Updated: 2019, Jun 11

Establishing a Gut Health Protocol: Where to Start?

By - Reviewed by CHD Team
Gut Health Product

When it comes to supporting gut health, many take action on ensuring to take their probiotic supplement of the day. Yet, they often don’t notice any changes in the overall health of their gut.
If our digestive system is not prepped to receive those probiotic supplements, the beneficial bacteria passes straight through us and the money from these expensive supplements literally gets dumped down the toilet.
So what can we do to actually colonize a healthy gut?
When I realized that my 2-year-old daughter was in dire need of a gut healing protocol, I found it beneficial to start at the very beginning: what is the actual definition of our “gut”??
The “gut” is the passage that food takes starting from your mouth all the way to your anus. Along that tract, we have a collection of bacteria, yeast, and fungi that we refer to as our microbiome.
When we refer to gut health, however, we most often are referring to the part of our gut that should house the vast majority of our microbiome, the large intestine.
The large intestine, in particular, is very important because it contains trillions of microbes that dictate not only the state of our digestion but the state of our overall health and mental well-being[1]. It is at this stage of digestion that our body absorbs the majority of our essential nutrients.

Stage of Digestion

I like to think the inner workings of our large intestine as a garden.
Imagine a thick layer of fertile soil full of earthworms, colorful flowers, a diverse selection of herbs and veggies, buzzing bees, ladybugs, and symbiotic fungi. This is what a healthy microbiome should look like.
Now imagine a garden with barren soil, overwrought with noxious weeds, aphids, slugs and little to no diversity. Unfortunately, this is a common scenario in our guts, especially after multiple doses of antibiotics and a constant stream of toxicities in our foods and environment.
The soil in this imagery represents a protective mucous layer and the foliage represent either harmful or beneficial microbes residing in our large intestine.
Surrounding the mucous layer of the intestines is what I like to think of as a mesh net. The healthier we are, the tighter knit this net is. When the net is intact, we can support a thicker mucous layer and the better we digest food and absorb proper nutrients.
Sometimes holes tear in this net and microbes, toxins, pesticides, sugar, gluten and other irritants literally escape our digestion, travel into our bloodstream and wreak havoc on our system.
This is the root cause of most inflammation in other parts of our body. These tears in the net are referred to as “leaky gut” and it is for this reason that many diseases stem from the gut.

Leaky gut

Another important fact to note is that the small intestine, on the other hand, should not have a high number of bacteria. Excess bacteria in the small intestine may use up the nutrients needed by the body.
As a result, a person may have an impeccably healthy diet but remain malnourished. This process often damages the lining of the small and large intestine, making it even harder for the body to absorb essential nutrients. This condition can be tested by your doctor and is known as SIBO[2] (small intestinal bacterial overgrowth).
So how do we begin cultivating a diverse garden in our large intestine?

1. Weed The Garden By Starving Out The Harmful Bacteria

This first step is crucial to creating space to plant beneficial microbes in our guts. The most common food for harmful bacteria and yeasts are sugars, alcohol, and empty carbs.
Another irritant that is crucial to cut down on at this stage is food laden with heavy pesticides/herbicides, such as GMO foods[3] and those found on EWG’s Dirty Dozen list.
I recommend that my clients start with at least a 1-2 week sugar and alcohol detox to starve out the harmful bacteria/yeasts. If your gut is in extreme dysbiosis, I also recommend temporarily cutting out all grains, especially gluten, as these can cause inflammation and feed the weeds.
The first few days are the hardest as these microbes experience die-off and send dire signals to the brain resulting in massive cravings. During this stage, I recommend upping water intake, healthy fats, fiber and magnesium to help battle cravings.
Small amounts of raw honey and pure stevia leaf extract can be used to sweeten your palate.

2. Fortify Your Garden Beds And Fertilize The Soil By Introducing Collagen-Rich Foods

Collagen-Rich Foods

This step can be tackled at the same time as the detoxing begins. As we weed out the harmful microbes, it is very important to nourish the soil and make a conducive environment for beneficial microbes to grow.
Collagen is very beneficial in tightening the mesh net lining of our intestine and increasing the thickness of our mucous layer.
Here are the couple of ways to get collagen in our diet:

  • Bone Broth: Bone Broth use as a base for soup, drink a cup by itself, cook into rice/quinoa or add to sauteed veggies
  • Gelatin From Grass – Fed Cows – I make homemade Jell-O with good quality gelatin and sweetened with stevia. We want to make sure the cows are not fed GMO feed, as herbicide residue is concentrated in the fatty, collagen-rich parts of the animal
  • Take Collagen Supplements – Can be in a capsule or added to drinks/smoothies

3. Introduce A Vast Variety Of Seeds To Your Renewed Garden By Eating Fermented/Cultured Foods

As we remove the noxious weeds in our microbiome and increase the health of the lining and mucous layer, we can begin to plant varietals in our garden.
This can be started at the same time as steps 1 & 2 and will even help curb the sugar cravings, nourish the protective lining and battle the harmful bacteria, but you may not start to feel the results until most of the weeds have disappeared.
The important part of this step is to introduce as much diversity into our garden as possible. It is possible to have an imbalance of beneficial bacteria if they leave no room for other important microbes to implant.
Here are some of the easiest foods to colonize the lining of our gut:

Sauerkraut And Kimchi (Must Be Raw/Not Pasteurized)

These traditional ferments are some of the easiest foods to digest and the vast amount of probiotics in them can quickly implant in fertilized soil

Goat Or Cow Milk Kefir/Yogurt

Cow Milk

These cultures introduce different type of probiotics to our revamped garden. Try to pick out yogurt/kefir with low sugar content and sweeten to taste with raw honey or stevia.
In general, goats milk products are easier on our system to digest

Water Kefir/Kombucha

Water kefir (you may know it by the popular brand, KeVita) is a yummy way to get probiotics into our system and is especially great for kids (it is what my daughter knows as soda) for its low sugar content, fizzy texture and lack of caffeine which Kombucha introduces.

Other Types Of Fermented Veggies

When we consume fermented vegetables, not only do we get a wide variety of probiotics, the fermenting process allows the nutrients in these foods to become more bioavailable to our system[4].

“Gut shots”

Most health food stores provide bottles of fermented liquid known as kimchi or gut shots. These are great to keep in your fridge and take a quick shot of every day before or after a meal
Please Note That Fermented Foods Are Not Intended To Be Eaten/Drank In Large Quantities By Themselves.
A small amount of a fermented food with each meal is a great way to easily introduce probiotics to our system and even aids in digesting the rest of the meal.
I like to think of using fermented foods as a condiment along with protein, healthy fats and fiber.
Traditional cultures used fermenting as a way to preserve food for long periods of time before refrigeration and condiments such as ketchup, mustard, pickles and hot sauces were all fermented products in origin.
Related Supplement To Explore: Thrive Plus Balance Review: How Safe And Effective Is This Product?

What About Probiotic Supplements?

Probiotic System

When probiotics are introduced into our system in a pill or powder form, we have to keep in mind that it may have a lower chance of colonizing in our gut.
When the bacteria is not in a food form, it can easily be destroyed by our stomach acid before it even makes it to our intestine. The remaining bacteria that make it to our intestine may not implant on the intestinal wall if the pH level of our internal environment isn’t perfect.
In addition to that, some of the bacteria that do implant may not have the necessary food (prebiotics) to sustain themselves and can die off quickly.
While we see most probiotic supplements have billions or even trillions of bacteria present, often the vast majority of them pass right through us[5] .
That being said, there is little risk in taking probiotic supplements and they can be a way to increase the biodiversity in our garden, I just don’t recommend them to be our only gut healing action.
If you would like to take a supplement, I suggest picking a brand that has multiple strains of bacteria or even finding ones that have digestive enzymes and prebiotics included in the supplement to increase chances of colonization.

4. Feed Your Seedlings By Incorporating Prebiotics Into Your Diet

Prebiotics are a specialized plant fiber that beneficially nourishes the good bacteria already in the large intestine. In short, prebiotics feed probiotics.
They are essential nutrients for our new seeds and will help ensure that these microorganisms will hold their ground against harmful microbes.
Here are the most common foods that contain prebiotics:

  • Cooked or raw onions
  • Raw garlic
  • Raw leeks
  • Raw banana
  • Raw chicory root
  • Raw asparagus
  • Raw dandelion greens
  • Raw Jerusalem artichoke

5. Keep In Mind That Consistency Is Key And Know What Can Set You Back

Maintaining our gut health

Just as maintaining a backyard garden takes a lot of patience and work, revamping and maintaining our gut health is a lifestyle change rather than a quick fix.
Depending on how depleted your garden was, to begin with, it may take years to build back a diverse, healthy garden.
It is also very important to note the effects of antibiotics on our gut health:

  • Antibiotics are very necessary at times and have done wonders to save lives.
  • That being said, antibiotics are often taken when it is not absolutely necessary and can create long-term problems.

Taking antibiotics is like dropping an atomic bomb in our digestive system.
It clears out all bacteria, good and bad.
The issue here is that once we finish our round of antibiotics, the weeds tend to take root and grow back extremely quickly while the good bacteria take a little longer to colonize.
Diversity is key in a healthy gut and this is extremely hard to achieve after a course of antibiotics. It often takes years to rebuild an abundant garden. One round of antibiotics alters the course of our microbiome for the rest of our lives[6].

  • This information is not to scare you from taking antibiotics but rather to build awareness to the effect it has on our gut health and double check with your doctor that the antibiotics are an absolutely necessary measure.
  • Keep in mind as well that many conventionally raised animals are fed antibiotics and trace amounts are found in their meat

I have seen the long-term effects of antibiotics from my gut health journey with my daughter. Due to a possible infection, she was put on IV antibiotics for the first 6 days of her life.
As a result, weight gain and getting proper nutrients from foods has been difficult for her. When she no longer received my breast milk (which was an aid in food digestion), her tummy was prone to getting extremely bloated and caused her digestive pain.

Her digestive pain

At that point, I put her on a 3-month diet with no grains or refined sugar and added collagen-rich and fermented/cultured foods into her diet. We were fortunate enough to have access to raw goat milk and I provided her with homemade yogurt and kefir from the milk.
After 3 months, I slowly added back in grains (gluten and sugar were the last additions) and I am happy to report that her tummy doesn’t bloat anymore and her digestion runs smoothly.
She is still very small for her age and we do not know if she will “catch up” or not, but we care most about her digestive system being happy.


While it may seem intimidating to take these steps to nourish your gut health, your body will reap the rewards of your hard work and dedication for years. Talk to your doctor about any possible contraindications of introducing this protocol into your lifestyle. You can also consider using a cleansing product such as Dr. Tobias Colon 14 Day Quick Cleanse along with the above-mentioned protocols. This product might help deliver speedy results.

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