Ten trillion cells make up the human body. There are 100 trillion bacteria that reside in and on us; these are known as the microbiome. There are approximately 35,000 varieties of bacteria that make up the human microbiome. These combined bacteria weigh 3–4 pounds — about the weight of the brain. Your gut and its bacteria are by far the largest immune system organ in your body. The gut and its bacteria provide about 80% of immune function. If these work poorly, your liver is asked to do much more. Because of their function, your gut and its microbiome are considered your second liver.

The neurons of the gut are so innumerable that many scientists are now calling it a second brain. The gut also produces many neurotransmitters and short-chain fatty acids. One of the neurotransmitters is serotonin (the “happiness neurotransmitter”) which helps create contentment; 80% of serotonin is produced in the gut.

All manner of disease is rooted in inflammation. With its immune giftedness, the gut is the greatest defense against inflammation. Bacteria are the first line of defense and teach our immune system how to proceed. It is now known that our weight, in part, is determined by the ratio of two types of bacteria colonies: firmicutes and bacteroidetes. If the percentage of firmicutes is higher than bacteroidetes, you will be heavier.

Keeping your gut and bacteria healthy requires your attention. Environmental chemicals and chlorinated water are examples of forces that work against our bacteria’s well-being. Don’t store food in plastic wrap or plastic with a recycle code of 3, PC, or 7. Don’t use nonstick pans, and don’t microwave food in plastic. Foods with high fructose corn syrup, gluten, and sugar cause harmful bacteria to proliferate. In large doses, cortisol (the “stress hormone”) can play havoc on your microbiome. Death to beneficial bacteria occurs with antibiotics and poor nutrition.

From the esophagus to the anus, your body is lined with only a single layer of epithelial cells. Known irritants to the gut, like those noted in the previous paragraph, create a widening of these cell junctures, resulting in a condition known as leaky gut, a huge pro-inflammatory condition that affects overall health. The brain seems to be especially vulnerable to leaky gut. The top irritants which cause leaky gut are gluten, sugar, and high fructose corn syrup.

A key to a healthy microbiome is fiber. A variety of fiber is essential for a more diverse microbiome. Keys are dark green vegetables, fibers that are grown above ground. These fiber varieties are also known as prebiotics. Onions, raw leeks, raw garlic, raw dandelion greens, raw asparagus, raw chicory root, gum arabic, and raw Jerusalem artichoke are considered some of the best sources of a prebiotic. You cannot be healthy without plant fiber.

What are the steps that will heal your gut? First, eliminate gluten from your diet and all manufactured fructose, limit fruit, and avoid chlorinated water. Choose foods rich in prebiotics. Consume fermented foods, such as pickles, sauerkraut, kimchi, kefir, yogurt, kombucha. Choose foods pickled in brine, not vinegar. Eat low carb. The more carbs consumed, the sicker the microbiome. Low-fiber and high-carbohydrate diets are linked to gut permeability, mitochondrial damage, immune compromise, and increased inflammation. Enjoy wine, tea, coffee, and dark chocolate; these are high in flavonoids. Choose foods rich in prebiotics — dark green vegetables that grow above ground. Use water that is filtered to remove chlorine.

Fasting is a powerful tool to change the percentage of your microbiome from bad to beneficial bacteria. This author prefers to fast four times a year, having a water-only fast lasting 24–72 hours. Come out of the fast with high-fiber foods or a prebiotic supplement and then follow with a probiotic. A good probiotic comes from these five core species:

1. Lactobacillus plantarum

2. Lactobacillus acidophilus

3. Lactobacillus brevis

4. Bifidobacterium lactic

5. Bifidobacterium longum

Eat high-quality fats, including coconut oil, butter, ghee, and olive oil. Reduce the amount of omega-6 fats and increase the amount of omega-3 fats. In addition, consume turmeric, vitamin D3, and alpha-lipoic acid.

The most effective way to administer a probiotic is by an enema. An oral probiotic has its benefits, but there are great changes in the microbiome through an enema. The right way to administer a probiotic by way of an enema is to take 3–6 capsules or 1/8 teaspoon of powder probiotic and add it to 12 oz. of filtered, non-chlorinated water and stir until dissolved. Fill an enema bottle. Lie on your side on a towel and insert the nozzle tip into the rectum; lubricate if needed. Slowly squeeze the bottle or bottles to get the 12 oz. of probiotic injected. Your goal is to hold the water for 30 minutes.

If you have been on aggressive antibiotic treatment, readminister three times a week for 4–6 weeks.  


Perlmutter, David, MD, and Kristin Loberg. Brain Maker: The Power of Gut Microbes to Heal and Protect Your Brain for Life. Boston: Little, Brown and Company, April 28, 2015.

Brian Rafool

Brian Rafool


Contact Me