The Microbiome Diet 101 Part 3 Spotlight On Supplements

In this third and last installment of our three part series, we’ll look more deeply at the details of the 4R program and supplements that are instrumental to healing the body and gut microbiome.

The 4 R’s of intestinal health


In Part 2 we discussed the details of The Microbiome Diet as well as touching on the first element of the 4R program that removes foods interfering with a healthy microbiome. In addition to diet, a key part of transforming the microbiome relies on specific herbs and compounds to remove unhealthy bacteria from the intestine. Great Microbiome Diet supplements include berberine, caprylic acid, garlic, grapefruit seed extract, oregano oil and wormwood are all useful to make shifts towards a positive bacterial balance. A good quality water filter should be used to lower the amount of toxins that we are all exposed to every day. Eat organically grown foods whenever possible to minimize any exposure to harmful chemicals and hormones in animals. Switch to natural versions of common household cleaners, cosmetics and personal care items, like make up and shampoo, to help lessen your body’s toxic burden even further. Additionally, we must stop the overuse of antibiotics, NSAID’s and drugs, like proton pump inhibitors, which decimate the microbiome, wiping out beneficial strains of bacteria.


Stomach acid and digestive enzymes play a key role in health by breaking down foods to their smallest components, making them easily absorbed into the intestine. Additionally, the acidic pH of the stomach creates a protective, hostile environment for pathogens hitching a ride on foods. Without enough of these important substances, nutrient deficiencies are common including B6, B12, folate, calcium and iron, plus microbiome imbalances are more likely. It is wise to replace hydrochloric acid and enzymes like protease, lipase, amylase and even some DPP IV, which can help breakdown gluten during accidental exposure. Apple cider vinegar is another great option that can help ignite the flames of digestion, as well as being antimicrobial by nature.


The intestine is home to the trillions of bacteria living in the gut microbiome and the majority of the immune system. It’s the place where our inner world meets the outside world, so having a well-maintained border is imperative. If the intestine is weakened or compromised, the immune system and microbes will suffer having a ripple effect through the entire body. In the repair phase, powerful healing compounds are used to stop and prevent leaky gut, and additionally protecting the body from over activity of the immune system that often happens as a result of large, undigested food particles slipping through a weakened gut wall. Zinc, carnosine, DGL, glutamine, marshmallow, N-acetyl glucosamine, quercetin, slippery elm, and Vitamin D, all help to soothe and heal intestinal damage.


While The Microbiome Diet emphasizes the use of probiotic foods, targeted probiotic supplements are also important and afford us the possibility of controlling the types of strains introduced to the ecology. In general, a good quality probiotic contains many diverse species. It has at least three types of Lactobacillus-acidophilus, rhamnosus, plantarum; contains different types of Bifidobacteria, when possible also has Acidophilus reuteri and should contain between 50 and 200 billion bacteria. Additionally, specific species can be added for specific conditions. In cases of autoimmunity and candida, we may add in Saccharomyces boulardii. For patients suffering with diarrhea, Culturelle’s strain of Lactobacillus GG is a great option, while B infantis 35624, found in Align, works wonders for high levels of inflammation as seen with elevated TNF-alpha levels.

When used in conjunction with The Microbiome Diet, The 4R approach can help restore a healthful microbiome balance, heal the intestine and rejuvenate the body.

For further details, complete food lists and meal plans please refer to The Microbiome Diet by Raphael Kellman, MD, available on

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