The Microbiome Diet: Can It Restore Your Gut Health?

The Microbiome Diet is a three-phase program aimed at helping you lose weight by restoring gut health.

It was developed by Dr. Raphael Kellman, a board-certified physician specializing in gut health.

It’s based on the idea that eating the right foods will help keep your gut microbiome healthy — which is instrumental to your overall health.

Your gut microbiome is made up of trillions of bacteria and other microorganisms — both friendly and unfriendly.

Maintaining the right balance of friendly and unfriendly bacteria in your gut is touted to improve digestion, reduce inflammation, decrease anxiety, and even improve brain function and mood.

A healthy balance of gut bacteria is also said to boost metabolism, eliminate cravings, and help you shed unwanted weight.

Summary

The Microbiome Diet is a three-phase program designed to improve gut health. It’s also claimed to boost metabolism, eliminate cravings, and help you lose weight.

The Microbiome Diet is divided into three distinct phases.

Phase 1: Your four R’s meal plan

This first phase lasts 21 days and aims to remove unhealthy bacteria from your gut and replace stomach acids and digestive enzymes.

It’s also designed to populate your gut with prebiotics and probiotics to repair its lining.

This phase is the strictest of the three and is based on the following “Four R’s” of intestinal health:

1. Remove: Cutting out all foods, toxins, and harmful chemicals that may cause inflammation or an imbalance in your gut bacteria. This includes pesticides, hormones, antibiotics, and certain medications.
2. Repair: Load up on plant foods and supplements that heal your gut and support the microbiome.
3. Replace: Eat certain herbs, spices, and supplements that can replace stomach acid, digestive enzymes, and improve the quality of bacteria in your gut.
4. Reinoculate: Repopulate your gut with healthy bacteria by eating probiotic- and prebiotic-rich foods and supplements.

In this phase, you are required to avoid a large variety of foods, including all grains, eggs, most legumes and dairy, as well as starchy fruits and vegetables.

Packaged and fried foods, sugar, fillers, coloring, artificial sweeteners, and some types of fats, fish, and meat should also be avoided.

Instead, you’re encouraged to eat an organic, plant-based diet with prebiotic-rich foods, such as asparagus, garlic, onion, and leeks. Fermented foods rich in probiotics — such as sauerkraut, kimchi, kefir, and yogurt — should also be included.

Certain supplements are strongly recommended, including probiotics, zinc, vitamin D, berberine, grapefruit seed extract, wormwood, and oregano oil.

Phase 2: Your metabolic boost meal plan

This phase is designed to last 28 days. By the time you reach it, it’s assumed that your gut and microbiome have gotten stronger, allowing you a bit more flexibility with your diet.

During this phase, you still need to avoid the supposedly gut-damaging foods from phase one — but only 90% of the time.

Concretely, this means that up to four of your weekly meals can include food not recommended on the food list from phase one.

In addition, dairy, free-range eggs, gluten-free grains, and legumes can be added back into your diet.

Finally, you can also start eating most fruits and vegetables again, such as mangoes, melons, peaches, pears, sweet potatoes, and yams.

Phase 3: Your lifetime tune-up

This last phase of the diet is considered the “maintenance phase.”

It has no recommended length, as you’re encouraged to follow it until you lose your desired amount of weight. Phase three is also meant to help you maintain the weight loss long term.

By this point, your gut and microbiome are believed to be almost fully healed. So, although the foods to avoid remain the same as in the first phase, you only need 70% compliance.

In other words, you can eat what you want 30% of the time — equalling about one meal per day. Still, it’s recommended to avoid processed foods and added sugar as much as possible.

Summary

The Microbiome Diet is split into three phases. Each phase eliminates the same foods but becomes increasingly flexible with how strictly these foods should be avoided.

The Microbiome Diet warns against eating an array of foods, which are thought to reduce the health of your gut and microbiome.

Thus, they should — at least initially — be completely avoided. These foods include:

• Processed and fried foods.
• Sugar and high-fructose corn syrup.
• Artificial sweeteners, except for small quantities of Lakanto.
• Trans and hydrogenated fats.
• Starchy fruits and vegetables, such as bananas, potatoes, corn, and peas.
• Deli meats high in salt and fats.
• Peanuts, soy, and other legumes, except for chickpeas and lentils.
• High-mercury fish.
• Dried fruit and fruit juices.
• All grains containing gluten.
• Eggs and dairy, except for butter and ghee.
• Yeast and foods containing it.

Summary

The Microbiome Diet excludes starchy fruits and vegetables, dried fruit, fruit juice, grains containing gluten, eggs, some dairy, and some types of fish and meats. It also discourages eating added sugar and processed or fried foods.

The following foods can be enjoyed throughout all phases of the Microbiome Diet:

• Wild salmon and grass-fed meat.
• Fermented vegetables, such as sauerkraut and kimchi.
• Non-starchy vegetables, such as asparagus, carrots, garlic, artichokes, leeks, onions, and radishes.
• Non-starchy fruits, such as tomatoes, avocado, apples, cherries, grapefruit, kiwi, oranges, nectarines, rhubarb, and coconut.
• Nuts, seeds, and their butter.
• Sunflower and olive oils.
• Chickpeas and lentils.
• Lakanto sweetener in small amounts.
• Herbs and spices.

In phase two of the diet, foods like free-range eggs, dairy, legumes, gluten-free grains, and certain starchy fruits and vegetables can be reintroduced.

Summary

The Microbiome Diet generally encourages eating non-starchy fruits and vegetables, fermented foods, grass-fed meat, and wild, low-mercury fish.

Aside from eating and avoiding certain foods, the Microbiome Diet has additional recommendations.

For starters, this diet encourages sticking to organic foods and avoiding chemicals in non-natural household cleaners and personal care products. It’s also encouraged to use a good water filter.

This is thought to improve gut health by lowering how many toxins, pesticides, and hormones your body is exposed to.

Moreover, the diet recommends various supplements as a way to reduce inflammation, remove unhealthy bacteria, and help strengthen your gut.

Examples of these supplements are zinc, glutamine, berberine, caprylic acid, quercetin, garlic, grapefruit seed extract, wormwood, oregano oil, probiotics, and vitamin D.

Dieters are also warned to avoid overusing certain drugs — such as antibiotics, nonsteroidal anti-inflammatory drugs (NSAIDs), and proton pump inhibitors — which may disrupt the balance of your gut bacteria.

Summary

The Microbiome Diet encourages eating organic foods, using a water filter, and taking various supplements. It discourages the use of non-natural household cleaners and personal care products, as well as the overuse of certain drugs.

The Microbiome Diet may improve gut health in various ways.

For starters, it promotes eating foods rich in probiotics and prebiotics — two compounds essential for a healthy gut.

Probiotics are live bacteria found in foods like yogurt, kefir, tempeh, kombucha, and unpasteurized fermented vegetables, such as sauerkraut, pickles, and kimchi.

These friendly bacteria help colonize your gut and prevent unfriendly bacteria from overpopulating it (1, 2, 3, 4).

Prebiotics are a type of fiber that helps feed these friendly bacteria. You can find them in foods such as asparagus, garlic, Jerusalem artichokes, onion, leek, and radishes — all of which are plentiful in the Microbiome Diet (5, 6).

Prebiotics and specific probiotic strains such as Lactobacilli and Bifidobacteria may also help seal gaps between intestinal cells, preventing leaky gut syndrome (6, 7).

Taken in supplements, probiotics may also help protect against infections with the H. pylori bacteria, one of the main causes of ulcers and stomach cancers (8, 9).

Antibiotics, along with proton pump inhibitors, are still the recommended therapies for H. Pylori. Probiotics help lessen antibiotic side effects but do not replace antibiotic therapy. (10, 11).

In addition, the Microbiome Diet also limits your intake of added sugar. The relationship to sugars in the diet and the effects on gut bacteria is very complicated. More human studies are needed (12).

The diet also warns against the overuse of antibiotics, NSAIDs, and proton pump inhibitors. Studies show that using these medications in greater amounts than prescribed” can damage the gut wall and wipe-out microorganisms — including friendly bacteria (13, 14, 15, 16).

Therefore, avoiding these medications whenever possible may contribute to a healthier gut as well.

Summary

The Microbiome Diet is rich in probiotics and prebiotics, as well as low in added sugar — all of which can contribute to a healthier gut. It also warns against the overuse of certain medications that could damage your gut.

The Microbiome Diet may provide additional health benefits.

The main benefit is that it encourages eating plenty of fruit, vegetables, healthy fats, lean protein, and other plant-based foods. It also recommends limiting added sugar as well as processed and fried foods.

Despite claims that a healthier gut will boost your metabolism, reduce cravings, and promote weight loss, research in humans to confirm these benefits is lacking (17).

That said, the Microbiome Diet tends to be naturally low in fat to the point of being restrictive, but rich in vitamins, minerals, and fiber — which may contribute to weight loss without the need to count calories or measure portion sizes (18, 19, 20).

Improving your gut health may protect against a variety of diseases (21).

These include obesity, type 2 diabetes, heart disease, metabolic syndrome, colon cancer, Alzheimer’s, and depression (22, 23, 24, 25, 26, 27).

What’s more, your microbiome is responsible for turning fiber into short-chain fatty acids that strengthen your gut wall and your immune system (28, 29, 30, 31).

A stronger gut wall can help prevent unwanted substances from entering your body and provoke an immune response (32).

Summary

The Microbiome Diet is highly restrictive and may help you lose weight. It contains nutrients which may boost your immunity and potentially protect against health conditions, such as diabetes and heart disease.

Despite its many potential benefits, the Microbiome Diet also has some drawbacks.

Restricts your intake of certain beneficial foods

The first phase of the Microbiome Diet is restrictive and requires that you eliminate a variety of foods — some of which may be nutritious and benefit your health. These include some fruits, starchy vegetables, all grains, and most legumes.

These foods are rich in vitamins, minerals, and other beneficial plant compounds.

Moreover, unless you’re intolerant to them, scientific evidence supporting that you need to avoid these foods to lose weight or maintain a healthy gut function is lacking. In fact, avoiding gluten can lead to a lack of fiber in the diet, which is counter to the research supporting a high-fiber diet for healthier microbiome.

There is no reason to avoid gluten unless you have been diagnosed with celiac disease or gluten sensitivity by a healthcare professional.

Emphasizes organic foods

The Microbiome Diet puts a strong emphasis on eating organic foods to avoid pesticides and hormones.

Yet, it fails to acknowledge that organic foods may be treated with pesticides as well. They contain organic pesticides rather than the synthetic ones found in conventionally-grown produce (33).

Both synthetic and organic pesticides can be harmful to your health when ingested in large doses. However, doses considered harmful are much larger than what you’d typically find in fresh produce (34, 35).

There is little scientific evidence supporting the notion that non-organic foods damage your gut. What’s more, diets rich in fruits and vegetables offer many health benefits — regardless of whether they’re organic or conventionally grown (36, 37).

Since organic produce tends to be pricier, a diet promoting eating only organic foods may limit the amount or variety of foods people can afford.

Heavy on supplements

The Microbiome Diet also recommends taking a wide variety of nutritional supplements. These are claimed to help reduce inflammation, remove unhealthy bacteria, and strengthen your gut.

Examples of recommended supplements include probiotics, vitamin D, glutamine, berberine, caprylic acid, quercetin, grapefruit seed extract, wormwood, and oregano oil.

Such supplements tend to be expensive. Moreover, besides probiotics and vitamin D — which can benefit gut health — most have only little scientific evidence backing their use to improve gut health (38, 39).

Summary

The Microbiome Diet starts off restrictive, excluding certain beneficial foods from your diet. What’s more, its strong emphasis on organic produce and supplements is unsupported by strong science.

Here is an example of a three-day meal plan on the first and strictest phase of the Microbiome Diet.

In phases two and three, your meal choices become increasingly more flexibility.

Day 1

• Breakfast: Fruit salad with Brazil nuts.
• Snack 1: Parsnip sticks with almond butter.
• Lunch: Chicken and vegetable soup.
• Snack 2: Roasted cauliflower with curry.
• Dinner: Grilled salmon with roasted Brussels sprouts, mixed greens, and fermented beets.

Day 2

• Breakfast: Pancakes made with almond flour topped with almond butter and fruit.
• Snack 1: Walnuts and cherries.
• Lunch: Vegetable salad topped with sauerkraut, chickpeas, and a parsley-lemon vinaigrette.
• Snack 2: Celery sticks with guacamole.
• Dinner: Zucchini noodles topped with marinara sauce and chicken meatballs.

Day 3

• Breakfast: Blueberry and almond breakfast cookies.
• Snack 1: Sautéed pineapple topped with shredded coconut.
• Lunch: Vegetable salad topped with miso-glazed cod.
• Snack 2: Carrots with hummus.
• Dinner: Flank steak tacos with steamed veggies, salsa, and guacamole.

Summary

The meals above are a good introduction to the strictest phase of the Microbiome Diet. More recipes can be found in the Microbiome Diet book.

The Microbiome Diet limits sugary, fried, and processed foods, focusing instead on fresh produce, lean protein, healthy fats, and probiotic- and prebiotic-rich foods.

It’s likely to aid gut health and weight loss but can be unnecessarily restrictive. Plus, its emphasis on supplements and organic foods is unsupported by science.

There is no one size fits all diet for gut microbiome health or for “repairing” the gut microbiome if there is a problem. Working with a healthcare professional, such as a registered dietitian, to individualize a healthy eating pattern is a good idea if you have concerns about your gut health.

Individualized advice is more likely to help than following a diet plan that doesn’t take into account your specific health issues and dietary needs.

That said, the Microbiome Diet does become less restrictive with time and is likely to be beneficial — as long as you can stick to it.