your New Baby Develop Optimal Gut Flora

Monday Health & Wellness: Optimal Gut Health

What Nutritional Deficiencies are Associated with Depression?

10 Ways To Feed Your Microbiome

Has your child struggled with gut flora levels?

This is the writings of:

I'm a mama to three boys who keep me busy and a wife to a supportive husband who has grown with me. I had a heart attack 4 years ago that you can read more about on my blog which has lead me to a more passionate pursuit of physical, mental, and spiritual health. My faith in Christ is the core of who I am. Without Him, I wouldn't be here. Come visit me at my blog reclaimed-life.com


  1. Wow your Story sounds so much like my niece, I have recently learned about gut health and am becoming more aware of it, since starting my son on some supplements he has had huge improvement and so has my whole family! love your article!


  2. These are good to know. I am very thankful that my kids never experienced these things because it’s so difficult to see them suffer from pain and other medical conditions.


  3. My 5 year old has 10/10 of these symptoms, we’ve been to the hat seems like every different kind of doctor and have gotten no where. All of them want to put him on medication for something they are just guessing is the cause without confirmation which I refuse to do! I’m feeling defeated and am trying to advocate for him but no one seems any sense of urgency to figure it out when it’s been going on for years..

    With that said, what products would you suggest or worked for you to fix all of these issues? I appreciate any insight!


  4. I would love more details on how you healed your son. My son has had similar issues and we have been working to fix them but still not sure we have all the fixes.


  5. What can you do for a child that has these issues?


  6. My son had his first ear infection at 2 months old and we battled with it until his 3rd set of tubes at age 4. He was on countless rounds of antibiotics. He has also been allergic to numerous foods and his palette is so thrown off that he only likes to eat a hand full of foods and his allergies make it even worse. He is now 8 and we have been educating him on the chemicals in the foods that trick his brain to think they are good so he is more willing to try new things but again this has been very difficult to achieve with allergies, ie tomatoes, onions, wheat etc. To top it off I HATE to cook and have a creative block when it comes to food and meals. Any suggestions on how to get him to to try good foods or cookbooks for kids with allergies with these basic ingredients. THANKS!


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Hi, I’m Kate.  I love medical freedom, sharing natural remedies, developing real food recipes, and gentle parenting. My goal is to teach you how to live your life free from Big Pharma, Big Food, and Big Government by learning about herbs, cooking, and sustainable practices.

I’m the author of Natural Remedies for Kids and the owner and lead herbalist at EarthleyI hope you’ll join me on the journey to a free and healthy life!

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