It’s no secret that millions of Americans suffer from leaky gut and intolerance issues. At our Prescott, AZ wellness center, we make gut health a priority. A record high number of prescription drugs being issued are affecting the levels of the correct gut flora in many people’s At Natural Health Sciences of Arizona, we offer naturopathic protocols that help to restore the balance in your gut, which assists in your overall health.

Probiotics and Gut Health

Probiotic bacteria supplements have become a mainstay of health food stores, natural medicine, and are used as a treatment for a variety of health conditions. These include IBS, inflammation of the bowel or inflammatory bowel disease, dysbiosis, an imbalance in gut flora due to overgrowth of toxin producing gram negative bacteria, parasites, pathogenic yeast and fungus that have in some cases essentially taken over the gut. Dysbiosis, it is often caused by excessive use of antibiotics such as the common outcome of antibiotic induced C. Dif overgrowth. Other possible reasons are exposure to mold toxins that the body attempts to detoxify through the gut, thereby killing good bacteria. Exposure to parasites that set up shop in the gut and produce a lot of toxins that damage and kill off the healthy gut bacteria.

Toxin-Producing Microbes in the Gut

A key point regarding this unfortunate condition of intestinal overgrowth of toxin producing microbes is that those who have it feel unwell, …all the time! They typically report feeling worse when eating sugar, or certain refined carbohydrates, but in some cases, they feel sick just from regular, or even healthy foods. This is because even healthy foods contain protein, fat, and carbohydrate in one form or the other, and all 3 can be metabolized into toxins by toxigenic microbes.

After years of doing everything imaginable to help people suffering from this condition, one thing has become very clear from doing gut bacteria intestinal genome testing, such as Ubiome, and more recently Viome, and G.I.Map, and that is the large amount of probiotics that these suffering individuals have taken have not made much difference over a period of years.

In our office we do energetic testing of any products before making recommendations. We recently began testing products that are fermented probiotics that contain 1000s of beneficial microbes instead of the 8-12 that are typical of probiotic supplements. I was introduced to some of these by my mentor, Lee Cowden M.D. at our recent detox retreat; others I have learned about from other sources.

Multistrain Probiotics

These multistrain probiotics are combined with recommendations for creating dairy free/soy free, fermented foods at home that contain large amounts of bifidus bacteria and spore bacteria such as bacillus subtilus. Based on feedback these unquestionably improve symptoms related to imbalance of gut flora. But, as always, there are some that use these products and these methods and still show severely imbalanced gut flora on Viome testing. What is going on?

Put simply, there is no probiotic or fermented food in existence as of now, that can reverse this condition of severe dysbiosis! These pathogenic microbes have worked their way into a position of dominance in the gut and control the battlefield so to speak in what is a war of attrition. As mentioned in the previous email, they are converting all macronutrients, fat, protein, and carbohydrate into toxins. Since most of us consume 2000-3000 calories of these macronutrients per day, you can see how this contributes to the tenacity of this problem. We have to eat to survive, and the dysbiotic microbes are using this against us.

Hope for Severe Intestinal Issues

This article though, is about hope! As a former severe Lyme patient whose intestinal issues required a full year of intravenous feeding and drastic natural interventions, I simply don’t accept that gut health issues that are causing people misery can’t be turned around. In part 3 I will answer the following questions:

  1. What role does biofilm production by pathogenic gut microbes have on the prevention of the implantation of good microbes in the gut and what can you do about it?
  2. Is FMT a critical component of rebalancing gut flora?

Biolfilm Production

Biofilm is a key way that pathogenic microbes evade the body’s defenses. It is an external goo or gel that is secreted by microbes if you will. It consists of polysaccharides (starch), in some cases cellulose (this is the primary structural component of plants, and bacteria such as Pseudomonas and salmonella produce cellulose in the gut as well), and mucins, AKA snot. In addition to gram negative bacteria, other heavy biofilm producers are candida albicans, and certain protozoan parasites.

Most bacteria and microbes that persist as chronic infections in the body live inside these complex biofilm communities and the bacteria in the gut are no exception. These can far outnumber planktonic bacteria (free floating) and intracellular pathogens. These biofilm communities are often made up of more than one type of pathogen. They are complex living communities and highly organized. From your perspective, the host dealing with the reality of these, the biofilm communities absorb nutrients and extrude toxins, and other highly antigenic substances that give you grief. What’s more, over time it appears very evident that this slime and cellulose and polysaccharide complex can eventually harden into a thick, mucoid lining plaque in the small intestine. This hardened plaque is not to be confused with live biofilm communities. It is causing gut problems but in a different way.

When you take the entire clinical picture into view it becomes very clear why no one is succeeding by swallowing probiotics, even the really good ones! What is that clinical picture?

The Mucoid Lining

A thick hardened mucoid lining in the small intestine that inhibits nutrient absorption and prevents removal of pathogenic bacteria (we address the removal of this as well as years of cumulative toxins in our Rapid detox retreats.)

Years of dominance by toxigenic microbes coupled with a progressive lowering of beneficial bacterial diversity. To make matters worse, each time you take a round of antibiotics you permanently worsen this condition by eradicating more beneficial microbes.

Active toxin producing biofilm communities.

The gut itself, in its entirety, becomes toxic with the many biotoxins and is in a degenerative state.

What are the solutions? Put briefly, you must do a protocol to eliminate the mucoid lining and the years of cumulative gut toxicity. It’s beyond the scope of this article to explain Doctor Cowden’s Rapid detox, but you may contact us for more information.

In addition you must eliminate the most toxigenic and destructive parasites from the gut ecology after the mucoid lining is gone, and this will require a biofilm busting protocol that is therapeutically powerful enough to accomplish that, so that your herbs or medications actually reach the parasites in therapeutic levels. Here is one thing you should know about biofilm busting. If you earlier in this article, biofilm contains cellulose. You will need the enzyme cellulase, taken with water away from food, to absorb systemically and dissolve the cellulose in the biofilm. (Cellulase taken with food converts fiber into glucose sugar so don’t take with food unless you’re a cow or a rabbit!)

Healthy Donor Fecal Microbiota Transplant (FMT)

Lastly, you will need to fully replenish ALL the needed beneficial microbes to restore gut health. In the case of this task, for some there is no option but a healthy donor fecal microbiota transplant (FMT). This is being done at Mayo Clinic and many clinics throughout the world. From a holistic standpoint, what really is a healthy donor? Clearly, they must be screened for common high-risk diseases, but does that screening make them ideal? in this area a new term has arisen called FMT Super Donors and these are assisting suffering people overcome a variety of G.I. problems. You are welcome to call us directly for more information about FMT.

If you are concerned about your gut health, you would benefit from speaking to a qualified naturopath. Prescott AZ and area residents may contact us at 928-227-0180 to schedule a wellness center visit.


Jack Miller, CTN