You’ve Damaged Your Gut Microbiome
– Now What? –

Dr. Al Danenberg Nutritional Periodontist

March 20, 2022 [printfriendly]

Amanda emailed me with a question. She asked, “I’ve been on several rounds of antibiotics recently, and I know I’ve damaged my gut. Now, what can I do to fix it?”

My first response was, “Amanda, you’re not alone.”

Then I followed up with, “While the damage from systemic antibiotics occurs immediately to the gut microbiome, it will take dedication and a structured program to fix the problem. But it is fixable.”

Finally, I assisted Amanda with the 5 steps to fix her gut.

But wait. There are many other “irritants to the gut” that could cause similar damage. Let’s dive into all this …


The Gut

It has been determined that there are about 38 trillion microbes in your body, and most are in your gut. Compare that to only 30 trillion human cells that make up your body.[1] That makes you “more microbial than human”! And what also is amazing is that an individual’s gut microbiome might be as unique to that individual as is his or her fingerprint![2]

Systemic antibiotics may kill many bad microbes but also kill many of the good guys. This creates an imbalance in the garden of gut bacteria, which allows potentially pathogenic species to overgrow (i.e., gut dysbiosis). In addition, the mucous layer and epithelial barrier of the gut can break down, resulting in the development of chronic diseases. And this can occur without any gut symptoms of bloating, constipation, or diarrhea.

The gut epithelial lining is just one-cell-layer thick. If it breaks down and becomes “leaky”, toxic elements and not-fully-digested nutrients from the gut begin to spill into the blood stream.

Then all havoc could break lose – the immune system could become overactive; organ systems could become dysfunctional; and chronic diseases could begin manifesting. The body might become unhealthy – even debilitated.[3]

However, the human body is resilient. For example, the cells of the intestinal wall replace themselves every 4-5 days.[4]

Amazingly, if all irritants to the gut were eliminated or avoided, and if they were not reintroduced into the body again, you would have a new gut epithelial lining after a week. But if irritants continued to affect the gut, gut dysbiosis and a leaky gut would continue to be factors causing chronic and debilitating diseases.

So, now what? Let’s discuss …

  • The irritants that can damage the gut
  • 5 steps to fix the damaged gut and rebalance the gut microbiome


Irritants to the Gut

  1. Systemic Antibiotics

I’ll first address Amanda’s concern about her rounds of antibiotic treatments.

Antibiotics have a purpose. When there is systemic infection creating potentially life-threatening disease, antibiotics may be critical. But the collateral damage to the body from administering these antibiotics needs to be addressed and properly treated concurrently with the administration of the antibiotic, if possible. Unfortunately, frequent rounds of antibiotics could cause repetitive and sometimes severe damage to the healthy balance of gut bacteria resulting ultimately in the development of various chronic diseases.


  1. Gluten

Gluten, which contains lectins, is a family of proteins that is present in wheat, rye, barley, and some other types of grains. It also is in many processed foods. In addition, gluten is an ingredient in many cosmetics, prescription medications, and nutritional supplements. The human body cannot completely digest gluten. One of the remnants of the incomplete digestion of gluten is gliadin. And gliadin causes dysbiosis and opens holes in the gut lining (i.e., leaky gut).[5],[6]


  1. Emotional, Physical, or Chemical Stressors

Chronic emotional or psychological stressors are serious but unrecognized causes of gut damage.[7],[8],[9],[10],[11]

An example of a significant chemical stressor to the gut is glyphosate herbicide (Roundup). It damages the DNA in human cells; deranges glycoprotein synthesis, structure, and function; inhibits the growth of healthy bacteria; and directly causes leaky gut.[12],[13]

Three other examples of chemical stressors to the immune system are metal ions leaking from titanium implants and mercury fillings (dental amalgams) placed in the body as well as chemicals leaking from breast implants.[14],[15],[16],[17]

Physical stressors like chronic over exercising will cause damage to the gut microbiome.[18]

Other stressors on the body and the immune system affecting the gut consist of chronic inflammation driven by infections and inflammation in the mouth and jawbone. (I discuss these in detail in Shoddy Dentistry & Mouth Splinters.)


  1. Lifestyle and Other Environmental Stressors

Included are heavy metal toxicity[19], sleep deprivation and sleep apnea[20], continuous exposure to dirty electromagnetic fields[21], disturbances in circadian rhythm[22], excessive blue-light exposure especially in the evening [23], and lack of proper sunlight that is essential to produce vitamin D3[24] – just to scratch the surface of a few offenders.


  1. Processed Foods

Overly processed vegetable and seed oils, high levels of linoleic acid, hydrogenated and partially hydrogenated fats and oils, processed sugars and carbohydrates, or other junk and chemicals in foods will have a harmful effect.[25],[26],[27],[28]


  1. Specific Plant Foods

Plants have the potential to irritate the gut by way of their anti-nutrients. Substances like phytates, oxalates, and lectins that exist in plants and are consumed in large quantities and continuously could damage the gut bacteria and intestinal barrier.[29],[30]


  1. Specific Medications

Over-the-counter and prescription medications such as non-steroidal anti-inflammatory drugs (NSAIDs), corticosteroids, alcohol, narcotics, antibiotics (already discussed), chemotherapy drugs, hydrogen peroxide, and birth control pills (and the list goes on) could result in leaky gut. [31],[32],[33],[34],[35],[36],[37]


  1. Low-Dose Ionizing Radiation

X-rays have an important purpose in diagnosing disease. They are critical when necessary. However, too many x-rays could have a cumulative and harmful effect. Over the course of time, they have the potential to cause damage to the microbiome, its metabolites, and the epithelial lining. Research on mice published in 2016 showed damage to the gut from low-dose radiation.[38]


  1. Anything that Disturbs the Delicate Balance of Microbes

Anything that irritates the gut could be the culprit.[39]


5 Steps to Fix a Damaged Gut and Rebalance the Gut Microbiome

#1: Remove

Remove irritants like anti-nutrients, infections, environmental stressors, and all other identifiable factors, which I have touched upon above. As I discussed with Amanda, after a round of systemic antibiotics is completed, the lingering damage to the gut microbiome needs attention. Ideally, implement the next 4 Steps as soon as possible. If practical, implement them concurrently with the course of systemic antibiotics.


#2: Replace

Replace your way of eating with one that includes the necessary bioavailable nutrients required by your body. My Better Belly Blueprint is a way of eating that provides the body with the bioavailable nutrients which it needs and avoids those foods that can be harmful. The overall eating plan is based on the percentage of the volume on a “plate of food” – at least 70% is “nose-to-tail” animal-based foods and no more than 30% is primarily fruits and possibly a select group of vegetables.

These animals must consume their organic natural diet and must be raised and butchered humanely. These animal foods include ruminant meats, animal fat, organs, bone marrow, and cartilage. The enormous amount of bioavailable nutrients in organs, bone marrow, and cartilage also are available if their desiccated forms (powder or capsules).

The remaining 30% of the “plate of food” consists of seasonal fruits, raw honey, and a limited number of vegetables that are low in anti-nutrients (i.e., phytates, oxalates, and lectins).


#3: Repair

Repair the gut’s mucous layer and epithelial barrier, both of which have been damaged by gut dysbiosis. One of the methods to assist the gut in repair is colostrum, which has many peer-reviewed medical articles describing how its unique concentration of nutrients can bind to LPS and other toxic elements in the gut as well as heal the mucous layer and epithelial barrier.[40],[41],[42]


#4: Reinoculate

Reinoculate the gut microbiome with the help of spore-based probiotics and prebiotics. [43],[44],[45],[46] Several studies demonstrate that spore-based probiotics not only germinate in the gut but also create various biochemicals (called metabolites). Prebiotics are elements that feed the gut bacteria. All of which can increase the diversity of species and the numbers of individual species in the gut to crowd out potentially pathogenic microbes.


#5: Rebalance

Rebalance your lifestyle to include and optimize techniques for stress reduction, restorative sleep, efficient exercise, relaxation techniques, and mindful eating.


It sounds like a lot to manage, but I promise you it can be done. And relatively quickly!  I’ve been through this process myself many times, and I can help you if you want some guidance.

Here’s a link to schedule a free 30-minute consultation with me to discuss.


















































Schedule a ”30-Minute Free Consult” with me to answer some of your questions and determine if we are a good fit for a coaching program! CLICK HERE.


If you don’t want to miss out on new posts, sign up for my Free “Belly Bites” Newsletter and receive your free copy of Dr Al’s “5 Things That Could Be Impacting Your Health Right Now” HERE.


Recommended Posts