The Microbiome Diet: Maintaining a Healthy Gut

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Are you a health-conscious person? Or are you looking for ways to secure a healthy gut? In that case, the microbiome diet might be of some interest. First introduced by Dr. Raphael Kellman, the diet revolves around consuming and avoiding certain foods to restore gut health. It's also said to have other advantages, like speeding up your metabolism. This article explains how the diet works, what it entails, what foods to consume, what to avoid, and how it can help you regain gut health.

What Is a Microbiome Diet?

The concept of the microbiome diet revolves around the cultivation of healthy gut bacteria inside the human body. Dr. Raphael Kellman studied the usefulness of the Bifidobacterium and Lactobacillus species and concluded the effectiveness of nurturing these bacteria in the human alimentary tract.

This diet's goal is to cultivate healthy gut flora; therefore, only foods that trigger bacterial growth in the gut are recommended, such as fresh fruits or vegetables that are high in fiber.

What's Inside the Human Gut Microbiome?

The microbiome consists of gut-friendly bacteria, protozoa, eukaryotes, viruses, and archaea. These microbes live symbiotically in our gut.

Gut microbes play a significant role in food digestion. They work along with the other digestive juices, such as bile, to break down food particles and offer controlled digestion.

Besides digestion, gut microbes benefit your immune system. They align potential immune cells, which trigger the production of healthy antiviral proteins. In return, these proteins fight viral infections in the human body. 

Benefits of Balanced Microbiome

Possible weight loss and a boosted metabolism are two of the key advantages of a balanced microbiome. The microbes in your stomach are so influential because they dictate how fast you digest food, how hungry you are, and what you crave.

What Makes the Microbiome Diet Special?

Microbiome diets are rich in probiotics and prebiotics. Prebiotic and probiotic foods activate the growth of beneficial microorganisms. Consequently, the production of these bacteria results in controlled food digestion and enhances the overall health of a person. 

With this diet, symbiotic meals that contain an equal proportion of prebiotics and probiotics are preferred because they strengthen the immune system. The intake of gut-friendly food also helps to shed off extra fat from the body and results in significant weight loss.

Moreover, the diet isn't tasteless or stagnant like other traditional diets. You can enjoy various fresh fruits, vegetables, and even low mercury salmon. There are a variety of mouth-watering meals to nourish your taste buds along with gut health.

3 Steps to the Microbiome Diet

The Microbiome Diet is a three-phase plan designed to help you lose weight and improve gut health. 

Phase 1: Follow the Four R's Plan

To cultivate gut microbiota, the first phase consists of following the four R's plan. It includes replacing toxic foods with healthy foods. 

This phase lasts 21 days and seeks to eliminate harmful bacteria in your gut and replace stomach acid. For maintaining sound intestinal health, here are the measures you have to stick with:

1. Remove

Get rid of processed foods, toxins, or hazardous chemicals that could trigger inflammation or a bacterial imbalance in your stomach. 

In the first phase of the microbiome diet, you have to cut down the consumption of foods rich in antibiotics, pesticides, and hormones, as well as medications. These foods inflate gut bacteria, and can lead to various health issues, such as inflammatory bowel disease.

2. Repair

Begin transitioning to a plant-based diet. Eat fresh fruits, fermented vegetables, legumes, beans, and very few components from animals. Kimchi and sauerkraut are the most popular fermented foods recommended for microbiome diets.

You can also use artificial sweeteners as a substitute for sugar. These sweeteners are gut-friendly and promote optimal functioning of the human alimentary tract. 

3. Replace

You should avoid processed foods and increase the intake of healthy plant-based foods. Also, start eating herbs, enzymes, or other natural food substitutes. The consumption of rich probiotic foods is highly recommended as well.

You should consider increasing your intake of free-range eggs, chickpeas, soy products, peanut butter, and gluten-free products. For a plant-based diet, you can consider eating garlic, leeks, carrots, onions, aspergillus, and lentils. These meals will boost the probiotic bacteria in your digestive tract and promote gut well-being.

4. Reinoculate 

You should constantly eat prebiotic foods that help cultivate healthy bacteria in this step. 

The best part of a microbiome diet is that it balances the consumption of healthy dietary fiber in the body. These fibers inoculate the healthy microbes in the gut lining and help maintain the overall health of your digestive tract.

Phase 2: Accelerate Your Immunity by Metabolism Plan

After practicing the microbiome diet for four weeks, your body has developed essential probiotic bacteria in your gut lining. However, you must continue to avoid the foods you eliminated during the first phase of the diet.

In other words, continue eating free-range eggs, gluten-free grains, and plant-based foods during this diet phase. All these natural foods will help you maintain the normal homeostasis of your body.

Phase 3: Reinvent Your Lifestyle

The third phase is also known as the "maintenance phase." There are no time constraints, as the microbiome diet should already have started to influence the day-to-day. During this phase, you have to be selective in food intake and keep avoiding unhealthy food.

Phase three is also designed to assist you in maintaining your weight loss over time. Practicing this diet will help you to lose extra fats from your body and boost your self-confidence. 

Foods to Eat and Foods to Stay Away From

To make things easier for you, we have prepared a list of foods you should eat during the microbiome diet, along with foods to stay away from.

Foods to Eat

According to Dr. Kellman, you should consider eating plant-based foods, such as:


During phase two, it is recommended to kick things up a notch by including: 


Non-starchy fruits and vegetables, fermented meals, grass-fed meat, and wild, low mercury fish are all recommended as part of this diet.

Foods to Stay Away From

Here are the foods you're strictly prohibited from eating during this diet:


Supplements to Use When Following the Diet

According to Dr. Raphael, supplements can help support gut health when you're doing the microbiome diet. Here are the essentials you should add to your diet at the beginning of phase one:

Antimicrobials – These include berberine, garlic, grapefruit seed extract, and oregano oil, which can kill pathogens

Acid and Enzymes – These include digestive enzymes such as lipase, protease, and amylase. These enzymes break down complex protein structures and extract vital nutrients from food.

Gut lining Supplements – These include slippery elm, glutamine, vitamin D, and zinc. These gut lining supplements support internal gut health.

Probiotics – These include the intake of probiotic food products that contain 50-200 billion probiotic bacteria. These foods encourage the growth of beneficial gut bacteria.

What the research says

Diet can help the microbiota, which in turn helps human health. A healthy microbiome may minimize illness risk because it has a role in immunity and inflammation.

According to a 2019 study, similar foods can have quite diverse effects on people's gut flora, depending on who they are. This means that the microbiota's response to nutrition is likewise unique.

Because heredity affects how variations in the microbiota affect human health, individuals may require a more personalized approach to nutrition than just a diet. This is especially true if the person has any underlying medical conditions.

Important Things to Remember

Dr. Raphael asks you to consider the following when you are practicing this diet:


Appetizing Microbial Meals

Although diets tend to get a bad rap, the microbiome diet still allows for tasty foods. With the help of a microbiome diet manual, you can use various ingredients to cook delicious meals. 

Here are some delicious meals for boosting the gut flora in your intestinal lining: 


The best part is that you will be eating healthy food while losing extra weight! 

Restoring Gut Health

This diet has numerous health benefits. The key advantage is that it promotes consuming a wide variety of fruits, vegetables, and healthy fats. It also suggests avoiding extra sugar and fried foods.

Despite suggestions that a healthier gut will accelerate your metabolism and help you lose weight, there isn't enough human evidence to back up these claims. On the other hand, the Microbiome Diet is naturally low in fat but high in vitamins, minerals, and fiber, which may help with weight loss.

Short-chain fatty acids support the health of your gut lining and immune system. Fiber is converted into short-chain fatty acids by your microbiota.

Prebiotics and certain probiotic strains like Lactobacilli and Bifidobacteria may help prevent leaky gut syndrome. According to research, probiotics may also help with digestive issues like irritable bowel syndrome.

Possible Drawbacks

One disadvantage of this diet is that it emphasizes eating organic foods. There is minimal scientific proof that non-organic foods are harmful to your gut. Whether organic or commercially cultivated, a diet rich in fruits and vegetables has numerous health benefits.

Because organic produce is more expensive, a diet that encourages people to eat only organic foods may limit the number and diversity of meals they can buy.

This diet also recommends a range of dietary supplements. Glutamine and berberine are some of the prescribed supplements. These supplements can be pretty expensive.


A microbiome diet is a great way to adopt a healthier lifestyle. You can practice this diet by following our suggestions asking an expert for guidance. 

Start by increasing your intake organic foods and eliminating packaged foods from your diet. Within a month or two of practicing the microbiome diet, you should feel significant changes in your overall health. The gluten-free products can help deter ulcerative colitis and inflamed bowel diseases.

New and exciting ways to improve gut health are also on the way. Designed with high-quality biometric sensors, the Çava Seat can track your gut health, heart health, fitness progress, and more, without changing your daily routine. Daily bathroom visits provide some of the best information needed to identify gut imbalances and food sensitivities.

By tracking your vitals, body composition, and waste quality the Çava Seat is able to learn over time and make recommendations to help you live a healthier life.


What do you eat on the microbiome diet?

There are lots of things you can eat on a microbiome diet, including fresh fruits, fermented vegetables, gluten-free products, free-range eggs, yogurt, flax seeds, nuts, almonds, and even low mercury salmon.

What foods heal the gut microbiome?

Yogurt, kefir, miso, sauerkraut, kimchi, sourdough, almonds, and olive oil are the potential foods that can heal your microbiome. You can also take digestive enzymes and prebiotic and probiotic supplements to foster the growth of probiotic bacteria in your intestinal lining.

What is the fastest way to heal the microbiome?


How can I improve my gut microbiome?

You can improve your microbiome by replacing your normal diet with a microbiome diet. Watch what you eat and stick to plant-based foods. Avoid eating processed and packaged foods, and drink lots of water. Lastly, be sure to increase your intake of foods rich in probiotics that boost your immune system.

Why is cultivating gut microbiomes essential?

Gut microbiomes are essential for controlled digestion. The microbiome diet initiates the production of beneficial gut bacteria and works to develop immunity against inflammatory bowel diseases, infectious diarrhea, antibiotic-associated diarrhea, and necrotizing enterocolitis.

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