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 support our body's natural defenses. It can be influenced by the foods we eat, our environment, and our lifestyle.

The Microbiome Diet may be an option for someone looking to support their overall health. This diet focuses on eating foods that may help maintain 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.

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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 supporting gut health and thus promoting overall well-being.

How To Follow the Microbiome Diet

The microbiome diet is a three-phase program aimed at supporting 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 may interfere with a healthy microbiome
Repairing the gut wall
Replacing stomach acid and pancreatic enzymes
Reinoculating with 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 that may help 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 may produce short-chain fatty acids that support gut barrier integrity and function, and may help modulate lipid and glucose metabolism, as well as the inflammatory response and immune system.

Probiotic Foods

Probiotic foods, such as kimchi and sauerkraut, may impact the gut microbiota composition. They can help support the body's natural defenses against pathogenic bacteria in the intestine and may help the host build a healthy intestinal mucosa layer. 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 consider avoiding 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

Supplements

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

The diet also suggests taking zinc, vitamin D, glutamine, marshmallow, quercetin, and slippery elm, to support the intestinal lining. Probiotics are suggested 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. Participants should continue to omit foods from phase 1 that they find inflammatory. 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 supported. 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 suggests 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 supports optimal health. In contrast, an impaired microbiome, known as dysbiosis, has been associated with an increased risk of many health conditions, including:

Summary

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 support health. 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 may 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.