What Is the Microbiome Diet?

The microbiome diet is a whole-food diet that focuses on consuming mostly fruit, vegetables, lean protein and a large amount of prebiotic and probiotic foods. It’s a three-phase program that starts out with an elimination diet, which creator Dr. Raphael Keller claims restores gut health in people who have been eating non-microbiome-friendly foods for a long time.

Your microbiome is the ecosystem of microorganisms that live throughout your digestive system. It’s also referred to as the gut microbiota, intestinal flora, gut flora, or simply the gut. Science has shown us that a healthy gut is critical to overall health, and that eating foods that nurture the gut can improve wellbeing — this is the premise behind the microbiome diet.

What Experts Say

“The Microbiome diet claims to optimize gut health. Experts agree eating prebiotic- and probiotic-rich foods and limiting added sugar both support gut wellbeing. However, phase one is unnecessarily restrictive and the supplement recommendations have little scientific support.”

Chrissy Carroll, RD, MPH


It’s likely you've already heard of probiotics as they relate to gut health: You’d be hard-pressed to find a health magazine (or yogurt brand!) that hasn’t covered the topic. Foods that naturally contain prebiotics and probiotics have risen to superfood status — and appropriately so. Both support the body in achieving and maintaining a healthy ecosystem of microorganisms in the digestive tract.

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

Though there are many ways to eat to optimize gut health, the “official” microbiome diet was developed by Dr. Raphael Kellman of the Kellman Center for Integrative and Functional Medicine, where Kellman treats thyroid disorders, autoimmune conditions, Lyme disease, digestive dysfunction, and more.

The Kellman Center primarily uses nutrition-based treatment approaches and claims to even treat autism and cancer by focusing on the microbiome.

In his 2014 book, The Microbiome Diet: The Scientifically Proven Way to Restore Your Gut Health and Achieve Permanent Weight Loss, Keller writes:

"Research reveals that when the microbiome goes out of balance, people often gain weight, even when they haven’t changed their diet or exercise. An imbalanced microbiome often dooms just about any diet to failure. When the microbiome is balanced, however, people often lose weight, even when they don’t make any other changes."

Additionally, Kellman posits that an imbalanced microbiome will cause you to crave sugar and unhealthy fatty foods, such as chips or fried foods; and that a balanced microbiome will increase your cravings for healthy foods.

With “probiotics” and “gut health” becoming buzz words in the mid-2010s, the microbiome diet exploded in popularity, with variations popping up all over the web. There is one element Dr. Kellman’s diet may be missing, though: An increasing body of evidence supports the idea that it’s not just bacteria that are crucial for gut health. Rather, the other microorganisms in our guts — particularly fungi — are just as important.

How It Works

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.

Phase 1: The Four R’s

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

Phase one is very restrictive and probably unnecessary for most people. During this 21-day phase, you’re required to avoid a vast amount of foods, including soy, dairy, grains, eggs, legumes, and starchy fruits and vegetables. You also can’t consume any sugar or artificial sweeteners, packaged foods, fillers or coloring.

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 2: The Metabolic Boost

This 28-day phase that 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 can be added back into your diet during phase two. You can also start eating some starchy fruits and vegetables again, such as sweet potatoes and bananas.

During phase two, you still need to avoid certain foods, but only 90 percent of the time. This essentially means that three to four times a week, you can enjoy the supposedly gut-damaging foods (soy, corn, potatoes, etc.).

Phase 3: The Lifetime Tune-Up

By phase three, your gut should be fully healed or almost to that point. Kellman calls phase three the maintenance phase of the microbiome diet, during which you can add back in even more foods. The Lifetime Tune-Up is aptly named because microbiome dieters are encouraged to maintain this way of eating for life.

A good rule of thumb, Kellman writes on his website, is to avoid the “damaging” foods, listen to your body’s cues, and pay attention to what foods work or don’t work for you.

Kellman also encourages people on the microbiome diet to avoid counting calories or tracking portions. This will help you learn to understand your body’s true hunger and satiety cues.

What to Eat

Compliant Foods
  • Non-starchy fruit and vegetables

  • Lean protein

  • Low-mercury fish

  • Nuts and seeds (except peanuts)

  • Prebiotic and probiotic foods

Non-Compliant Foods
  • 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


For the purposes of this article, we’ll describe the compliant and non-compliant foods in the first phase.

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 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 actually 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 provides 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 kombucha, sauerkraut, pickles, tempeh, miso, kefir, and yogurt, but remember that soy and dairy aren’t allowed during the first phase of the microbiome diet.


Packaged Foods: Packaged foods are often full of fillers, additives, colorings, and chemicals, not to mention 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 warns you to look out for signs of intestinal discomfort.

Soy: Soy and soy products remain controversial. This is mostly because of the fact that 90 percent of soy is genetically modified and contains isoflavones, which led to the idea that soy causes breast cancer (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 actually contain a good amount of prebiotic fiber.

High Fructose Corn Syrup and Added Sugars: HFCS or added sugars, in association with the western diet (high fat, high carbohydrate, and low fiber), may alter microbes negatively promoting cognitive issues, insulin resistance, and increase risk for metabolic disease, inflammation, and inflammatory intentional disease.

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 needed.

Trans Fats and Hydrogenated Oils: Artificial trans fats and hydrogenated fats are made by pumping hydrogen molecules into vegetable oils, which turns the oil from a liquid at room temperature into a solid. Crisco, the popular baking ingredient, is a hydrogenated product. These kinds of fats have scary influences on all sorts of diseases, including heart disease, diabetes, and arthritis. Trans fats also have a negative impact on gut bacteria and can result in dysbiosis.

Corn and Potatoes: It’s true that starchy foods can impact the composition of your gut microbiome. Many starches are resistant to digestion and can result in the digestion by bacteria, influencing and altering 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.

Peanuts: Often mistaken for a tree nut, peanuts are actually legumes. Legumes are often shunned by many diet groups, including paleo followers. Peanuts are a major allergen that can be adverse for many people. However, it’s been found that peanuts might actually improve gut health.

Fried Foods: You probably already know that fried foods aren’t high up on the list of superfoods. 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: You should avoid fruit juice and dried fruit on the microbiome diet because they contain concentrated amounts of sugar.

Eggs: It’s not eggs themselves 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 until phase two of the microbiome diet when you can begin eating probiotic-rich kefir and yogurt.

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. Keller recommends taking a handful of supplements on the microbiome diet in addition to focusing on gut-friendly foods. Here’s a list of supplements to take on the microbiome diet:

  • 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 help round out your diet and fill in any gaps in your nutrient consumption.

Recommended Timing

There’s no timing aspect to the microbiome diet. Rather, Dr. Kellman encourages intuitive eating, or to eat when you’re hungry and stop when you’re full.

Resources and Tips

If you’re interested in following the microbiome diet, Dr. Kellman’s book, The Microbiome Diet, will provide you with a detailed structure of the diet, as well as his scientific reasoning for the diet. There are several books with similar names on the market, so make sure to choose one by a respected and experienced researcher or health professional.

The web is home to vast and diverse microbiome diet recipes, but you can also benefit by following anti-inflammatory recipes and Mediterranean recipes.


To make the microbiome diet more doable, it’s recommended that you don’t start with the first phase. Phase one of the microbiome diet is unnecessarily restrictive, and it’s 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 would be a big change for many. If you currently eat a lot of artificial sweeteners, packaged foods, sodium, fried foods, and sugar, you could see great benefits just by following phase three of the microbiome diet.

Pros and Cons

  • Promotes nutritious food choices

  • Improves gut health

  • Limits sugar intake

  • May aid weight loss

  • May protect against disease

  • Restrictive

  • Expensive

  • Unsubstantiated health claims


Promotes Nutritious Food Choices: The microbiome diet encourages people to choose whole, nutrient-dense foods such as fruit, berries, vegetables, fish, nuts and seeds, and lean protein. All of these food groups provide loads of vitamins and minerals, and they all 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, avocadoes, citrus fruits and more all have prebiotic or probiotic qualities. Prebiotics and probiotics work together to achieve optimal gut health.

Limits Sugar Intake: Copious amounts of sugar in your diet can be a driver of many diseases and 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.

May Aid in 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 be in a caloric surplus even when you’re eating healthy foods.

May Protect Against Disease: 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.

Additionally, your microbiome is critical in keeping your immune system in tip-top shape — so by nurturing your microbiome, you also nurture your ability to fend off illness.


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: Health claims regarding the gut are over-exaggerated and have not been substantiated by independent evidence. The diet as a whole hasn't been fully studied on effectiveness, efficacy, and safety.

How It Compares

USDA Recommendations

The federal dietary recommendations include five food groups: fruit, vegetables, grains, dairy, and protein. The key recommendations in the federal guidelines include:

  • “A variety of vegetables from all of the subgroups—dark green, red and orange, legumes (beans and peas), starchy, and other
  • Fruits, especially whole fruits
  • Grains, at least half of which are whole grains
  • Fat-free or low-fat dairy, including milk, yogurt, cheese, and/or fortified soy beverages
  • A variety of protein foods, including seafood, lean meats and poultry, eggs, legumes (beans and peas), and nuts, seeds, and soy products
  • Oils
  • Limited saturated fats, trans fats, added sugars and sodium”


It’s important to know how many calories you should be consuming each day in order to reach your weight goals, whether your goal is to lose, maintain, or gain weight. Our Weight Loss Calorie Goal Calculator can help you determine your daily caloric needs.

Most people need around 2,000 calories per day. Smaller-framed women and children may need less; men and very active people may need more. Note that calorie needs are extremely individual. Age, height, weight and activity level all play a role in your caloric needs.

Similar Diets

Anti-Inflammatory Diet: The anti-inflammatory diet is based on the idea that chronic inflammation is a root cause of disease, and choosing anti-inflammatory foods can reduce your risk of disease. The anti-inflammatory diet is focused on vegetables, fruits, healthy fats, and spices. It limits processed meats, added sugars, refined grains, and hydrogenated oils. Because the anti-inflammatory diet aims to reduce inflammation, it’s gut-friendly by default.

Mediterranean Diet: The Mediterranean diet also focuses on fruits, vegetables, whole grains, and healthy fats, with a particular emphasis on herbs. Many of the foods on the Mediterranean diet are microbiome-friendly. The Mediterranean diet has been associated with a decreased risk of heart disease, and it's also been shown to reduce blood pressure and bad LDL cholesterol.

DASH Diet: The DASH Diet — or Dietary Approaches to Stop Hypertension — is another healthful eating pattern that emphasizes fresh produce, lean protein, and whole grains. The DASH Diet largely focuses on salt intake, because sodium is the main culprit behind hypertension. The DASH Diet was developed to treat high blood pressure, but anyone can benefit from this diet and it’s regularly named one of the by U.S. News & World Report.

A Word From Verywell

The microbiome diet has the potential to be a very healthy and beneficial diet. However, the first phase is extremely restrictive and not necessary for most people. Most people would benefit just by changing their diet to match phase three of the microbiome diet.

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

Avoiding high-sugar, fried and packaged foods is a surefire way to improve your health and vitality on all levels. This is similar to other popular diets such as DASH and the Mediterranean diet. If you experience severe digestive discomfort or other symptoms, talk to a physician or registered dietitian who can help you make smart diet choices.

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Article Sources
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Additional Reading
  • Iliev ID, Funari VA, Taylor KD, et al. Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science. 2012;336(6086):1314-7.

  • Liguori G, Lamas B, Richard ML, et al. Fungal Dysbiosis in Mucosa-associated Microbiota of Crohn's Disease Patients. Journal of Crohn's & colitis. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4957473/. Published March 2016.

  • Mar Rodríguez M, Pérez D, Javier Chaves F, et al. Obesity changes the human gut mycobiome. Scientific reports. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4600977/. Published October 12, 2015.

  • Zhernakova A, Kurilshikov A, Bonder MJ, et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science. https://science.sciencemag.org/content/352/6285/565. Published April 29, 2016.