(Woodpath is an education site focused exclusively on gut health. Our articles are researched by clinical nutritionists and contain citations at the end of the page.)

The gut microbiome is made up of 300-500 bacterial species and nearly 2 million genes. (Quigley, 2013)

It's important to maintain a balance of good to bad bacteria. A healthy gut can lead to a host of health benefits, including:

  • A better functioning brain
  • More stabilized moods
  • Improved digestion
  • Metabolism and energy increase
  • Reduction in unhealthy food cravings
  • Decrease in inflammation

When the gut has too much of a pathogenic bacteria — or not enough good bacteria — digestion becomes sluggish. You may have increased cravings for carbs and sugar. Inflammation and weight may increase, as may symptoms of depression and anxiety. You may also experience a decrease in mental clarity and functioning.

Maintaining gut balance can be tricky, leading to gut dysbiosis. Several factors cause this, including a poor diet high in processed foods and sugar, particular medications such as PPIs/antacids, and the overuse of antibiotics.

The Microbiome Diet

The microbiome diet was developed by Dr. Raphael Kellman, a board-certified physician who specializes in gut health. It focuses on improving the gut, the immune system, and the overall health of the body. This article is an overview of his approach.

These improvements are made by consuming foods that balance gut bacteria.

The microbiome diet contains three phases:

Phase 1

The first phase is strict and lasts three weeks. The objective is to rid the gut of unhealthy bacteria, replace stomach acids and digestive enzymes, and repopulate the gut with prebiotics and probiotics to repair the stomach lining.

This phase also follows the four Rs of intestinal health:

1. Remove: Cut out all foods that disrupt a healthy microbiome. This means all foods that have come into contact or were produced with:

  • Pesticides
  • Chemicals
  • Hormones
  • Antibiotics
  • Other medications

2. Repair: Consume a plant-based diet and taking supplements that repair the gut and support the microbiome

3. Replace: Consume ingredients and supplements that help to increase stomach acid and pancreatic enzymes that aid in digestion. Make sure to eat:

  • Apple cider vinegar
  • Ginger
  • Fermented vegetables
  • Peppermint, anise, cardamom, and coriander
  • Pineapple

4. Reinoculate: Repopulate your gut with healing, healthy bacteria by taking supplements as well as eating foods rich in prebiotics and probiotics such as:

  • Garlic
  • Asparagus
  • Jerusalem artichokes
  • Edible seaweed
  • Leafy green vegetables
  • Fermented foods such as sauerkraut and kimchi
  • Miso
  • Kombucha

Strive only to eat organic foods, and avoid all foods containing grains, eggs, legumes, dairy, and starchy fruits and vegetables. Also avoid all processed foods and foods containing sugar, preservatives, food coloring, and artificial sweeteners.

The following supplements are recommended during this phase because they help reduce inflammation, leaky gut and the amount of bad bacteria living in the gut:

  • A high quality probiotic supplement. We recommend Culturelle and Florastor
  • Zinc
  • Glutamine
  • Vitamin D
  • Oregano oil

Phase 2

By this time the intestines have started to heal, there is a decrease in inflammation, and the microbiome is steadily getting healthier and much stronger.

In phase 2, you continue to eliminate foods that damage the gut. But you add new healthy foods that were previously avoided.

This part of the diet lasts four weeks. In addition to Phase 1, allowable foods now consist of:

  • Dairy: Grass-fed goat or cow milk, cheese, yogurt, and kefir  
  • Eggs: Organic, free-range eggs. Local, if possible.
  • Fruit: Mango, melon, papaya, and peaches
  • Gluten-free grains: Quinoa, wild rice, brown rice, millet, buckwheat, amaranth
  • Legumes: Chickpeas, lentils, kidney beans, pinto beans, and navy beans
  • Some starchy vegetables such as Sweet potatoes and yams

Phase 3

Phase 3 is often considered the maintenance phase — it doesn't have to be followed for any specific amount of time.

The goal of this phase is to help you maintain feeling your best, to maintain continuous health, and to maintain a healthy weight or continued weight loss until you reach your personal goal.

At this point, you should have balance and restoration in your gut microbiome and digestive system. However, to maintain optimum health and avoid regressing, it is best to continue avoiding processed foods, sugar, and anything else containing toxins, chemicals or hormones.

Additional Foods that Restore Gut Health

You can have any of the foods below at any point throughout the diet:

  • Healthy fats: Avocado, wild salmon, other low mercury fish, and olive oil
  • Non-starchy vegetables: Carrots, arugula, artichokes, leeks, onions, and radishes.
  • Non-starchy fruits: Melon, apples, strawberries, cherries, grapefruit, oranges, and coconut.
  • Nuts and seeds: Chia seeds, pumpkin seeds, pistachios, almonds, walnuts, and cashews.
  • All herbs and spices

Additional Foods to Temporarily Avoid in Phase 1

It is essential that you eliminate foods that may contribute to inflammation, dysbiosis and SIBO. These include:

  • Fried foods
  • High-fructose corn syrup
  • Trans and hydrogenated fats
  • Starchy vegetables: Potatoes, corn, lima beans, and peas
  • Starchy fruits: Bananas, pumpkins, and plantains
  • Deli meat
  • Some nuts: Peanuts and soy
  • Fish high in mercury, such as tuna
  • Dried fruit
  • Fruit juice
  • All grains that contain gluten
  • Foods containing yeast: Bread, salad dressing, alcohol

Woodpath Editor's note: The above recommendations are a summary of those made by Dr. Raphael Kellman. All practitioners practice differently and may recommend different dietary choices and supplements. Always work with your healthcare provider to discuss your individual needs and concerns before starting a new healthcare regime.

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Research Citations

  • Ng M, Fleming T, Robinson M, Thomson B, Graetz N, Margono C, et al. Global, regional, and national prevalence of overweight and obesity in children and adults during 1980-2013: a systematic analysis for the Global Burden of Disease Study 2013. The Lancet. 2014;384(9945):766-81. doi: 10.1016/S0140-6736(14)60460-8.
  • Harakeh SM, Khan I, Kumosani T, et al. Gut Microbiota: A Contributing Factor to Obesity. Frontiers in Cellular Infection Microbiology. 2016;6:95. doi:10.3389/fcimb.2016.00095
  • Quigley E.M.M. Gut Bacteria in Health and Disease. Gastroenterology & Hepatology. 2013; 9(9): 560–569.

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