Microbiome Diet, Did You Know

Synopsis of Diet Plan. This diet involves three phrases, and, throughout all phases, dieters are encouraged to take “microbiome supersupplements” (ingredients such as garlic, berberine, wormwood and grapefruit seed extract), digestive enzymes, prebiotics and probiotics. Kellman also suggests apple cider vinegar supplementation.

Plate Diagram of acceptable foods


Synopsis of Diet Plan

The first phase is devoted to the removal of unhealthy bacteria, replacement of digestive enzymes, reinoculation with pre- and probiotics and repair of the intestinal wall. Dieters follow Phase 1 for three weeks by removing processed or packaged foods, juices, some fruits, gluten, all grains, sugars and sweeteners, dairy products, eggs, soy, processed or deli meats, peanuts, potatoes and most legumes, among other foods. The second phase lasts four weeks, and dairy, eggs, fruits, gluten-free grains, legumes and sweet potatoes are added back in. Dieters are asked to follow the diet with 90-percent compliance. The final phase, which lasts in perpetuity, promotes all foods allowed in Phase 2 with 70-percent compliance.


Nutritional Pros and Cons.

Kellman urges readers to eat foods that feed healthy gut bacteria and avoid foods that nourish harmful gut bacteria, a commendable dietary approach. He also encourages readers to change their relationship with food and describes the perils of stress eating. By Phase 3, the Microbiome Diet calls for a generally healthy diet with 70-percent compliance, allowing for more flexibility and the occasional indulgence.

Bottom Line.

Kellman believes all health begins in the gut and he thoroughly explains the relationship between gut bacteria and health, as well as the value of mindful eating and creating a healthy relationship with food. Unfortunately, the benefits of healthy gut bacteria are often overlooked – or perhaps poorly understood or publicized – as is the potential risk of harmful gut bacteria on obesity and chronic disease.

The Microbiome Diet centers around the idea that the key to optimal body function—and in turn, high metabolism and weight loss—is a thriving internal ecosystem of bacteria. “Research reveals that when the microbiome goes out of balance, people often gain weight, even when they haven’t changed their diet or exercise,” Kellman writes. “An imbalanced microbiome often dooms just about any diet to failure. When the microbiome is balanced, however, people often lose weight, even when they don’t make any other changes.”

It makes plenty of sense: 90% of our cells are bacterial, and there’s strength in numbers. “These intestinal organisms—bacteria—digest your food, govern your appetite, control your metabolism, orchestrate your immune system, influence your mood, and even help determine how your genes are expressed,” Kellman says. “They have a major impact on whether your heart is healthy, whether your bones develop properly, and whether your brain feels sharp and clear or fuzzy and unfocused. They sustain the gastrointestinal tract so your food is properly digested and you get all the nourishment you need. They produce crucial vitamins and other nutrients. They even manufacture natural antibiotics.”https://www.byrdie.com/microbiome-diet


Processed foods of all kinds are out of the question, as are sugar, eggs, soy, gluten, dairy, yeast, dried fruits, and fungus. Even gluten-free grains like quinoa and brown rice and starchy vegetables and legumes like potatoes, peanuts, and kidney beans are off-limits, as the sugars in those foods can feed bad bacteria. 


Most non-starchy veggies and fruits are just fine, with a special emphasis on fermented foods like pickles, sauerkraut, and kombucha (which contain digestion-friendly bacteria strains). Chickpeas and lentils are the only legumes permitted, and Kellman advises sticking with coconut oil or ghee. For protein, beef, chicken, low-mercury fish, lamb, and shellfish are all fine (though as low-processed as possible).Kellman also suggests a variety of bacteria-promoting supplements to ingest daily, the most important of which being a probiotic and prebiotic. And here’s where things take a turn for the amazing: A couple cups of coffee per day are allowed, as are wine and beer, since they’re fermented.

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.

https://kellmancenter.com/2016/11/the-microbiome-diet-101-part-2/For complete food lists and meal plans please refer to The Microbiome Diet by Raphael Kellman, MD available on Amazon.com.

Thank you for reading 🙂


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