What Is the Microbiome Diet?

Microbiome Daughter

Verywell / Debbie Burkhoff

At Verywell, we believe there is no one-size-fits-all approach to a healthy lifestyle. Successful eating plans need to be individualized and take the whole person into consideration. Prior to starting a new diet plan, consult with your healthcare provider or a registered dietitian, especially if you have an underlying health condition.

Your microbiome is a vast ecosystem of 100 trillion microorganisms living in your digestive tract. It’s also referred to as the gut microbiota, intestinal flora, gut flora, or simply the gut. Research has shown that a healthy gut is critical to overall health and that eating foods that nurture the gut can improve health and wellness. This is the premise behind the microbiome diet.

Though there are many ways to eat to optimize gut health, the microbiome diet was developed by Raphael Kellman, MD, author of "The Microbiome Diet: The Scientifically Proven Way to Restore Your Gut Health and Achieve Permanent Weight Loss." Dr. Kellman treats thyroid disorders, autoimmune conditions, Lyme disease, digestive dysfunction, and other health conditions at his Kellman Center for Integrative and Functional Medicine by focusing on the gut microbiome.

The microbiome diet is a three-phase program that begins with an elimination diet, which claims to restore gut health in those who've been eating non-microbiome-friendly foods for a long time. Phases two and three are less restrictive, but all three phases focus on consuming mostly fruits, vegetables, lean protein, and a large amount of prebiotic and probiotic foods.

Dr. Kellman posits that an imbalanced microbiome causes cravings for sugar and unhealthy fatty foods and that a balanced microbiome will increase your cravings for healthy foods. However, Dr. emerging evidence shows that it’s not just bacteria that are crucial for gut health. The other microorganisms in the gut—particularly fungi—are just as important.

What Experts Say

“The microbiome diet claims to optimize gut health. Experts agree that eating prebiotic- and probiotic-rich foods and limiting added sugar both support gut well-being. However, phase one is unnecessarily restrictive and the supplement recommendations have little scientific support.”
Chrissy Carroll, RD, MPH

What Can You Eat?

The microbiome diet is a three-phase program that begins with an elimination diet, removing common “trigger” foods such as soy, corn, eggs, and dairy. The diet becomes less restrictive as you move throughout the phases, and by the end of phase three, you should be eating a primarily gut-friendly diet.

Microbiome diet recipes can be found in abundance on the internet, but you can also try anti-inflammatory recipes and Mediterranean recipes, many of which are also good for your gut. The full details of the microbiome diet can be found in Dr. Kellman's book (note there are several books with similar names).

What You Need to Know

There’s no timing aspect to the microbiome diet. During all three phases of the plan, Dr. Kellman encourages intuitive eating, or eating when you’re hungry and stopping when you’re full. Those on this plan are also encouraged to avoid counting calories or tracking portions. This will help you learn to understand your body’s natural hunger and satiety cues.

Phase 1: The Four R’s

The first phase of the microbiome diet is the most restrictive and is likely unnecessary for most people. During this 21-day phase, you’re required to avoid a vast amount of healthy foods, including soy, dairy, grains, eggs, legumes, and starchy fruits, and vegetables. But you'll also cut out sugar and artificial sweeteners, packaged foods, fillers, and coloring, which can be a boon to your health.

The main foods encouraged in phase one are organic, prebiotic-rich foods, such as asparagus, garlic, leeks, and onions, and fermented foods such as sauerkraut and yogurt, which are rich in probiotics. Phase one is based on the "Four R's":

  1. Remove: Eliminate any and all substances that may contribute to an unbalanced microbiome. This includes all processed foods, added sugar, hormones, antibiotics, and pesticides.
  2. Repair: Consume large portions of plant-based foods and supplements to help heal the gut after years of harming it with processed foods and toxins.
  3. Replace: Use herbs and spices and take supplements that can replace stomach acid and digestive enzymes to improve the quality of bacteria in your gut.
  4. Reinoculate: Eat foods with high probiotic and prebiotic content to repopulate your gut with beneficial bacteria. 

Phase 2: The Metabolic Boost

This 28-day phase allows for a little more flexibility based on the assumption that the first 21 days helped your gut grow stronger. Dairy, free-range eggs, legumes, and gluten-free grains are now allowed, as are some starchy fruits and vegetables, such as sweet potatoes and bananas.

During phase two, you still need to avoid certain foods about 90% of the time. This essentially means that you can have just a few servings a week of supposedly gut-damaging foods like soy, corn, and potatoes.

Phase 3: The Lifetime Tune-Up

By phase three, your gut should be fully "healed" or almost to that point, according to Dr. Kellman. Phase three is the maintenance phase of the microbiome diet, during which you can add back even more foods. Followers of the microbiome diet are encouraged to maintain this style of eating for life.

As a general rule, Dr. Kellman writes on his website, avoid the “damaging” foods, listen to your body’s cues, and pay attention to what foods work or don’t work for you.

What to Eat
  • Non-starchy fruit and vegetables

  • Lean protein

  • Low-mercury fish

  • Nuts and seeds (except peanuts)

  • Prebiotic and probiotic foods

What Not to Eat
  • Packaged foods

  • Grains and gluten

  • Soy

  • High fructose corn syrup and added sugars

  • Artificial sweeteners

  • Trans fats and hydrogenated oils

  • Corn and potatoes

  • Deli meat

  • Peanuts

  • Fried foods

  • Fruit juice and dried fruit

  • Starchy fruit and vegetables

  • Eggs

  • Dairy (except butter and ghee)

  • Legumes (except chickpeas and lentils)

  • Yeast and foods containing yeast

Non-Starchy Fruits and Vegetables

On the microbiome diet, you’re encouraged to eat a substantial amount of berries, leafy greens, and other non-starchy produce, which is thought to have a variety of anti-inflammatory and antioxidant effects on the body. Non-starchy fruits include avocados, cherries, kiwi, citrus fruits, coconut, and tomatoes. Non-starchy vegetables include asparagus, artichokes, onions, radishes, and leeks.

Lean Protein

Almost all sources of animal protein are allowed on the microbiome diet, except eggs, which can be reintroduced later. Dr. Kellman encourages people to eat grass-fed meat. If you’re choosing ground meats, look for ones with the lowest fat content possible.

Low-Mercury Fish

Mercury is toxic to humans, and like many health experts, Dr. Kellman recommends avoiding fish with high mercury levels. Low-mercury fish include salmon, trout, whitefish, mackerel, catfish, and sardines.

Nuts and Seeds

With the exception of peanuts (which are a type of legume), you can enjoy all kinds of nuts and seeds—and nut butters without added sugar—throughout the microbiome diet. Nuts and seeds are full of healthy fats, protein, and fiber that can help lower your cholesterol levels, aid in weight loss, and reduce inflammation.

Prebiotic and Probiotic Foods

These are the basis for the microbiome diet, and you should fill your diet with both prebiotic and probiotic foods. Prebiotics are a type of dietary fiber that provide food for the probiotic bacteria. Foods rich in prebiotics include artichokes, leeks, onions, dandelion greens, asparagus, and bananas—but remember that you can’t eat bananas until phase two of the diet.

Probiotic foods include fermented foods, such as kombucha, sauerkraut, pickles, tempeh, miso, kefir, and yogurt. However, soy and dairy aren’t allowed during the first phase of the program.

Packaged Foods

Packaged foods are often full of fillers, additives, colorings, and chemicals, not to mention added sugar and sodium. Because packaged foods contain so many ingredients that may be harmful to the gut, they should be avoided at all times on the microbiome diet.

Grains and Gluten

Grains, especially those with gluten, are associated with inflammation in some people. You should avoid grains completely until phase two when you can reintroduce gluten-free grains such as quinoa and amaranth. You can start adding other whole grains back into your diet when you reach phase three, but Dr. Kellman advises watching for any signs of intestinal discomfort.


Discouraged on the microbiome diet, soy and soy products remain controversial. This is mostly because most soy is genetically modified and contains isoflavones, which led to the idea that soy causes breast cancer—though according to most studies, that isn’t true.

However, more recent evidence suggests that soy foods could actually have a beneficial effect on the gut microbiota. Whole soy products contain a good amount of prebiotic fiber.

High Fructose Corn Syrup and Added Sugars

High fructose corn syrup and other added sugars, in association with the standard American diet (high fat, high carbohydrate, and low fiber), may negatively alter gut microbes. These sugars are also associated with cognitive issues, insulin resistance, and increased risk for metabolic disease and inflammation.

Artificial Sweeteners

Some artificial sweeteners may alter the gut microbiome environment in both a positive and negative manner. However, the true mechanism of how artificial sweeteners interact with the human gut is not fully known. Further research is still needed.

Trans Fats and Hydrogenated Oils

Artificial trans fats and hydrogenated fats are made by pumping hydrogen molecules into vegetable oils, which turn the oil from a liquid at room temperature into a solid. Crisco, the popular baking ingredient, is a hydrogenated product.

These kinds of fats can have detrimental effects on health and are associated with heart disease, diabetes, and arthritis. Trans fats also have a negative impact on gut bacteria and can result in dysbiosis (a microbial imbalance).

Corn and Potatoes

It’s true that starchy foods can impact the composition of your gut microbiome. Many starches are resistant to digestion, which can alter the microbe environment. Not all starches have been tested, which is why it’s recommended that you initially avoid corn, potatoes, and other starchy fruits and vegetables.

Deli Meat

Processed meat is to be avoided as fresh, lean meats are healthier alternatives.


Often mistaken for a tree nut, peanuts are actually legumes. Legumes are often shunned by many diet groups, including paleo followers. Peanuts are also a major allergen. However, it’s been found that peanuts might actually improve gut health in those who can tolerate them.

Fried Foods

You probably already know that fried foods aren’t very good for you. The main reason for avoiding them is that they tend to reduce diversity in the gut bacteria. Generally, the more diverse your gut microbiome is, the healthier it is, too.

Fruit Juice and Dried Fruit

Fruit juice and dried fruit are to be avoided on the microbiome diet because they contain concentrated amounts of sugar.


It’s not eggs themselves that Dr. Kellman is concerned about—it’s how they’re produced. All eggs should be avoided until phase two, but when you add them back in, you should choose free-range, antibiotic-free eggs.

Dairy (Except Butter and Ghee)

Dairy, or rather the milk sugar lactose, is a common digestive irritant. Dr. Kellman recommends avoiding dairy, with the exception of butter and ghee, until phase two of the microbiome diet. Then you can begin eating probiotic-rich kefir and yogurt made from cow's milk.

Legumes (Except Chickpeas and Lentils)

Legumes have a bad reputation when it comes to gut health, primarily because they contain lectins. Lectins are naturally occurring proteins in many foods, and they have been associated with inflammation and damage to the gut lining. But we know that legumes have many beneficial effects, too.

Yeast and Foods Containing Yeast

It’s recommended that you avoid yeast on the microbiome diet because too much yeast consumption could lead to Candida overgrowth or other fungal infections in the gut.


Dr. Kellman recommends taking a handful of supplements on the microbiome diet in addition to focusing on gut-friendly foods.

  • Berberine
  • Butyrate
  • Caprylic acid
  • Carnosine
  • Garlic
  • Glutamine
  • Glucosamine
  • Grapefruit seed extract
  • Oregano oil
  • Probiotic supplements
  • Quercetin
  • Vitamin D
  • Zinc

You don’t have to take all—or any—of these supplements to have a healthy diet, but taking certain supplements can sometimes help to fill any nutrient gaps. Just remember that health claims made by manufacturers of dietary supplements are largely unregulated by the U.S. Food and Drug Administration (FDA).

Pros and Cons

  • Promotes nutritious food choices

  • Improves gut health

  • Limits sugar intake

  • Restrictive

  • Expensive

  • Unsubstantiated health claims


As with all diets, the microbiome diet has its benefits and drawbacks, and it's important to understand them before you decide to follow a particular eating plan.

  • Promotes nutritious foods: The microbiome diet encourages whole, nutrient-dense foods such as fruit, berries, vegetables, fish, nuts and seeds, and lean protein. All of these food groups provide many vitamins and minerals and have health-boosting properties.
  • Improves gut health: More specifically, the fruits and veggies on the microbiome diet are gut-friendly foods. Asparagus, leeks, onions, artichokes, sauerkraut, kimchi, radishes, avocados, citrus fruits, and more all have prebiotic or probiotic qualities. Prebiotics and probiotics work together to achieve optimal gut health.
  • Limits sugar intake: Excess sugar intake can be a driver of many chronic diseases and cause immediate symptoms such as lethargy, difficulty focusing, and mood swings. By limiting your sugar intake, the microbiome diet may help improve your day-to-day functioning.


There are several challenges to be aware of when considering the microbiome diet.

  • Restrictive: The microbiome diet can be very restrictive, especially in the first phase. It isn’t usually necessary for most people to cut out as many foods as the first phase requires. Corn, soy, eggs, grains, legumes, and dairy can have a very healthy place in most people’s diets.
  • Expensive: The microbiome diet encourages organic foods, free-range meats, and cage-free eggs. These kinds of foods can be much more expensive than their traditional counterparts, so cost may be a limiting factor for many people on the microbiome diet.
  • Unsubstantiated claims: Some health claims regarding the gut are exaggerated and have not been substantiated by independent evidence.

Is the Microbiome Diet a Healthy Choice for You?

The key tenets of the microbiome diet are similar to other well-established diets that may support gut health. For example, The Mediterranean diet also focuses on fruits, vegetables, whole grains, and healthy fats, with a particular emphasis on herbs. Many of the whole foods on the Mediterranean diet are microbiome-friendly.

When compared to federal dietary recommendations, phase three of the microbiome diet is the most aligned. The restrictions of phases one and two eliminate many healthy foods recommended for a balanced diet. The U.S. Department of Agriculture suggests consuming a variety of fruit, vegetables, grains, dairy, and protein. The recommendations in the federal guidelines suggest consuming:

  • Vegetables of all types—dark green; red and orange; beans, peas, and lentils; starchy; and others
  • Fruits, especially whole fruit
  • Grains, at least half of which are whole grain
  • Dairy, including fat-free or low-fat milk, yogurt, and cheese, and/or lactose-free versions and fortified soy beverages and yogurt as alternatives
  • Protein foods, including lean meats, poultry, and eggs; seafood; beans, peas, and lentils; and nuts, seeds, and soy products
  • Oils, including vegetable oils and oils in food, such as seafood and nuts
  • Limited saturated fats, trans fats, and added sugars
  • Limited in sodium and dietary cholesterol

Avoiding high-sugar, fried, and packaged foods is a surefire way to improve your health and vitality. But for weight loss, it’s helpful to know how many calories you're consuming each day in order to reach your goals—whether your goal is to lose, maintain, or gain weight.

Most people need around 1,500 calories a day for weight loss and about 2,000 calories a day for weight management, but these numbers vary based on an individual's age, height, weight, and activity level. Try this calculator to help determine your daily calorie needs.

Phase one of the microbiome diet eliminates many healthy foods recommended by federal dietary guidelines. Because of these severe restrictions, this diet is not recommended by experts. However, phase three of the plan is mostly compliant with USDA recommendations for a well-rounded diet.

Health Benefits

The microbiome diet as a whole hasn't been fully studied on effectiveness, efficacy, and safety. But there is some evidence that it can be beneficial.

Health Maintenance

Research increasingly shows a strong link between a healthy diet and a healthy gut, and between a healthy gut and a generally healthy body.

Weight Loss

Because the microbiome diet requires you to eat mostly fruit, vegetables, and lean protein, it may inherently help you lose weight. Keep in mind, though, that it’s still possible to take in more calories than you're burning even when you’re eating healthy foods, which contributes to weight gain.

Disease Prevention

Some of the foods that have microbiome-friendly effects also have protective qualities against a number of diseases. For example, higher consumption of nuts and seeds has been associated with a reduced incidence of coronary heart disease, and gallstones (in both men and women), and diabetes in women. Limited evidence also suggests beneficial effects on hypertension, cancer, and inflammation.

Health Risks

Especially during the restrictive phases, the microbiome diet may not provide the nutrition most people need for good health.

Nutrient Imbalances

Phase one of the microbiome diet eliminates many healthy foods like whole grains, dairy products, eggs, starchy fruits and vegetables, and most legumes for 21 days. While these restrictions are temporary, they could result in nutrient imbalances.

Nutrition experts recommend skipping the first phase as it is unlikely that you need to cut out all of the foods it bans. Instead, it might be helpful to start with a more inclusive version, perhaps with the second phase.

Even beginning with the third phase might be a big change for many people. For instance, if you currently eat a lot of artificial sweeteners, packaged foods, sodium, fried foods, and sugar, you could experience benefits just by following phase three of the microbiome diet, which is far more nutritionally balanced than phases one or two.

Disordered Eating

Some regimented diets with severe restrictions such as those found in phase one of the microbiome diet can lead to an unhealthy obsession with food. To that end, the microbiome diet may not be a healthy choice for those who have had or are at risk for developing an eating disorder.

A Word From Verywell

By following phase 3 of the microbiome diet and focusing on fresh fruits and vegetables, lean protein, healthy fats, and fermented foods, you’ll naturally help to balance your gut microbiota. Be advised, however, that more research is still needed to validate the complex relationship between food, the gut, and overall health.

If you experience severe digestive discomfort or other symptoms on the microbiome diet, talk to a physician or registered dietitian who can help you make personalized dietary choices. It's also a good idea to consult with your healthcare team before you begin a new diet plan, especially if you're trying to lose weight.

Remember, following a long-term or short-term diet may not be necessary for you and many diets out there simply don’t work, especially long-term. While we do not endorse fad diet trends or unsustainable weight loss methods, we present the facts so you can make an informed decision that works best for your nutritional needs, genetic blueprint, budget, and goals.

If your goal is weight loss, remember that losing weight isn’t necessarily the same as being your healthiest self, and there are many other ways to pursue health. Exercise, sleep, and other lifestyle factors also play a major role in your overall health. The best diet is always the one that is balanced and fits your lifestyle.

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Additional Reading

By Amanda Capritto, ACE-CPT, INHC
Amanda Capritto, ACE-CPT, INHC, is an advocate for simple health and wellness. She writes about nutrition, exercise and overall well-being.