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 In this article we will be addressing how to create a healthy gut microbiome also called colonic microbiota.  We will also address risk factors associated with an unhealthy microbiome and its impact on overall health.

When I was about 25 years of age I started having some GI problems. It started occasionally and then became more and more consistent.

Ok, it is a topic most people don’t like to talk about. Diarrhea! Yup. I said it. Now it is out. Everybody now knows about my little problem.

After going to multiple doctors and specialists and trying a variety of medications that didn’t work or made matters worse I started to do my own research and 17 years later was able to successfully treat my condition.

I now live a normal life. Well, at least my bowel habit is normal(ahem).

What are some of the problems that might be caused by poor gut health?

Poor Digestion

When your gut isn’t working properly you may experience bloating, gas, constipation, diarrhea, nausea, heartburn, acid reflux, indigestion, and abdominal pain.

Food Allergies/Intolerance

If you have a leaky gut then you could develop food intolerances or even allergic reactions to foods. This occurs due to undigested proteins entering the bloodstream where they cause an immune response.

Autoimmune Disease

A study published in 2017 found that patients with autoimmune diseases such as Crohn’s Disease had higher levels of bacteria associated with leaky gut than healthy controls.

Celiac Disease

Celiac disease affects 1% of Americans but only 5-10% know they have it because symptoms mimic other conditions. It is estimated that up to 50 million Americans suffer from celiac disease. The connection between celiac disease and poor gut health is not fully understood yet. However, studies show that gluten intolerance leads to increased intestinal permeability. Gluten is a protein found in wheat, barley, rye, and oats.

Depression and Anxiety

Depression is one of the leading contributors to suicide worldwide. There is evidence suggesting that depression, anxiety, and other behavioral health conditions are linked to gastrointestinal dysfunction. In fact, many antidepressants target serotonin receptors located within the GI tract.

Our Second Brain

Do you think our stomach is strictly for processing the food we eat? Think again. Our gut has been called the second brain by some scientists.

Our “gut”, also called our alimentary or digestive system goes from our mouth to our anus and is approximately 30 feet long.

It is called the second brain due to the similarities to our “1st brain”. The gut is embedded with sheaths of neurons and a lot of them. About 100 million which is more than either the spinal cord or the peripheral nervous system according to Michael Gershon who is an expert in the field of neurogastroenterology and the author of the 1998 book, The Second Brain: A Groundbreaking New Understanding of Nervous Disorders of the Stomach and Intestine. This system known as the “enteric nervous system” sends and receives messages, and responds to emotions just like the brain. This is called the gut-brain axis.
So although the gut cannot think deeply or intellectually it can affect the entire physiology of the body just as our brain can.
The brain can affect our gut and our gut can affect our brain potentially contributing to depressive disorders and mental health issues.

Irritable Bowel Syndrome

Irritable bowel syndrome is characterized by chronic abdominal discomfort accompanied by changes in stool frequency and form. It is believed to have a strong link to poor gut health because most IBS sufferers report having experienced at least two episodes of acute gastroenteritis before developing their condition. Some researchers believe that bacterial overgrowth in the small intestine may be responsible for the symptoms of IBS.

Inflammatory Bowel Disease

Inflammatory bowel diseases include ulcerative colitis and Crohn’s disease. These illnesses result in severe inflammation of the colon and small intestine respectively. Recent evidence suggests a connection between diet and intestinal bacteria reflected in the composition of the gut microbiome.


Diabetes has become an epidemic all across America. According to the CDC, about 29 million adults aged 18 years and older were diagnosed with diabetes in 2016. Of these individuals, approximately 2.8 million children under age 20 also had type 1 diabetes.

Poor gut health has been shown to be a potential risk factor for diabetes As a result, there is growing interest in understanding how dietary factors influence the development of this illness. A review led by Dr. Victor Gerdes reviewed several studies analyzing the connection between the gut microbiota in obesity and type 2 diabetes.

This review suggests that an imbalance of beneficial microbes can lead to insulin resistance while excessive growth of harmful species can contribute to glucose intolerance.


Heartburn or acid reflux occurs when stomach contents back into your esophagus causing burning pain behind your breastbone. Small intestinal bacterial overgrowth is thought to be one of the causes of acid reflux symptoms. This occurs because bacteria meant to be only in the large intestine finds its way into the small intestines where it produces gas as well as other substances which irritate the lining of the digestive system.

Skin Conditions

The bacteria in your intestines can have a huge impact on your skin’s health. Bacteria produce chemicals such as short-chain fatty acids like acetate, propionate, and butyrate that nourish cells throughout the body. SCFAs help maintain normal blood sugar levels, regulate immune responses, and promote cell survival. They’re even linked to anti-aging effects! But too many bad bugs could cause problems.

When you don’t get enough good bacteria from food sources, they might move up through your GI tract and out into your bloodstream. That means they end up circulating around your entire body—including your skin. And since most of those bacteria aren’t friendly to humans, they may trigger inflammation and damage sensitive tissues. Some of the skin conditions potentially caused by these bad bugs are acne, eczema, psoriasis, rosacea, dandruff, and dermatitis.


The link between cancer and the gastrointestinal tract was first recognized in the early 1900s. Since then, research has focused on identifying the role played by certain types of bacteria in tumor formation. A recent study published in Cell Metabolism showed that certain types of cancerous tumors contain fewer than 10% of their usual number of bacteria. Researchers believe that this decrease in microbial diversity contributes to tumor progression and metastasis. It has been suggested that probiotics may reduce the incidence of colorectal cancer due to their ability to inhibit the production of carcinogens produced by fecal bacteria.


The role of intestinal bacteria in relation to inflammation in the body has recently become an area of intense interest among researchers. Studies suggest that bacterial metabolites play important roles in regulating inflammatory processes. These include mediators involved in innate immunity and adaptive immunity. Certain species of beneficial bacteria appear to protect against chronic diseases including diabetes, obesity, cardiovascular disease, arthritis, asthma, allergies, celiac disease, Crohn’s Disease, ulcerative colitis, and multiple sclerosis. Leaky gut syndrome occurs when there is an increase in intestinal permeability which allows toxins into the bloodstream through the intestines. This causes inflammation throughout the body.

Heart disease

A new review paper suggests that heart attacks occur because of changes in the composition of our gut microbes. The authors found that people who had suffered a myocardial infarction were more likely to develop another one within five years if they lacked specific strains of Lactobacillus reuteri. In addition, mice lacking L. reuteri developed atherosclerosis at younger ages than did control animals.


A team led by Dr. David Relman reported in Nature Medicine last year that patients suffering from Alzheimer’s have lower levels of two kinds of microorganisms: Bifidobacterium longum subsp. infantis and Akkermansia muciniphila. Both of these organisms help keep the immune system functioning properly. “We think that having less of them leads to increased susceptibility for infection,” says Dr. Relman.

Wow, that is an extremely long list of health problems!

So how do we perfect the health of our intestinal microbiota?

The number one thing we want to do is make sure our microbiota are balanced.


Here is my 8 step system to see optimal health benefits.

1. Consume a variety of fruits and veggies

Don’t just eat the same old banana every morning or green beans, corn, or peas with your pork chop.

Experiment with different varieties and make sure to include all the colors. This will help increase the number of different kinds of beneficial bacteria and create a bacterial diversity which will make your army even stronger against the bad guys.

2. Consume Fermented foods

These will increase the number of lactobacilli which are very good guys!!

You would not believe how easy it is to ferment your own veggies. This book, Home Fermentation: A Starter Guide will give you all the information necessary to become a master fermenter.
that will give you everything you need to get started on your new hobby.
  • Yogurt (beware many yogurts are full of sugar or artificial sugar which is not good for healthy bacteria)
  • Kefir
  • Kimchee
  • Kombucha
  • Sauerkraut
  • Tempeh
  • Fermented veggies


3. Eat Clean

A study published in Nature Medicine highlights the direct correlation between the types of food eaten and the amount and type of healthy gut flora

“In contrast, a more diverse gut microbiome was tied to healthy dietary patterns (high-fiber vegetables like spinach and broccoli, nuts, and, heathy animal foods such as fish and eggs) and was linked to measurements tied to lower risk of certain chronic diseases. In addition, the study found that polyunsaturated fats (found in fish, walnuts, pumpkin, flax and chia seeds, sunflower, safflower, and unhydrogenated soybean oils) produce healthy gut species linked to a reduced risk of chronic disease.”

Learn more about clean eating by reading my free downloadable E-Book.

4. Add Prebiotics

You may be getting some of these without even knowing about it. But some folks may find it hard to get enough of these in their diet. What are they? Food for the probiotics!

  • Garlic
  • Onions
  • Bananas
  • Oats
  • Berries
  • Legumes(beans, peas)
  • Chicory root
  • Berries
  • Jerusalem artichokes
  • Dandelion greens
  • Asparagus
  • Leeks

5. Consume Bone Broth

Some studies have shown promising benefits of amino acids that are in bone broth to be helpful for digestion. The amino acid called glutamine seems very promising.

Glutamine helps heal the intestinal barrier according to a 2017 study in the journal Current Opinion in Clinical Nutrition and Metabolic Care This may be very beneficial with conditions such as leaky gut where the mucosal lining of the intestines becomes irritated and inhibits the body’s ability to digest food.

What is interesting is what was documented in the journal Nutrients based on another study in 2017. They state people with inflammatory bowel disease tend to have lower levels of some amino acids.

Consuming bone broth on a regular basis may be a simple way to get anti-inflammatory amino acids into the body.

Here is a recipe that calls for adding eggshells for additional benefits of highly absorbable calcium along with other needed nutrients.

6. Get off those PPI’s!

Proton Pump Inhibitors(PPI’s) are not meant for long-term use. If you have been on them longer than a month or two talk to your doctor about how you can taper off.

Proton Pump Inhibitors are those anti-acid meds your doc gives you for acid reflux (Omeprazole, Prevacid, Prilosec, Aciphex, Protonix, etc).

You should not attempt this without the help of your medical provider.

There are many natural alternatives to help you with this but you will have rebound acid while trying to get yourself off of them.

The stomach is supposed to have an acidic environment. When we change that for an extended length of time it creates an uncomfortable environment for our healthy bacteria(aka the good guys).

If you decide to stay on the PPI’s then you need to work a little harder to keep the good guys strong and healthy.

7. Eat your oats!

High fiber foods, including whole grain are digested in the large intestine and increase the amount of the good guys!! Whole grains also contain a lot of nutrients, decrease chronic inflammation, and create a feeling of fullness.

8. Finally, (and what I started with) a quality probiotic. 
They are not all the same. Many over-the-counter expensive name brands do not have all the necessary strains or the number of active cultures your GI tract is lacking.

I had actually tried some of those common ones you see advertised (I won’t mention any names) and they did not help me at all.

The effects of probiotics can be astounding. This is a major component of gut health. I now maintain my gut health by utilizing the steps above but initially, I took this brand because of the high number of strains and cultures, and within 3 weeks I was normal for the first time in 17 years.

Again, I realize this only normalized my bowels and not all the other aspects of my life but we have to start somewhere right?

A healthy gut is just one of the benefits of clean eating. Download my free E-Book now.


Everyone Needs to Know About Gut Microbiome and How to Perfect it