The microbiome diet was the idea of Dr. Raphael Kellman to encourage beneficial gut bacteria to grow in the digestive tract. Keeping the gut bacteria healthy is essential for human health.

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This article looks at how the diet works, what it involves, foods to eat and avoid, and what the research says.

We will also look at the pros and cons of the microbiome diet.

a woman preparing food that she is going to eat as part of her microbiome dietShare on Pinterest
The microbiome diet focuses on plant-based foods.

The “microbiome” refers to the collection of microorganisms present in a person’s intestines. These microorganisms include bacteria, fungi, and archaea. Having a diverse range of “good” gut flora benefits a person’s health.

However, gut flora can become less diverse and less beneficial for many reasons. The microbiome diet aims to improve the microbiome and overall health, as a result.

Dr. Kellman, who specializes in holistic and functional medicine, developed the microbiome diet. The Kellman Wellness Center website states that looking after the microbiome is important for the following reasons:

  • In the right balance, most strains of gut bacteria contribute to human health.
  • The microbiome creates short chain fatty acids (SCFAs), which decrease inflammation, boost brain function, and help the immune system.
  • Microbes in the gut help regulate a person’s metabolism and mood.

The microbiome diet has three phases. The first two phases take a total of 7 weeks to complete. The final phase is a long-term maintenance diet.

Phase 1

The first phase of the diet lasts for 3 weeks, and focuses on:

  • removing disruptive food, bacteria, pathogens, and toxins
  • repairing the gut lining
  • replacing stomach acid and pancreatic enzymes
  • reinoculating with beneficial bacteria strains

During this phase, Dr. Kellman advises that people avoid the following foods and ingredients:

  • gluten
  • dairy products, except butter and ghee
  • grains
  • eggs
  • packaged foods
  • soy
  • fruit juice
  • potatoes and 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
  • fried foods

Dr. Kellman advises that people focus on plant-based foods that increase microbiome diversity, such as:

  • prebiotic foods, such as Jerusalem artichoke, onions, and garlic
  • probiotic foods, such as sauerkraut and kimchi
  • fruits, such as apples, berries, cherries, grapefruits, kiwi, nectarine, orange, and rhubarb
  • healthful fats from fish, avocado, nuts, and seeds
  • oils, including flaxseed, sunflower, and olive oil

If a person eats animal proteins, Dr. Kellman recommends focusing on wild fish and grass fed meat.

Phase 2

After phase 1, a person following this diet can start to introduce a wider range of foods over the next 4 weeks, including:

  • sheep or goat’s milk dairy and kefir
  • organic, free-range eggs
  • mangos, melons, peaches, and pears
  • gluten-free grains, including amaranth, buckwheat, millet, gluten-free oats, quinoa, brown, basmati, and wild rice
  • beans, including, green, black, red, white, and kidney beans
  • sweet potatoes and yams

Phase 3

The final phase of the microbiome diet aims to maintain the results of phases 1 and 2. Dr. Kellman advises that people continue avoiding foods that damage gut flora and the gut lining.

In addition to dietary changes, the microbiome diet recommends the following supplements during phase 1:

  • Antimicrobials: These include berberine, caprylic acid, garlic, grapefruit seed extract, and oregano oil to kill pathogens.
  • Acids and enzymes: Supplements containing digestive enzymes, such as protease, lipase, and amylase, to help break down proteins, fats, and carbohydrates in food. The diet also recommends taking apple cider vinegar to stimulate stomach acid production.
  • Gut lining supplements: These can include zinc, vitamin D, glutamine, marshmallow, quercetin, and slippery elm, among others, to benefit the intestinal lining.
  • Probiotics: These should be products with 50–200 billion bacteria with strains such as Lactobacillus acidophilus, Rhamnosus, Plantarum, bifidobacteria, and Acidophilus reuteri.

Dr. Kellman also recommends that people following the diet:

  • use a good quality water filter
  • eat organic foods to limit exposure to pesticides and hormones
  • switch to natural versions of household and personal products
  • avoid the overuse of antibiotics
  • avoid nonsteroidal anti-inflammatory drugs, such as ibuprofen
  • avoid proton pump inhibitors, which reduce stomach acid production

No studies have proven explicitly that the microbiome diet works to improve a person’s microbiome or that it can treat health conditions.

However, the idea that diet can benefit the microbiome and that this, in turn, can benefit human health, does have evidence to support it.

As the microbiome plays a role in immunity and inflammation, a healthy microbiome may reduce the risk of diseases, such as:

The food a person eats can positively impact the microbiome in the gut.

A 2013 study showed that dietary changes could rapidly affect the abundance of specific species of bacteria in people’s digestive tracts. As such, switching to a different diet will change the microbiome.

A review in 2019 noted, more specifically, that a plant-based diet may promote a healthy diversity of gut flora. As the microbiome diet contains many plant foods, it may have similar benefits.

Another key element of the microbiome diet is probiotics. Research into the potential benefits of probiotics is ongoing. A 2017 review found evidence they could help with:

However, scientists are still trying to understand how specific foods and bacterial species affect the microbiome.

A 2019 study found that similar foods could affect people’s gut flora in very different ways, depending on the individual. This suggests that how a diet influences the microbiome is also individualized.

As genetics have an impact on how changes to the microbiome affect human health, people may need a more personalized approach to nutrition than the microbiome diet. This is especially true if a person has any underlying health conditions.

Overall, scientists need to carry out more research on the ways that specific food choices and probiotic strains impact the microbiome.

Evidence suggests that a healthy and diverse microbiome is beneficial to human health. The microbiome diet could support this by encouraging people to eat plant-based foods.

Plant-based diets can also benefit people who are overweight to reach a healthier weight.

Some people may notice the benefits of the microbiome diet from its focus on vegetables, fruits, healthful fats, and lean proteins.

However, others may experiences side effects from the restrictions and supplements the microbiome diet recommends. For example, some people experience bloating and gas with a sudden increase in fiber, and when taking probiotics.

These effects typically resolve over time as the body gets used to a higher fiber intake. Probiotic treatment, on the other hand, should be individualized as not everyone benefits from the same strains.

Additionally, it may not be necessary for a person to take antimicrobials and other supplements. Many of the herbal supplements the microbiome diet recommends do not have high quality research to support their use, and they may be expensive and unnecessary.

A person should always consult a doctor before using supplements, particularly if they are pregnant, breastfeeding, take medication, or have a chronic health condition.

It is also a good idea to talk to a dietitian before following a restrictive diet to ensure a person gets the nutrients they need.

If someone is experiencing digestive issues, such as nausea, reflux, bloating, and diarrhea, it is important to consult a doctor for advice before starting a new diet. These symptoms can be a sign of an underlying medical condition that may need immediate attention.

Learn more about the side effects of probiotics here.

The microbiome diet is a plant-based diet that may promote beneficial microorganisms in the gut. A diverse microbiome reduces the risk of some diseases, and probiotics can improve the symptoms of conditions, such as IBS and eczema.

However, studies have not verified the health benefits of the microbiome diet specifically. The diet also includes a variety of supplements and removes some foods from the diet permanently. It is a good idea to talk to a doctor or dietician about this first to prevent unwanted side effects.

Typically, a diet that promotes fruits, vegetables, healthful fats, and good sources of protein is likely to benefit health compared with the standard Western diet. A personalized approach to food choices may help people find the best diet for them.