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The Microbiome Diet: Everything You Need To Know

The Microbiome Diet: Everything You Need To Know

The gut microbiome is an essential part of the human body. It is made up of microorganisms, like bacteria and fungi, that live in our digestive system. The microbiome helps us to digest food, absorb nutrients, and protect us from disease and can be affected by the foods we eat, our environment, and our lifestyle.

The Microbiome Diet may be an excellent choice for someone looking to improve their overall health. This diet focuses on eating foods that support a healthy microbiome, such as probiotics, prebiotics, and fiber-rich foods. It also includes foods that are low in processed sugars and refined grains.

This article discusses The Microbiome Diet and its possible health benefits.


What is the Microbiome Diet?

The Microbiome Diet was created by Dr. Raphael Kellman, MD, a physician of Integrative and Functional Medicine, and is based on eating and eliminating certain foods for specific periods of time in the hopes of restoring gut health and thus promoting optimal overall health.

How To Follow the Microbiome Diet

The microbiome diet is a three-phase program aimed at restoring gut health. 

  • phase 1 (the strictest of the 3 phases, also known as the elimination diet) lasts for 21 days
  • phase 2 (a period of more flexibility) lasts for 28 days
  • phase 3 (the maintenance phase), which can last indefinitely

Phase 1-The 4 R's

Phase 1 of the diet lasts for 21 days and focuses on the 4 Rs:

  • Removing foods that interfere with a healthy microbiome
  • Repairing the gut wall
  • Replacing stomach acid and pancreatic enzymes
  • Reinoculating with large amounts of beneficial probiotic bacteria

Foods to Incorporate

The focus of phase 1 is to shift to an organic, plant-based diet that includes "Microbiome Superfoods." These foods contain prebiotic fibers necessary to feed and nourish the healthy strains of intestinal bacteria, giving them the energy to grow, multiply and thrive. The foods include:

Prebiotic Foods

Prebiotic Foods such as artichokes, onions, and garlic produce short-chain fatty acids that improve the gut barrier integrity and function, modulate lipid and glucose metabolism, and the inflammatory response and immune system.

Probiotic Foods

Probiotic foods, such as kimchi and sauerkraut, impact the gut microbiota composition. They can inhibit the colonization of pathogenic bacteria in the intestine, help the host build a healthy intestinal mucosa layer, and enhance the host's immune system. These foods include:

  • fruits, such as apples, nectarine, berries, grapefruits, kiwi, oranges, cherries, and rhubarb
  • healthful fats from fish, nuts, avocado, and seeds
  • oils, including flaxseed, sunflower, and olive oil

Foods to Avoid

During this phase, it is advised that people avoid the following foods and ingredients: 

  • gluten
  • dairy products (except butter and ghee)
  • grains
  • eggs
  • packaged foods
  • soy
  • fruit juice
  • potatoes
  • corn
  • peanuts
  • legumes (except chickpeas and lentils)
  • high mercury fish
  • deli meat
  • artificial sweeteners
  • high-fructose corn syrup
  • fillers and colors
  • trans or hydrogenated fats and fried foods


In addition to dietary changes, the microbiome diet recommends the use of some supplements during Phase 1, such as antimicrobials (berberine, caprylic acid, garlic, grapefruit seed extract, and oregano oil to kill pathogens), acids (apple cider vinegar) and enzymes (protease, lipase, and amylase), to help break down proteins, fats, and carbohydrates in food. 

The diet also recommends taking zinc, vitamin D, glutamine, marshmallow, quercetin, and slippery elm, to benefit the intestinal lining. Probiotics are recommended from strains such as Lactobacillus acidophilus, Rhamnosus, Plantarum, Bifidobacterium, and Acidophilus reuteri.

Phase 2 – The Metabolic Boost

Phase 2 introduces a wider range of foods over the next 28 days. By this time, it's assumed that the gut and microbiome have gotten stronger, allowing more flexibility with the diet. Patients should continue to omit inflammatory foods from phase 1. The foods that can be consumed are:

  • sheep or goat's milk dairy 
  • kefir
  • coconut yogurt
  • organic, free-range eggs
  • melons, mangos, peaches, and pears
  • gluten-free grains, including quinoa, buckwheat, amaranth, millet, gluten-free oats, basmati, brown, and wild rice
  • beans
  • sweet potatoes and yams

Phase 3 – The Lifetime Tune-Up

After Phase 2, the gut and microbiome are believed to be almost fully healed. Phase 3 aims to maintain the results obtained in phases 1 and 2. Phase 3 has no recommended length; participants are encouraged to continue the diet and avoid processed foods and added sugar as much as possible. In the case of severe digestive discomfort or other symptoms on the microbiome diet, individuals should talk to a physician or registered dietitian. 

An integrative practitioner can run specialty tests like a comprehensive stool or food sensitivity test to see what is going on at a deeper level. It is always recommended to consult a healthcare team before beginning a new diet plan.

Evidence Supporting the Use of The Microbiome Diet

Research into the human microbiome continues to emerge and demonstrates that a healthy gut flora is associated with optimal overall health and well-being. It is now also known that diet is a vital component of the relationship between humans and their microbial residents. In fact, experiments have shown that dietary alterations can induce gut microbial changes in as little as 24 hours. 

There are no specific studies evaluating The Microbiome Diet; however, it is well known that a diverse and healthy gut flora promotes optimal health. In contrast, an impaired microbiome, known as dysbiosis, has been associated with an increased risk of many health conditions, including:


Diet is a key modifiable factor that has been shown to influence the composition of the gut microbiome. As a healthy and diverse microbiome has been linked with reducing the risk of numerous health conditions, it stands to reason that if there were a diet that positively impacts our gut microbiome, it could be helpful to follow it. No current studies specifically address the purported benefits of the Microbiome Diet. Still, many strategies, such as incorporating more fiber-rich plant foods and avoiding processed and packaged foods, are known to reduce disease risk. Thus, The Microbiome Diet may help some people achieve a healthier and more balanced gut microbiota. Working with a dietician or functional medicine provider to address gut health through dietary changes will likely provide health benefits, especially when compared to consuming a Standard American Diet.

Disclaimer: *Rupa Health is not affiliated with Dr. Kellman, and this article is not an endorsement of The Microbiome Diet.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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