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January 18th, 2021

The responses to the questions from 2 weeks ago are emblematic of
the difficulty that we all face. 2/3 of respondents state that they do not consume 20 grams of fiber a day or do not know because they do not count. This is a root cause of gut health dysfunction and one that we need to spotlight for change. The second question is an unknown at this point but is leaning toward individual bacterial extinction events based on antibiotic use and dietary influences.

Targeted therapy in the coming years will be to replace these friends via supplementation. There is still much to learn.

 Do you consume 20 grams of fiber daily? Do you count fiber grams?
66% Say no

If a species of microbe dies out because of a lifestyle choice , it is gone for good? 96% Say no

Microbiome Health and Probiotics

We have established that the intestinal microbiome is loaded with bacteria that can work for us in synergy or against us in pathology. The choice on which fork in the road is taken and walked to disease or health is based on our decisions and those of our parents. I can tell you that the two common themes to early onset autoimmune disease in children are over exposure to antibiotics and chronic poor quality food consumption. The former can and often is heavily driven by disorders like milk protein intolerance and non celiac gluten sensitivity. It saddens me often to see a child with full body autoimmune skin rashes that could have been prevented.

I think of a case where this child had classic milk protein intolerance and maintained a diet full of dairy driving mucous production throughout her body. This led to recurrent ear infections and sinus disease. By 10 years of age, this person had had 15 treatment courses of antibiotics. His intestinal microbiome on culture testing was devoid of two major classes of intestinal bacteria. His RNA analysis showed dysbiosis which is a dysfunctional pattern of bacteria that were working against him. Without getting into the details, he could have been devoid of disease by simply avoiding dairy as a child which would have dramatically eliminated the mucous that drove the bacterial infections necessitating antibiotic therapy which ultimately leads to disease. This reality has been proven in animal models where antibiotic overuse drives autoimmunity and shows up repeatedly in humans.

Antibiotics are not good for us unless you must use them. I don't think that there is any debate here anymore. What can we do to prevent as much of this as possible?

In a recent publication in the Journal Gut, Dr. Yeoh and colleagues analyzed the microbiome of COVID19 patients and noted abnormal microbial makeups were associated with worse disease. They state, "Gut microbiome composition was significantly altered in patients with COVID-19 compared with non-COVID-19 individuals irrespective of whether patients had received medication. Several gut commensals with known immunomodulatory potential such as Faecalibacterium prausnitzii, Eubacterium rectale and bifidobacteria were underrepresented in patients and remained low in samples collected up to 30 days after disease resolution. Moreover, this perturbed composition exhibited stratification with disease severity concordant with elevated concentrations of inflammatory cytokines and blood markers such as C reactive protein, lactate dehydrogenase, aspartate aminotransferase and gamma-glutamyl transferase." What the authors are saying directly relates to the entire microbiome discussion. If we choose the wrong lifestyle choices chronically, we will end up with a dysfunctional microbiome that increases the risk of severe COVID disease.

There is a direct link between our lifestyle choices, microbiome composition, disease morbidity and finally COVID death risk. 95% of deaths are defined by this paradigm.

How do we protect our microbiome from perturbation, disease and pandemic risk?

1) CRITICAL – Avoid all antibiotics, antacids and non steroidal anti-inflammatory drugs where possible during pregnancy, during child birth and for your child afterwards. These drugs and many others adversely effect the healthy gut microbes of an infant and child
2) CRITICAL – Eat a predominantly plant based whole foods diet. This means shunning processed flour and sugary “white” foods. Consuming fermented foods like kefir, kimchi, kombucha, yogurt and sauerkraut are direct bacterial sources for the gut. Avoid all refined and processed foods that are low fiber, high fat and sugar bombs.These same foods drive insulin resistance further exacerbating physiology
3) Avoid non-nutritive sweeteners like saccharin, aspartame and sucralose which promote the growth of unhealthy bacteria. Instead use stevia, allulose or monk fruit natural sweeteners. One caveat here is to chew gum with xylitol after meals to improve the microbial health of your mouth which is the entrance to your whole GI tract
4) Avoid endocrine disrupting chemicals, EDC. Visit for lists of chemicals to avoid. Go old school with plain soap and vinegar as disinfectants. Targeted bleach for raw animal-based food residue on countertops in the kitchen is useful. EDC's can be found in plastic eating and drinking vessels, face makeups, creams, and many other everyday products
5) Consider taking high quality probiotics in the range of a 100 billion bugs. (Only with the advice of your provider.)
6) Eat local organic foods until we have definitive proof that Round Up/ glyphosate and other chemicals in our food supply are truly safe. The early research on these chemicals and the microbiome are not encouraging
7) CRITICAL – Meditate and reduce stress daily. Get into a rhythm of daily gratitude and prayer to engender a mindset of happiness no matter where you find yourself or how much external stress is pushing on you. Avoid negativity in all its forms. Negative mind sets only promote stress and stagnation of spirit.
8) Consider an elimination diet if you are suffering from chronic fatigue, gut bloating/irritable bowel syndrome, chronic headaches or other symptoms. Removing trigger foods can stop food gut induced inflammation that can damage the microbiome. Trials of 1-2 months off of offending foods often answers the question as your body will feel dramatically different if you have a food sensitivity. Eliminating gluten, dairy, corn, egg, soy, tree nuts, peanuts and shellfish accounts for most food reactions that are not anaphylactic and classified as allergy/sensitivity. Never try elimination re-challenge diets with foods that cause anaphylactic symptoms like vomiting, wheezing, oral swelling, loss of blood pressure. Seek expert help when working on elimination diets.
9) Consider taking a prebiotic supplement to enhance the growth of the good bacteria that you already have. Great in smoothies and cold beverages. Prebiotics are mother nature's perfect bacterial food source. For example, breastmilk has 8% prebiotic milk oligosaccharides present in it to feed the infant's gut microflora. Fiber from vegetables, fruits and legumes are great sources of prebiotics.
10) Exercise daily to a sweat. Enhances microbial quality and helps the body rid itself of toxins.
11) Get adequate sleep to reduce stress.
12) CRITICAL – Aim for a vaginal delivery every time. No scheduled cesarean sections unless medically indicated.
13) CRITICAL – Breastfeed exclusively until 6 months. I recommend whole foods for your baby from 6 months on. NO white refined foods.
14) If you are really struggling with gut health, despite trying the above recommendations, find a functional/integrative medicine or gastroenterologist practitioner versed in analyzing the intestinal microbiome to assess for overgrowth of bad bacteria or yeast. Treatments for these problems are very specific and complicated.
15) Finally, anything that you perceive as chronic stress is a real stressor for you. You must change the narrative in your mind. Accept the current reality until you can remove yourself from the stressor or mitigate it somehow. Jesus Christ and the philosopher stoics understood this philosophy well. Turning the other cheek, forgiveness, boundaries, standing strong in the storm, whatever you want to call it, will help you maintain a reduced-stress life. We will always have stress. It’s our perception and reaction to the stress that dictates our physiologic outcome.

In 2021, this is the best path to a healthy microbiome and thus a healthy body.

Dr. M

Yeoh Gut
Cani Gut
Kho Frontiers in Microbiology
Functions Table