Gut Issues: The 5R Protocol

“Hey Doc,” he says “I can’t believe how much better I’m feeling. I haven’t had any gas, bloating or stomach pain since I followed your directions. It’s awesome!”

Balancing the gut

I hear this all the time and let me tell you how blessed I feel to be a witness to health conditions and symptoms being resolved without medication. Let’s talk gut issues…again. The reason I talk about them so frequently is because almost everyone who walks into my clinic has them. There is a protocol that is routinely given from functional health practitioners, like yours truly. It is used because it works, but only if you work it. I can tell you what to do and how to do it all day long, but you have to do the heavy lifting and actually follow my advice. You will, you say? Great, here it is.

What is the 5R protocol?

The 5R protocol consists of 5 steps that help restore the natural balance of the gastrointestinal (GI) system. The GI system needs special attention because it is so important to have it functioning properly. There are many physiological processes that occur here like absorbing nutrients, identifying toxins, producing and using enzymes to break down food, housing several pounds of necessary bacteria and more. This is why balance in this system is so darn important.

What are the five components?


It’s first important to identify and remove any organisms or sensitivities that irritate the system or cause it to function sub-optimally. I use muscle testing, blood work, stool tests, and breath tests to identify the culprits. Those culprits may be bad bacteria or fungi, food sensitivities or heavy metals. It can even be good bacteria in the wrong place. These are things that can cause irritation and damage to the gut as well as throw off the way this system is meant to function. The way we remove them may be food avoidance, NAET, supplements, and herbs. Occasionally medication is called for as well.


There are many substances and compounds that are needed for a properly functioning GI system. Digestive enzymes like hydrochloric acid, amylase, protease, and lipase. Vitamins like methylated folate, vitamin D, B vitamins and minerals are needed as well. If these are not present or are in low supply they will need to be supplemented. We can often identify which of these are needed with an extensive history and/or stool testing.


All those trillions of bacteria in your belly are important…yes I said trillions! This is your good bacteria or your microbiome. Antibiotics you take for infection and even the antibacterial agents in antibacterial hand soap can affect them. Stress, lack of sleep and a poor diet can alter them as can radiation, chemicals, and toxins, like the sweetener Splenda. We reinoculate with fermented foods like sauerkraut, pickles, and kefir. We also use probiotic supplements to increase the numbers of good bacteria. This is especially important to prevent fungal infections like Candida albicans which is normally in the gut but kept in check by the good bacteria.


The cells of the intestinal lining are like a world unto itself. These are the gatekeepers to your bloodstream and your insides. They identify the undesirables that need to be kept out and they actually keep them out, if these cells are healthy. They constantly die and are replenished. If they are damaged they need to be repaired. A healthy high fiber diet and supplements such as L-Glutamine, flax, chia, acacia, aloe, and plantains are helpful in repairing the intestinal lining.


The last step is to pull everything together and shift it to meet the needs of the healing gut. As healing happens different components are needed at different times. Work with me to make sure we are resolving your symptoms and reestablishing a healthy gut system.

The GI system is complex but it’s my favorite system to work with because the rewards are so great. Better energy, better skin, better elimination, better nutrient absorption…it is a rewarding effort, I promise.

Cheers to the gut!

Dr. Stacey

One response to “Gut Issues: The 5R Protocol

  1. I’m so grateful for all you’ve done to help with my digestive issues. A couple of months ago, I would never have been able to predict that I could feel this good! Thanks so much, Dr. Francis!

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