The Microbiome Diet 101 Part 2

In this second installment of our three part series, we’ll look at the details of The Microbiome Diet plan and get ready to take a deeper dive into supportive and healing compounds in part three.

The Microbiome Diet Phase 1-The 4 R’s

The 4R approach to intestinal health works to rebalance gut flora by:

  1. Removing foods that interfere with a healthy microbiome, disruptive bacteria, pathogens and toxins
  2. Repairing the gut wall
  3. Replacing needed stomach acid and pancreatic enzymes
  4. Reinoculating with large amounts of healing, probiotic bacteria

Diets high in refined carbohydrates, fat, sugar, processed foods, coloring, and fillers are what creates the perfect storm to allow opportunistic strains of bacteria to overgrow, as well as pathogens to dominate the balance of the ecology. By removing them, the intestine can heal and the composition of the microbiome begins to change for the better. Patients are advised to avoid the following for the first 3 weeks:

  • Packaged foods
  • Gluten
  • Soy
  • Fillers/Color
  • High-fructose corn syrup
  • Artificial sweeteners
  • Trans/hydrogenated fats
  • Potato/Corn
  • Deli meat
  • Peanuts
  • Fried foods
  • High mercury fish
  • Fruit juice
  • Eggs
  • Grains
  • Dairy (except butter/ghee)
  • Legumes (except chickpeas/lentils)

The focus should shift to an organic, plant based diet that includes “Microbiome Superfoods”. These are foods that contain prebiotic fibers necessary to feed and nourish the healthy strains of intestinal bacteria, giving them the energy to grow, multiply and thrive. Since these fibers are indigestible by us humans, they make it into the intestine intact, where they are fermented and broken down by our tiny friends. In the process, compounds called Short Chain Fatty Acids (SCFA) are released, which have many positive effects on our health. It’s a win/win for everyone! Asparagus, garlic, Jerusalem artichoke, Jicama, onion, leek, and radish are all terrific examples of prebiotic foods.

Probiotic foods are equally as important, as they loaded with huge amounts of healing bacteria. Fermented vegetables, kimchi, sauerkraut, plus sheep, and goat’s milk products like kefir and yogurt, contain exponentially more healing bacteria than supplements do. A true Microbiome Diet includes liberal use of these foods to boost the quantity and types of strains that should be found in great numbers in the ecology.

Fruits such as apples, berries, cherries, coconut, grapefruit, kiwi, nectarine, orange and rhubarb are also included. To round things out, healthy fats from nuts, seeds (natural nut/seed butters), avocado, fish, and oils from flaxseed, sunflower and olive are all great choices. When it comes to animal proteins, make the healthiest choice possible by focusing on organic, free range and cruelty-free versions.

We will explore more on the 4R’s and healing supplements in Part 3.

Phase 2 – The Metabolic Boost

After the first 21 days on the diet, the intestine have begun to heal, inflammation is down, and positive shifts are already taking place in the microbiome. In this next phase, we continue to omit damaging foods, while adding in the following for the next four weeks.

  • Dairy – goat or sheep’s milk products such as milk, cheese and yogurt, kefir of all types including cow’s milk, and coconut yogurt
  • Eggs – organic, free range
  • Fruits – mango, melon, peaches, and pears
  • Gluten free grains – including mmaranth, buckwheat, millet, oats (certified GF), quinoa, brown rice, basmati rice, and wild rice.
  • Legumes – green beans and all types of beans, including black, kidney, red and white
  • Sweet potatoes and yams

Phase 3 – The Lifetime Tune-Up

At this point in the process, the intestine is healing or has fully healed and so has the microbiome! A good rule of thumb is to always try to avoid the damaging foods, listen to your body, and follow your inner guide as to what foods work or don’t work for you. By maintaining The Microbiome Diet principles, the health of the bacterial communities is ensured.

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

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