Reboot Your Microbiome With Our 3-Day Gut Health Makeover

A few years ago, a study published in the journal Nature found that eating a high-fiber, plants-only diet positively shifted people’s microbiome makeup in just 24 hours, compared with eating a meat- and cheese-heavy diet—suggesting the former might be a better way of eating for gut health. (Conversely, the animal-based diet rapidly shifted the microbiome in a way that implies it could trigger inflammatory bowel disease.)

Interestingly, one group of gut bacteria—the genus Prevotella—that represents microbiome diversity (which you want) did not change on the short-term plants-only diet, suggesting that to see the full benefits, you will need to make a commitment to a high-fiber diet for the long haul.

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But to help you quickly reboot your gut flora, we offer this easy-to-follow three-day plan. It’s an all-plants (aka vegan) diet based on whole foods, zero added sugars, and lots of fiber to feed the good bugs in your belly. Each day provides around 47g of fiber. That’s 88% more fiber than the current daily recommendation for women, so if your usual diet is lacking in fiber, you might want to start slow here to prevent—ahem—ill side effects.

RELATED: This New Probiotic Food Might Surprise You

We give you a shopping list and some get-ahead recipes to make the plan easier to stick with. It’s affordable (about $52 for one person), and servings are generous—so you’ll stay satisfied over the three days. Use the plan to jump-start your commitment to better gut health or as a guide to long-term changes. Either way, your gut will thank you.

Don’t let these foods destroy your gut.

Plan Ahead

We kept our meal plan fast, easy, and affordable. Here’s what you need to get your gut in gear—all for $52.15. (Cost includes three days of breakfast, lunch, dinner, and two daily snacks for one person.) Download our 3-Day Gut Health Makeover Shopping List.

Make Ahead

You’ll use these two recipes over the course of the one-person meal plan. Each one makes several portions that are spread out over three days.

Make Ahead: Smoky Roasted Chickpeas

Image zoom Jennifer Causey

These crunchy chickpeas will serve you well over the three-day meal plan as both a snack and a crunchy, protein- and fiber-rich topping for salads. For the crunchiest texture, cook them until they’re just shy of burning. They’ll stay crisp in an airtight container at room temperature for up to a week.

Make Ahead: Simply Seasoned Bulgur

Image zoom Jennifer Causey

Make a batch of whole grains ahead of time to enjoy in various forms throughout the three days—as part of breakfast, lunch, and dinner. For a gluten-free option, you can use the same amounts and cook times to make a batch of quinoa. Per serving, the quinoa version will contain 124 calories, 4g fat, 4g protein, and 2g fiber.

Day 1 Menu

Breakfast: Strawberry Bulgur Bowl

Image zoom Jennifer Causey

While you might not think of turning bulgur into porridge, it’s a delicious whole-grain breakfast with a texture similar to instant oatmeal. Mashed dates naturally sweeten and enrich almond milk for a creamy, satisfying, no-added-sugar bowl. You can make the porridge ahead of time and simply reheat before serving; then add the berries and nuts.

A.M. Snack

5 oz. frozen edamame pods, steamed and tossed with 1/8 tsp. kosher salt (155 calories, 7g fiber)

Lunch: Tabbouleh with Avocado

Image zoom Jennifer Causey

Crunchy, lemony, fresh, and filling—this hearty tabbouleh makes a fine lunch. If you’re packing it up to go, store the chickpeas separately so they’ll keep their crunch. Save the other avocado half; you’ll use it in the next day’s lunch. Keep the pit in the avocado half, and wrap it tightly with plastic wrap to limit browning.

RELATED: How to Shop the Grocery Store for Gut Health

P.M. Snack

3 dates and 12 unsalted roasted almonds (152 calories, 4g fiber)

Dinner: Pasta with Green Peas and Almond Gremolata

Image zoom Jennifer Causey

We chose chickpea pasta here for its mild flavor and higher fiber content (when compared with whole-wheat pasta). The gremolata topping truly makes the dish; it’s herby, crunchy, fragrant, and citrusy. Serve the pasta immediately for the best texture and taste.


Day 2 Menu

Breakfast: Raspberry-Date Smoothie

Image zoom Jennifer Causey

You’ll often find silken tofu in shelf-stable packages on the Asian foods aisle. We call for Mori-Nu brand because one package will provide exactly what you need for this three-day meal plan. The squeeze pack of almond butter is convenient and contains only what you need for this recipe. But if you have almond butter in your fridge or pantry, just use 2 tablespoons.

A.M. Snack

1/2 cup Smoky Roasted Chickpeas (229 calories, 6g fiber)

Lunch: Green Pea Fritters with Avocado Puree

Image zoom Jennifer Causey

P.M. Snack

1 medium apple (95 calories, 4g fiber)

Dinner: Summery Lentil Soup

Image zoom Jennifer Causey

This veggie-packed soup serves double duty: Eat for dinner tonight, and save the rest for breakfast the next day. For a little heat, add a pinch of crushed red pepper.


Day 3 Menu

Breakfast: Veggie Bowl with Tofu Scramble

Image zoom Jennifer Causey

Last night’s soup powers this morning’s breakfast; just cook off most of the liquid to give the soup a porridge-like texture. The seasoned, sautéed tofu is pretty much a dead ringer for scrambled eggs, especially if you opt to add golden turmeric.

A.M. Snack

1 medium apple (95 calories, 4g fiber)

Lunch: Kale Salad with Spiced Chickpeas and Berries

Image zoom Jennifer Causey

To make this salad ahead of time, pour the dressing into the bottom of a portable container, and arrange the kale and the toppings (except for the chickpeas) on top without mixing. When you’re ready to eat, stir together the salad components to coat with dressing. Bring chickpeas in a separate container so they’ll stay crunchy, and toss them in at the last minute.

P.M. Snack

1 cup strawberries and 12 unsalted roasted almonds (138 calories, 5g fiber)

Dinner: Edamame, Okra, and Green Pea Korma

Image zoom Jennifer Causey

If you have Madras curry powder, use it for slightly more heat and richer flavor; standard curry powder will also be great.


Recent Articles

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Imagine your gut is like a garden: Every garden has a mix of flowers and weeds, but its overall health depends on the balance of the two. Like a garden, your gut contains elements that help it thrive (good bacteria) and elements you’d like to have less of (bad bacteria).

These bugs – the bacteria, fungi and other microbes that reside in your gut – are collectively known as the microbiome, and they serve numerous important functions. They impact your immune system, control inflammation, affect digestion, create neurotransmitters that influence mood and help make certain vitamins. Research has shown that a healthy microbiome is linked to protection from diseases including type 2 diabetes, obesity, metabolic syndrome and many autoimmune conditions.

When the ratio of good bacteria to bad bacteria is off, called dysbiosis, disruptions to certain gut bacteria communities occur. Some of the causes of this imbalance include antibiotic usage, chronic stress and gastrointestinal infections. According to a 2015 study published in the International Journal of Molecular Sciences, dysbiosis can lead to chronic diseases such as inflammatory bowel disease (IBD), obesity and cancer. Just like maintaining a healthy garden, to maintain a balanced microbiome and ward off disease, you have to give it the right kind of nourishment. A gut-healthy diet includes fiber- rich foods (vegetables, fruits, whole grains, nuts, seeds, legumes), plenty of polyphenols (coffee, tea, red wine, dark chocolate) and lots of water. The weeds (bad bacteria) love processed grains and sugar, so a gut-healthy diet will help keep them in check. This one-week meal plan is tailored specifically to provide your gut with the nourishment it needs to thrive – and none of what it doesn’t.

8 Steps to a Healthier Microbiome

Meal Plan

Shopping List

How to Eat for a Healthy Gut: The Microbiome Diet

Seen the headlines? We are not alone! We share our bodies with trillions of microbes. The majority live in our guts, and these tiny critters play a key role in keeping us healthy.

Science is still piecing it all together. But the initial insights are intriguing. Our gut microbes fight off intruders, help digest food, make vitamins, prep and protect our immune systems. Recent research points to an association between the microbiome and behavior, including mood and emotions, as well as to links between our gut microbes and disorders like Alzheimer’s, Parkinson’s, epilepsy, and autism.

Taking care of our microbes helps them take care of us. We can start by being good hosts: feeding our friendly microbial guests what they’re hungry for — lots of fresh produce, whole grains, fermented foods — and by staying away from refined sugars. Here are 8 ways to eat for a healthy gut, along with top-rated Microbiome Diet recipes.

1. Eat a Wide Variety of Plants, Fruits, and Veggies

Sound familiar? There’s really nothing new about this advice. Just like their human hosts, the beneficial bacteria that make up our microbiome thrive on a diversity of fiber-rich plants and fruits. So go big on bananas, beans, onions, leeks, oats, whole grains, nuts, avocados, leafy greens, broccoli, asparagus; and fermented foods like yogurt, kimchi, and sauerkraut. The key is variety because it seems that different types of fiber benefit certain bacteria, which in turn benefit the body in specific ways.

Image zoom Avocado Salad | Photo by SunnyByrd

Pictured: Avocado Salad. This 5-star salad boasts a bunch of healthy, diverse, and delicious fresh veggies.

Need another reason to choose whole, fiber-rich foods? Research is finding that certain food additives intended to emulsify, artificially sweeten, stabilize, thicken, and/or create pleasing textures in highly processed foods may also be doing serious harm to our gut microbiomes. These additives aren’t digested by humans; instead, researchers contend, they feed dangerous pathogens in our guts (like C. diff and E. coli) and may also harm the protective layer of mucus that coats the intestines. As unintended consequences go, these are doozies. Writing in The New York Times, science writer Moises Velasquez-Manoff explains that “a growing body of evidence that common food additives can push our microbial communities in unhealthy directions…encouraging diseases like obesity, diabetes and inflammatory bowel disease.” For more, read Velasquez-Manoff’s article, The Germs That Love Diet Soda.

2. Don’t Overcook the Veggies

Soft, overcooked veggies are quickly digested. Leave a little crunch, and the microbes down the line have more to munch on.

Image zoom Photo by Molly

Pictured: Broccoli Mango Salad. This fresh, funky salad is a fruit and veggie mashup, combining broccoli, mango, and mandarin oranges.

3. Chomp on More of the Plant

Eat further down the veggie stalks and stems, not just the soft tips and florets. Your gut will thank you. A healthy, happy gut may actually boost our sense of well being, since gut microbes, along with their other tasks, also assist in processing mood-regulating neurotransmitters like serotonin.

Image zoom Photo by ALFANN02

Pictured: Roasted Vegetable Medley. This medley goes for gut-health gold with asparagus, yams, parsnips, carrots, zucchini, and red peppers. So much good stuff!

4. Eat Fermented and Cultured Foods

Enjoy yogurt for breakfast, a little sauerkraut on sandwiches and salads for lunch, and this homemade kimchi with grilled or roasted meats.

5. Give an A+ to Artichokes, Asparagus, and Avocados

These fiber-rich foods earn top marks. Also, don’t forget about Jerusalem artichokes. Full Disclosure: Jerusalem artichokes are not really from Jerusalem; they’re not even artichokes. But despite the fibs, the truth is, they’re among the gut-friendliest of foods.

Image zoom Photo by naples34102

Pictured: Zucchini and Artichoke Salad. This simple salad combines sliced chicken breasts with artichokes, garbanzo beans, and zucchini.

6. Be Keen for Greens

Your good bacteria love the fiber in kale, spinach, bok choy, and other leafy greens.

Image zoom Photo by Linda LMT

Pictured: Roasted Yam and Kale Salad. This one pairs fresh kale with caramelized onions, garlic, and yams.

7. Seek Out Leeks

Leeks are legendary for helping promote good gut health. Watch Chef John make his simple Sexy Fish Stew with lots of leeks, shallots, and fennel bulbs.

8. And, Finally, a Word About Kraut

Sauerkraut’s not just for hot dogs. Sneak this fabulous fermented food into summer salads and stir-fries, and onto sandwiches, pork chops, even your scrambled eggs.

Image zoom Photo by Caroline C

Pictured: Sauerkraut Salad. Sauerkraut, onions, celery, bell peppers, carrots, and pimento peppers mingle with a tangy, slightly sweet dressing. Let the flavors meld overnight. Delicious.

Why is dietary fiber good for us? As we’ve said, when we eat dietary fiber, we’re feeding the critters in our guts. The billions of bacteria benefit first by feeding on the fiber that’s indigestible to humans. Healthy gut microbes lead to a healthier gut, which translates to a healthier immune system. Also, after the bacteria in the gut break down the fiber, they leave behind short-chain fatty acids, which keep the cells of the intestines healthy and may help calm aggressive immune system responses. Diets rich in dietary fiber may also help defeat obesity and reduce the risk of heart disease, diabetes, along with immune disorders like irritable bowel syndrome. For a slightly more in-depth look at the health benefits of eating fiber-rich foods, check out Learning More about Fiber’s Benefits in The New York Times.

Want more? Check out our top-rated Microbiome Diet Recipes, for eating with your microbes and a healthy gut in mind.

Is the Microbiome Diet the Best Way to Promote Gut Health?

Photo: Anfisa Kameneva / EyeEm / Getty Images

At this point, you’re either well-versed in or sick of everything gut-related. Over the past few years, a ton of research has focused on the bacteria that inhabit the digestive system and how it’s linked to overall health. (It’s also been linked to brain and skin health.) Naturally, diets geared toward promoting healthy bacteria in your gut microbiome have been gaining traction, like the plant paradox, autoimmune paleo, and low-FODMAP diets. Then there’s the microbiome diet, which is intended to maintain a healthy gut bug balance by cycling through three phases of elimination. We’re talking a complete overhaul, not just a daily bottle of kombucha. Here’s everything you should know.

What Is the Microbiome Diet?

Holistic doctor Raphael Kellman, M.D., created the diet and spelled it out in his 2015 book, The Microbiome Diet: The Scientifically Proven Way to Restore Your Gut Health and Achieve Permanent Weight Loss. While Dr. Kellman is behind *the* microbiome diet, dozens of other experts have come out with similar books describing gut-focused diets before and since The Microbiome Diet hit the shelves. (One example is the anti-anxiety diet.) Dr. Kellman categorizes weight loss as a side effect, but not the main aim of the diet.

Phase one is a three-week elimination diet that calls for cutting out foods that are detrimental to gut health, according to Dr. Kellman. You completely avoid a list of foods including grains, gluten, sweeteners, dairy, and eggs, and focus on eating a lot of organic, plant-based foods. And it doesn’t stop at food. You should opt for natural cleaning products and limit the use of antibiotics and NSAIDs (nonsteroidal anti-inflammatory drugs such as aspirin and ibuprofen).

During phase two, which lasts four weeks, you can start reintroducing some of the foods eliminated in phase one, like certain dairy foods, gluten-free grains, and legumes. A rare cheat meal is allowed; you should aim for 90 percent compliance.

The final phase is the “lifetime tune-up,” which is all about intuiting which foods work and don’t work well with your body. This is the most relaxed phase, meant for the long term, calling for 70 percent compliance. (Related: You Need Way More Nutrients for Good Gut Health)

What Are the Potential Benefits and Negative Effects of the Microbiome Diet?

Studies have shown a potential link between gut makeup and conditions like diabetes, heart disease, and cancer. So if the microbiome diet does improve the microbiome makeup, it could bring major perks. It promotes a lot of healthy eating habits, says Kaley Todd, R.D., staff nutritionist for Sun Basket. “It really encourages the consumption of fresh fruits and vegetables, avoiding processed foods and heavy sugars, and it really focuses on vegetables and meats and good fats,” she says. “And I think the more people can eat those whole foods the better.” Plus, it doesn’t call for calorie counting or restrictive portions.

Calories aside, the diet is restrictive, especially during phase one, which is a major drawback. “You’re eliminating large groups of food such as dairy, legumes, grains,” Todd says. “You’re taking those foods that do have nutrient-dense qualities and do offer nutritional benefits and completely eliminating them.” Because gut health is so individualized, she doesn’t recommend following a boilerplate diet to try to fix a gut-related health condition: “It’s best to work with an appropriate health professional along the way to maximize the benefits and really go down the correct path.” (Related: These Juice Shots Put Sauerkraut to Good Use for a Healthier Gut)

Plus, while research on how diet can benefit the gut microbiome is promising, a lot is still unclear. Researchers haven’t definitively pinpointed exactly how to eat to achieve the perfect balance. “We have data to show that diets change the microbiome, but not that specific foods will change the microbiome in a specific way for a specific individual,” Daniel McDonald, Ph.D., scientific director of the American Gut Project and a post-doctoral researcher at the University of California, San Diego School of Medicine, recently told Time.

Sample Microbiome Diet Food List

Each phase is a little different, but as a general rule, you’re going to want to add foods that contain probiotics and prebiotics and avoid processed foods. Here are some of the foods you should and shouldn’t eat once you’ve made it onto phase two:

What to Eat On the Microbiome Diet

Foods to Avoid On the Microbiome Diet

  • Packaged foods
  • Gluten
  • Soy
  • Sugar and artificial sweeteners (Lakanto sweetener is allowed in moderation)
  • Trans fats and hydrogenated fats
  • Potatoes (besides sweet potatoes)
  • Corn
  • Peanuts
  • Deli meat
  • High-mercury fish (e.g., ahi tuna, orange roughy, and shark)
  • Fruit juice

Dr. Kellman also suggests taking supplements in conjunction with the microbiome diet, especially during the first phase.

Supplements to Take On the Microbiome Diet

  • Berberine
  • Caprylic acid
  • Garlic
  • Grapefruit seed extract
  • Oregano oil
  • Wormwood
  • Zinc
  • Carnosine
  • DGL
  • Glutamine
  • Marshmallow
  • N-acetyl glucosamine
  • Quercetin
  • Slippery elm
  • Vitamin D
  • Probiotic supplements

Sample Microbiome Diet Meal Plan

Want to give it a try? Here’s what a day of eating might look like, according to Todd.

  • Breakfast: Fruit salad with avocado, topped with toasted cashews or unsweetened coconut
  • Midmorning snack: Sliced apple with almond butter
  • Lunch: Veggie chicken soup
  • Afternoon snack: Roasted curried cauliflower
  • Dinner: Salmon with turmeric, roasted asparagus and carrots, fermented beets, and kombucha
  • By Renee Cherry @reneejcherry


Your microbiome is your key to weight loss success. We used to think that the bacteria in our intestines (microbiome) were essentially there and not doing much. We now know differently. These little critters are highly active and powerful in terms of their ability to dictate what we eat, our cravings, how hungry we are, and how many calories we extract from the food we are eating. They’re also to blame for unwelcome food cravings.

Our microbiome plays a starring role in creating healthy fat genes by eating specific types of fiber called prebiotics that create short-chain fatty acids such as butyrate, which helps reduce our genetic predisposition to weight gain.

It turns out that lean people have more gut bacteria and a more diverse microbiota than those who are overweight or obese. An imbalance of gut bacteria may cause low-grade inflammation in your body, contributing to weight gain, obesity, and difficulty losing weight.

The good news? Gut microbes respond quickly to a change in diet. We can begin to take control and lose weight by eating the types of food that healthy gut bacteria thrive and multiply on.

Adding just one to three servings a day of the right prebiotic (foods that feed beneficial bacteria) and/or probiotic foods (foods that contain beneficial bacteria) to feed and nurture your microbiome will help stop sugar and carb cravings while you are beefing up your army of good healthy microbes to create weight loss success.

According to the Centers for Disease Control and Prevention, more than 35 percent of adults in the United States are obese. With obesity linked to a lengthy list of scary health conditions, including cardiovascular disease, diabetes, high blood pressure, and some cancers, it’s no wonder that many Americans’ ears perk up when a new diet is discussed. Unfortunately, many diets turn out to be fads that fade without making any real dent in waistlines.

A microbiome diet is different. It doesn’t restrict calories, involve strict recipes, or vilify particular food groups. Instead, a microbiome diet focuses on promoting overall wellness by fueling one of your body’s natural resources: gut microbes. The benefits of a diverse microbial community include a healthy weight and a stronger immune system, and a microbiome diet can help you cultivate that. Are you eager to explore your microbiome and learn how a microbiome diet works?

Exploring the Microbiome

What is a microbiome? Why should you care? An author, professor of genetic epidemiology, and scientist with King’s College London, Tim Spector is deeply interested in the microbiome, and he makes a convincing case as to why you should be too. Basically, the microbiome is the community of microbes that thrive in the human gut. While you may think of yourself as an individual, you are never truly alone. More than 100 trillion microbes live in your gut. These microbes impact your digestive and immune systems and contribute to the production of vitamins, minerals, and crucial brain chemicals like serotonin. According to Spector, the diversity of your microbial community has a significant impact on your health. Fortunately, you can influence your microbiome and your health with your diet.

How a Microbiome Diet Works

When you’re carrying extra weight, trying fruitlessly to shed unwanted pounds can be incredibly frustrating. If counting calories, exercising like crazy, and trying the latest diet tip hasn’t done the trick, it’s time to explore how a microbiome diet works. Actually, learning about this diet is smart even if you aren’t trying to lose weight because following a microbiome diet may provide significant wellness benefits.

The Benefits of a Balanced Microbiome

A balanced microbiome is linked with clear thinking, good digestion, a stable mood, and general good health. In contrast, experts believe that a microbiome that is out of whack can contribute to brain fog, depression, insomnia, skin issues, and obesity (source). In fact, when scientists reduced the diversity of animals’ microbiomes, the animals became ill.

While your microbiome is unique, it’s not set in stone. Microbes have short lifespans, and the composition of your microbiome can be changed fairly quickly. This complex ecosystem is influenced by a variety of factors, including your environment, stress, exercising, your sleep habits, your medications, and your diet. When you follow a microbiome diet, you opt for foods that fuel a healthy microbiome.

Fueling with Food

Antibiotics are notorious for killing both good and bad bacteria in the gut. Sugar, artificial sweeteners, and chemical preservatives often nourish bad bacteria that promote inflammation and encourage weight gain, allowing them to crowd out more helpful microbes, and restricting yourself to a limited diet can reduce the diversity of the microbes that live in your gut. However, consuming probiotics, fiber, and a wide assortment of healthy foods can help a multitude of good bacteria thrive, creating a balanced, diverse microbiome that helps you to stay healthy.

What to Eat

Now that you know how a microbiome diet works, are you ready to make the transition? When you follow a microbiome diet, your focus isn’t on counting calories or eliminating fats or carbs. Instead, your goal is to consume reasonable portions of a wide array of foods that support good gut microbes. Fermented foods like sauerkraut, pickles, kimchi, kefir, unprocessed yogurt, and kombucha are all great choices, and a daily probiotic can be helpful. Choose foods high in dietary fiber, mainly through vegetables (asparagus, leeks, broccoli, brussels sprouts, peas), as fiber feeds many of the bacteria in the gut (source). When filling your plate, don’t be afraid to mix it up. Eating an assortment of foods feeds more types of microbes, which expands the diversity of your microbiome.

Chicken Soup for the Microbiome

Chicken soup has long been a home remedy for illness, so it’s no surprise that chicken broth fits beautifully into a microbiome diet. Would you like to incorporate chicken broth into your microbiome diet? IDF’s SIP Bone Broth Protein is a conveniently delicious option that promotes good gut bacteria, which leads to a better immune system and reduces the body’s anti-inflammatory response. When your goal is to fuel your microbiome effectively, IDF’s broths make it easy to combine good nutrition and great taste.

When you want real ingredients from real food, you can count on IDF. To discover more about our bone broths or to see our full range of products, including CHiKPRO® Chicken Protein Isolate Powder, contact us today.

The Microbiome Diet

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A new trendy diet that you must know about is the “Microbiome Diet” by Dr. Raphael Kellman. It is all about knowing what food to eat and not to eat in order to restore optimal gut health and achieve weight loss.

What Is this “Microbiome Diet?”

Dr. Kellman is a board-certified doctor that specializes in gut health. He developed the Microbiome Diet–which is basically a three-phase program that focuses on gut health restoration and weight loss.

The whole concept of this diet is choosing the right foods to maintain a healthy gut microbiome. The human gut is composed of trillions of bacteria–both good and bad.

Having the proper balance of these bacteria is necessary for boosting digestion, supporting metabolism, improving mood, reducing inflammation, and even enhancing brain function.
The Microbiome Diet is not as simple as you think. It is divided into three unique phases.

The First Phase: The 4 R’s of Gut Health

The first phase of this diet lasts for 21 days. Its main objective is to eliminate unhealthy gut bacteria and replace digestive enzymes and stomach acids. In addition, it is intended to fill the gut with both probiotics and prebiotics to repair the gut lining.

The first phase is the strictest of all three phases because it follows the “4 R’s” of gut health:

  1. Remove: Removing all foods that cause inflammation or harm to your gut is a must, such as processed foods, or foods with hormones, pesticides and antibiotics.
  2. Repair: Repair your gut by taking supplements and consuming plant-based foods that soothe your gut and support your microbiome.
  3. Replace: Replace your digestive enzymes and stomach acid by eating certain herbs and spices. Doing so will also enhance the quality of your gut bacteria.
  4. Reinoculate: Reinoculate your gut with beneficial bacteria through consumption of prebiotic- and probiotic-rich supplements and foods.

In the first phase, it is imperative to stay away from a wide range of foods, such as grains, eggs, dairy, starchy fruits, starchy vegetables, processed foods, fried foods, artificial sugars, fillers, and colorings. A few types of meat, fish and fats must be avoided too.

Instead, it is recommended to consume a plant-based diet that is purely organic. Your diet must consist of prebiotic food sources, such as onion, garlic, and asparagus. Probiotic food sources are also recommended such as yogurt, kimchi, kombucha, and kefir.

Aside from food sources, this phase also recommends certain supplements such as vitamin D, zinc and grapefruit seed extract.

The first phase of the Microbiome Diet runs for 21 days with the objective of eliminating “bad” gut bacteria and replacing them with stomach acids and digestive enzymes. It consists of the “4 R’s of gut health:” remove, repair, replace, and reinoculate.

The Second Phase: Metabolic Boost

The second phase of the Microbiome Diet lasts for 28 days. Reaching the 28th day assumes that your gut microbiome is stronger and healthier, allowing flexibility to your new diet.

It is still necessary to avoid foods that harm your gut, but only about 90% of the time. You may also put back dairy, and gluten-free grains in your daily diet. Most vegetables and fruits are also allowed to be consumed, such as pears, mangoes, yams, and sweet potatoes.

The second phase of the Microbiome Diet runs for 28 days. After strengthening and healing the gut microbiome during the first phase, the second phase allows flexibility to your diet.

The Third Phase: Lifetime of Maintenance

Unlike the first and second phase, the third phase doesn’t have any recommended duration. In fact, you can follow it for as long as you want. Most people stop once they reach their weight loss goals, while some doesn’t ever stop.

At this time, it is expected that your gut is almost completely well. You still need to avoid some foods, but for only 70% of the time.

You read it right! 30% of the time, you can freely eat anything you want. However, it is best to still avoid sugary and processed foods.

The third phase of the Microbiome Diet can last for a lifetime. This is also called the “maintenance phase” because it aims to maintain the healthy condition of your gut. There are still foods to avoid, but only 70% of the time.

Foods to Stay Away From

There is a wide range of foods that the Microbiome Diet warns us about. These foods negatively impact the condition of your gut and the proper balance of your gut bacteria.

Especially during the first two phases, harmful foods must be avoided, such as:

  • Processed foods
  • Fast foods
  • Fried foods
  • Sugary foods
  • Foods with artificial sweeteners
  • Foods with hydrogenated and Trans fats
  • Starchy vegetables, like potatoes
  • Starchy fruits, like bananas
  • Peanuts, soy, and certain legumes
  • Dried fruit and fruit juices
  • Grains that contain gluten
  • Foods that contain yeast
  • Eggs and dairy (with the exception of butter)

Foods Allowed for Consumption

Throughout the three phases we talked about, these are the foods that may be freely consumed:

  • Grass-fed meat
  • Wild salmon
  • Non-starchy vegetables, like onion, garlic and carrots
  • Non-starchy fruits, like apples, kiwi, and oranges
  • Fermented vegetables, like kimchi
  • Nuts and seeds (including their butter)
  • Sunflower oil
  • Olive oil
  • Chickpeas and lentils
  • Herbs and spices

Take note that in the second phase, you may re-introduce certain foods into your diet including:

  • Eggs (free-range)
  • Dairy
  • Grains (gluten-free)

Extra Recommendations

Knowing what foods to eat and avoid is not the only thing you should remember. There are extra recommendations that the Microbiome Diet provides.

Here are some of them:

  • Go for organic foods as much as possible.
  • Lower your exposure to chemicals, such as household cleaners, non-organic lotions and makeup products.
  • Make sure to use a water filter.
  • Lower the toxins and pesticides that you are exposed to.
  • Avoid the overuse of certain drugs, such as proton pump inhibitors and antibiotics.
  • Take supplements that are good for your gut, such as zinc, vitamin D, and glutamine.

Sample 3-Day Meal Plan

Let me share with you a sample meal plan that you can use in the Microbiome Diet’s initial phase.

Phase 1, Day 1

  • Breakfast: Fruit salad and Brazil nuts
  • Snack 1: Walnuts
  • Lunch: Vegetable salad with chickpeas, sauerkraut, and lemon vinaigrette
  • Snack 2: Celery sticks and guacamole dip
  • Dinner: Grilled salmon with fermented beets and mixed greens

Phase 1, Day 2

  • Breakfast: Pancakes (use almond flour) with toppings of fruit and almond butter
  • Snack 1: Roasted cauliflower with curry
  • Lunch: Vegetable salad with toppings of miso-glazed cod
  • Snack 2: Parsnip sticks with almond butter
  • Dinner: Zucchini noodles topped with chicken meatballs and marinara sauce

Phase 1, Day 3

  • Breakfast: Almond breakfast cookies
  • Snack 1: Carrots with hummus
  • Lunch: Chicken and vegetable soup
  • Snack 2: Sautéed pineapple
  • Dinner: Flank steak tacos with steamed veggies, salsa, and guacamole.

There are more recipes in the Microbiome Diet book if you want more ideas.


The Microbiome Diet truly helps in achieving optimal gut health and weight loss. It focuses on consuming foods that are gut-friendly, and avoiding foods that negatively impact the gut and the microbiome.

Always remember that when our gut microbiome flourishes, so do we!

What Is The Microbiome Diet?

Modern society is experiencing different health problems due to many reasons: poor eating habits, lack of exercise, exposure to chemicals/toxins, tremendous stress, and more. But one of the most critical factors that cause health issues among people is poor diet.

Eating the wrong foods can wreak havoc to your gut health. Find out why you should take your gut’s health seriously and how you can improve your overall well-being with the right diet.

What You Should Know About the Microbiome Diet

The microbiome diet aims to restore and improve gut health with the proper food. The human microbiome is important because it’s home to the beneficial microorganisms in your digestive system. It’s also called the gut, gut flora, intestinal flora, or gut microbiota.

The microbiome diet emphasizes the importance of gut health and how eating certain foods will benefit it entirely.

The main staples are fruits and vegetables, lean meat, and a variety of probiotic and prebiotic foods. Dr. Raphael Keller, the creator of the Microbiome Diet, suggests that a special diet can restore gut health. This will benefit people who have not been eating a gut-friendly diet for some time.

Microbiome Diet: How It Works

If you want to optimize or improve your gut health, you should consider switching to a Microbiome diet. The diet has three phases and is less restrictive as you go on with the diet. By the time you reach stage three, you’ll be consuming primarily gut-friendly food.

Phase 1: The Four R’s

Phase one of the microbiome diet is very restrictive. The first phase spans 21 days and requires avoiding certain foods, such as dairy, eggs, grains, legumes, starchy fruits, soy, and some vegetables. You’re not allowed to consume food with sugar (including artificial sweeteners), packaged foods, and food products with coloring or fillers. Instead, you can eat organic foods that are rich in prebiotics, like asparagus, onions, leeks, and garlic.

It’s also recommended to include fermented, probiotic-rich foods. like yogurt and sauerkraut. Those following the microbiome diet should follow the four R’s:

  • Remove: Don’t consume any food that can cause a disrupted or unbalanced microbiome, including processed foods, food products with sugar, antibiotics, hormones, or pesticides.
  • Repair: Consume plenty of plant foods that’ll help repair the gut that was harmed through prolonged consumption of processed foods and unknown chemicals or toxins.
  • Replace: Consume spices, herbs, and supplements to help replace digestive enzymes and stomach acid with better-quality substances.
  • Re-inoculate: Consume foods with high prebiotic and probiotic content so that the gut is repopulated with good bacteria.
Phase 2: The Metabolic Boost

Phase two of the microbiome diet allows more flexibility in the diet because the first phase of the diet has helped heal and repair the gut. You can now add dairy, gluten-free grains, legumes, and free-range eggs to your diet. Your diet can now include bananas, potatoes, and other starchy foods or vegetables.

However, you should still avoid some foods, but only to a certain extent. It means you can enjoy corn, potatoes, soy, and other foods that can harm the gut for about three to four times each week.

Phase 3: The Lifetime Tune-Up

In phase three of the microbiome diet, your gut is expected to be healed entirely or almost fully healed. During this maintenance phase, you can add more food types to your daily diet. Individuals in the third phase of the microbiome diet should maintain these eating habits for life.

Dr. Kellman discourages calorie-counting or food portioning, but instead focus on the quality of food consumed regularly. Intuitive eating is also encouraged, which means waiting for your body to tell you to eat or stop eating.

The Pros and Cons of the Microbiome Diet

Following the microbiome diet have several benefits and a few drawbacks:

  1. Encourages proper food choices
  2. Improves or repairs the gut
  3. Reduces the intake of sugar
  4. Helps to remove extra weight
  5. Possibly prevents diseases
  6. Enhances the mood and mind

There are some disadvantages to following the microbiome diet. First, the diet is very restrictive and requires cutting back on many types of foods. Second, the diet is not budget-friendly since it involves the consumption of organic foods, cage-free eggs, gluten-free grains, and free-range meat. These foods are more expensive compared to their regular counterparts.


There’s no doubt that the microbiome diet is beneficial to those who want to have a healthier gut. In general, avoiding processed foods, oily, and sugary foods will help in improving your overall health.

If you wish to follow the microbiome diet, reach out to a registered dietitian or your physician for evaluation and recommendations.

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It’s not hard to stumble across any number of articles and papers proclaiming the next wonder food to improve your gut health. As scientists increasingly discover the central role that gut bacteria play in our overall health, it’s tempting to latch on to these promises to try to revitalise everything from your weight to mental wellbeing.

But the science has a way to go before we know exactly what nutrition is best for your gut. BBC Future spoke to leading gut health and microbiome researchers to sift fact from fiction on gut health “wonder foods”, probiotics, prebiotics and what changes to your diet could genuinely boost your gut health.

The interest in how to improve your gut health is so high because recent advances have begun to unpick how the microbiome affects many conditions beyond those affecting the digestive system. Studies have linked gut bacteria – known collectively as the microbiome – to changes in mood and mental health, tendency to obesity and to cardiovascular health. For people who want to maintain a healthy weight and mental health, the goal would be a way to “hack” their gut bacteria.

“The general belief is that a diverse gut microbiota is a synonym for health, since are helping us produce nutrients and essential substances that our cells cannot,” says Sonia Fonseca, a researcher studying the interactions between the diet, gut, microbiome and brain at the Quadram Institute. “So feeding our microbes with a diverse diet and creating a comfortable environment for them seems the right thing to do.”

You might also like:

  • What we do and don’t know about gut health
  • Can detoxing help your gut health?
  • How dirty air could be affecting your gut health

But finding a way to hack your microbiome might be harder than it sounds. For one thing, like much of health research, even though a study finds a link between one food and an improvement in gut bacteria, it doesn’t mean that food has caused the change in the microbiome.

“Many studies are based on finding correlations, which even sometimes are contradictory, but only a few are interested in explaining causation,” says Fonseca. “That is the challenging part.”

While headlines may be moving faster than solid science, some clear trends are emerging on things we can do to make a real impact on gut health, says Kevin Whelan, professor of dietetics at King’s College London. The majority of evidence supports that there are four main ways to do this.


The first is taking foods or supplements with probiotic bacteria in them. These are bacteria that are generally thought to be part of a healthy microbiome – particularly common ones in supplements and “live” yoghurts (meaning they contain living bacteria) are called bifidobacteria and lactobacillus.

“In general, what we know is that if you take a probiotic yoghurt with those bacteria, we know it will increase the number of those strains in your gut,” says Whelan.

Best foods for microbiome

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