This 3-Day Microbiome Cleanse Will Eliminate Bloat, Improve D

Photo:Functional Food

Over two decades as a holistic, functional doctor in New York City, I have treated tens of thousands of patients who have brain fog, anxiety, and lack of clarity. I’ve developed an approach to brain and microbiome health that goes far beyond conventional medicine, which I detail more in my book, The Whole Brain: The Microbiome Solution to Heal Depression, Anxiety, and Mental Fog Without Prescription Drugs.

In just three days, you can begin your journey of microbiome health for life. Of course, like any habit, it will take more than three days to achieve significant results; this three-day reboot is to provide the tools that you need for a lifelong shift in your diet, your health, and your mood.

Day 1: Laying the foundation.

When you eat the foods that support your brain, microbiome, and gut—and when you avoid foods that undermine them—you create a healthy ecology throughout your entire body. This healthy ecology is crucial for overcoming depression, anxiety, and brain fog.

The diet couldn’t be simpler. To reap the benefits, you don’t need to worry about how much you’re eating, as long as you are careful to stick to the right foods. The good news is that I don’t want you counting calories, fretting over such things as grams of carbs, or measuring out amounts. I just want you to focus on making good whole food choices at every meal, and this will do the work of rebalancing your microbiome, healing your gut, and supporting your brain.

Because your brain is composed primarily of fat, you need healthy fats to support your brain. Healthy fats are first and foremost those found in nature. Thus trans fats, which are made only in factories, are not healthy—your cells don’t know what to do with them, and these fats can actually damage your cells and, therefore, your brain.

The rest of your brain is composed of protein; therefore, your brain needs healthy proteins as well. Proteins contain amino acids, which are needed to preserve the integrity of your cells and to produce the enzymes necessary for digestion and other aspects of metabolism. Any organically raised protein can be healthy; however, studies have shown that when proteins are too high in fat, your microbiome can suffer. I recommend "clean, lean proteins."

For the three days of this diet, stock your fridge and pantry with these foods, and try to largely consume what's on this list.

  • Avocado oil
  • Coconut oil
  • Olive oil
  • Wild fish
  • Organic meats and poultry, pasture-raised and antibiotic-free
  • Organic grass-fed sheep and goats' milk dairy products
  • Kefir, yogurt
  • Fermented vegetables
  • Kimchi
  • Raw sauerkraut
  • Kombucha
  • Cultured buttermilk
  • Asparagus
  • Dandelion greens
  • Gluten-free grains (such as millet, quinoa, rice)
  • Jerusalem artichoke
  • Jicama
  • Leeks
  • Legumes (beans, garbanzos, lentils)
  • Potatoes (when roasted and cooled)
  • Radishes
  • Seeds
  • Tomatoes
  • Nuts (raw, never roasted)
  • Microbiome super spices: cinnamon, turmeric, ginger
  • All organic vegetables
  • All organic fruits—but in moderation, please! At most, enjoy two fruits a day, and if you’re struggling with sugar or carb cravings, keep it to one serving. Otherwise, you may be feeding the wrong types of bacteria too much sugar.

It’s not just WHAT you eat; how you eat is just as important. What is crucial is that you eat in a stress-free way, taking time to enjoy every bite of food.

One of the saddest things I see as a physician is when patients come to me at odds with their own bodies. I understand how it can happen. You come in with painful digestive issues and perhaps also struggle with excess weight, and you’ve learned to view both food and your own body as your enemy. Each meal is a challenge, full of temptations, obstacles, pitfalls, dangers. In such circumstances, it’s very difficult to find pleasure in a delicious taste, a shared meal among friends, the joy of feeling full and satisfied.

Rushed, stressful eating activates the nervous system, which triggers a cascade of stress hormones and disrupts digestion, with disastrous consequences for your brain. A calm mealtime, with gratitude for the food and the mental space to savor every bite, triggers the parasympathetic nervous system and creates significant benefits for gut and brain health, as well as weight. Chew each bite 20 times longer than you are used to, which literally cues your relaxation response.

If you can rediscover the joys of eating, the pleasures of food, the value of a meal with people you love, you will go a long way toward healing your gut—and your brain.

Now that you’ve added the essentials, the next step of this challenge is to eliminate the foods that disrupt your ecology: toxins, inflammatory foods, and foods that undermine your brain function.

For the next three days, try to avoid these foods as much as possible:

  • Canola oil and cottonseed oil
  • Corn and cornstarch
  • Cow’s milk dairy products
  • Dried or canned fruits
  • Gluten (found in wheat-, barley-, and rye-based foods)
  • High-fructose corn syrup
  • Iceberg lettuce
  • Juices
  • Peanuts or peanut butter
  • Processed meats or deli meats
  • Processed and packaged foods
  • Soy—except soy lecithin and organic fermented soy: soy sauce, tempeh, miso
  • Sugars and sweeteners, natural or artificial, except Lakanto
  • Trans fats and hydrogenated fats

Bonus points if you can do the following:

  • Don’t store food in plastic. Glass containers are optimal.
  • Use "clean" personal products and cosmetics, shampoos, lotions, shaving products, etc. By "clean" I mean without parabens, phthalates, fragrances, or other chemicals.
  • Use "clean" household products: cleansers, detergents, polishes, etc.
  • Drink only filtered water. Avoid bottled water—molecules from the plastic migrate into the water.

Day 2: Get your supplement game on.

While there are no "one-size-fits-all" supplement plans, there are certain supplements that support your health in a variety of ways.

Pruning the excess bacteria.

As probiotics have been getting more media attention these days, you may have read about "supporting the good bacteria" and "eliminating the bad bacteria." To me, that’s a human-made construct that has nothing to do with how nature actually works. My approach understands there are no "bad" bacteria. In the right context, all bacteria have the potential to do good, contributing to the health of the whole body ecology. Health problems occur when some bacteria proliferate unchecked. So our goal is not to "eliminate the bad" but rather to restore balance, pruning the naturally occurring bacteria in your gut that have overgrown to excess while still maintaining a diverse and vibrant ecology.

Some supplements can help you reduce the excess. To prune your microbiome, look for a combination product that contains at least two of the following ingredients, and follow the directions on the bottle:

  • Berberine
  • Wormwood
  • Caprylic acid
  • Grapefruit seed extract
  • Garlic
  • Oregano

Boosting digestion.

Short-chain fatty acids (SCFAs) offer enormous benefits to digestion and gut function. They are a fuel source for the cells of your large intestine, improve insulin sensitively while increasing energy expenditure, modulate your immune system, and protect against inflammation. SCFAs have also been shown to be neuroprotective, which is important for your brain, while also improving brain plasticity for those with neurological disease.

To improve digestion, brain function, and gut function:

  • Butyrate
  • Digestive enzymes—look for a product that contains protease, lactase, amylase, DPP IV, alphagalactosidase

Gut motility and brain function.

These supplements help your digestive tract keep food moving, which aids in digestion as well as the elimination of toxins. Both via the gut and through their impact on the brain itself, they also support brain function.

  • 5HTP
  • Curcumin
  • Alpha-lipoic acid
  • Probiotics: The more strains included, the better! Ideally, you want at least 50 billion CFU, but diversity is even more important than total quantity.

In my practice, I work with individual patients to create their own personal probiotic combination based on their blood work and other testing—probiotics are not, unfortunately, "one size fits all"! Hence the term "Microbiome Medicine"—I find what particular bacteria strains are deficient and causing the brain fog or other health symptoms.

The most important two strains are called bifidobacterium (B.) and lactobacillus (L.), which have been shown to aid in improving a number of neuropsychiatric disorders and dysfunction including anxiety, depression, OCD and memory issues.

Studies have also shown that the following bacteria also help with depression:

  • L. casei
  • L. acidophilus
  • B. longum
  • B. infantis
  • L. helveticus
  • L. rhamnosus
  • B. bifidum
  • B. breve
  • L. plantarum PS 128
  • B. longum Rosell 175
  • L. rhamnosus

Brain fog is another condition that can be effectively addressed with supplements. The following are good for targeting brain fog:

  • Yucca
  • Arginine
  • Ornithine
  • Prebiotics are important to ensure the health of bacteria already living and growing within the intestine.
  • Inulin powder
  • Arabinogalactans

Breakfast, Day 2: Breakfast sundae of yogurt, apple, berries, and walnuts

Snack, Day 2: Cucumber, cherry tomatoes, and radishes with sea salt and olive oil dips

Lunch, Day 2: Curried Chicken Salad With Apple, Jicama, Fennel & Walnuts

Here’s your chance to use up the leftover chicken from the Chicken Bone Broth. The jicama, radishes, and tomatoes are all "microbiome superfoods," loaded with just the kind of prebiotic fiber that your microbiome needs to be diverse and strong. The healthy fats in the nuts and vinaigrette help support your brain, plus the nuts, fennel, and garbanzos have plenty of microbiome-friendly fiber.

Ingredients, Lemon Vinaigrette

  • 1 teaspoon finely grated lemon zest
  • 2 tablespoons freshly squeezed lemon juice, plus more if needed
  • ½ teaspoon Dijon mustard
  • ¼ teaspoon salt, plus more to taste
  • 3 tablespoons olive oil
  • Freshly ground black pepper

Ingredients, Curried Chicken Salad

  • ¼ teaspoon curry powder
  • 1 cup cooked chicken, cut into ½-inch chunks
  • 1 (½-inch) slice peeled jicama, diced
  • ¼ cup canned garbanzos, drained and rinsed
  • ¼ cup diced fennel
  • ¼ heaping cup cored and diced apple
  • Salt and freshly ground black pepper
  • 1 heaping cup mixed salad greens
  • 2 radishes, cut into ¼-inch slices
  • 6 cherry tomatoes, halved
  • 1 roughly chopped tablespoon cashews or walnuts


  1. Make the lemon vinaigrette: Combine the lemon zest and juice in a small, bowl. Add the mustard and ¼ teaspoon of salt. Whisking, slowly add the olive oil. Add additional salt, pepper, and lemon juice as needed.
  2. Make the curried chicken salad: Mix the curry powder into the lemon vinaigrette.
  3. Combine the chicken, jicama, garbanzos, fennel, and apple in a bowl with 1½ tablespoons of the curried lemon vinaigrette. Add salt and pepper to taste.
  4. Place the salad greens in the middle of a plate. Scoop the chicken mixture on top and fan the radishes and halved tomatoes around it.
  5. Sprinkle the nuts on top and serve with the remaining vinaigrette.

Snack: Caribbean-Spiced Garbanzos, leftover from Day 1

Dinner: Mediterranean Fish Stew With Assorted Salad Greens and Lemon Herb Vinaigrette

This quick-and-easy fish stew can be made with a variety of firm-fleshed white, low-mercury fish, such as cod or halibut. The onions and carrots are "microbiome superfoods" that nourish and replenish your gut bacteria. The fat in the fish and salad vinaigrette helps support your brain cells and the cells in your gut wall while the resistant starch in the Herbed Rice is terrific for both gut and microbiome.


  • 1 pound cod, cut into 2-inch pieces
  • 2 tablespoons freshly squeezed lemon juice, plus more if needed
  • ½ teaspoon salt, plus more if needed
  • ½ teaspoon freshly ground black pepper, plus more if needed
  • 2 large garlic cloves
  • 5 anchovy fillets, rinsed
  • 2 tablespoons olive oil
  • ¾ cup chopped onion
  • ¾ cup chopped carrot
  • ¾ cup chopped fennel
  • 1 (28-ounce) can organic tomatoes, with liquid
  • ½ teaspoon fresh thyme leaves
  • 2 teaspoons snipped fresh tarragon
  • 1 teaspoon roughly chopped parsley, plus 1 teaspoon finely chopped, for garnish
  • Herbed Rice (leftover from Day 1 dinner), for serving
  • Assorted salad greens


  1. Place the fish in a small, nonreactive bowl with the lemon juice, salt, and pepper. Marinate for 15 minutes.
  2. Place the garlic in a food processor and chop finely. Add the anchovy fillets and process until smooth. Set aside.
  3. In a large Dutch oven, heat the olive oil and add the onion, carrot, and fennel. Cook for about 5 minutes, or until the onion is soft. Add the anchovy mixture and cook for a minute over low heat. Add the tomatoes. Cook for about 10 minutes, or until the tomatoes have begun to break down.
  4. Add the thyme, half of the tarragon, the roughly chopped parsley, and the fish. Simmer until the fish turns opaque and flakes when prodded with a fork.
  5. Add 1 teaspoon of the tarragon and taste for seasoning, adding salt and pepper and lemon juice to taste. Garnish with the finely chopped parsley.
  6. Serve with the herbed rice and vinaigrette-dressed salad greens.
  7. Refrigerate the extra portion for another dinner or a fish salad lunch.

Day 3: Reactivate your will.

The foundation of healing is to activate your will—to tap into your own innate desire to receive and to give. This can be done at a very fundamental level, by connecting to your purpose or through a sense of awe. Let your gut instincts guide you to which suggestions will be most healing for you.

Some of these suggestions may strike you as difficult. That’s because your will may be a bit out of shape, just as your body gets out of shape when you don’t exercise. Those first few exercises can be scary and uncomfortable—but soon your body welcomes the exertion. In the same way, I invite you to train your will, making it stronger and more muscular. Slowly but surely, you will feel more empowered and strong, in both your receiving and your giving.

Some of these suggestions may seem too small to make much difference. Don’t be fooled! These seemingly tiny actions can create big, unexpected shifts in your will, helping you to transform your brain and body and return you to a stronger sense of self.

Try these microbiome-enhancing activities.

Quiet time: Find a safe, comfortable place where you can sit or lie quietly for at least five minutes: in a cozy chair, on a couch or bed, in a scented bath. Allow your body to relax and simply be quiet. Allow yourself to receive the physical comfort of that moment. Then think of a time when you received something—from a family member, friend, stranger, animal, or even a special place. What you received might have been a helping hand, a smile, a sense of peace—something large, small, or in between. Sit or lie quietly, receiving now what you received then.

Reach out: Think of something you need that would make you feel cared for and nurtured. It might be a physical object, or it might be someone to help you clean your house or take care of your kids for an hour. Find a person you trust and ask for what you want. Allow yourself to receive it.

Say hello: Next time you are in a public situation—at work, in a store, or walking down the street—say hello to at least one person with your warmest smile. This is an especially good exercise if you don’t feel like smiling—if you’ve been having an awful day or feel especially depressed. See whether you can activate just a tiny flicker of connection with other people—a smile as they hand you change or as you pass them by. Notice their response and how it makes you feel.

Shift the focus: In a situation where you feel hopeless and powerless—a long line, a doctor’s waiting room—find someone else to focus on. Ask someone how he or she is doing or comment on your shared situation in a sympathetic way. Make it your secret project to cheer the other person up for just 60 seconds. I bet you’ll emerge from the experience feeling more empowered and cheerful than you were before.

Music: Choose a piece of music that you enjoy. Sit quietly for five to 30 minutes and savor the music, allowing yourself to receive whatever it offers. If you’d rather sway, tap, clap, or dance in response to the music, by all means, let your body go! Sing or hum or shout along, as the spirit moves you. In a very real sense, listening is your receiving of the music; dancing and singing are your giving back to it.

Team sports: There’s nothing like a team sport for giving and receiving—for experiencing how those two aspects of your will are really one. If you like sports, or think you might like them, go for it!

Group projects in the arts, politics, etc.: Joining a group of any kind, for any purpose, can set off a powerful exchange of receiving and giving. Find an activity you like or would like to know more about. Join a group, and discover the pleasures of giving and receiving.

Discover/rediscover: Give yourself five to 30 quiet minutes in a safe, pleasant space. Write one of the following sentences at the top of the page—your choice:

  • What's my purpose?
  • What gives my life its meaning?
  • What do I contribute to the world?
  • What makes me feel most inspired and alive?

Then, for five to 30 minutes, write whatever comes to mind. Set a timer for the duration of your choice and don’t stop writing until it goes off. If you don’t know what to say, write, "I don’t know what to say" over and over until you find yourself writing something else. Unless you truly hate the physical act of writing, use a pen and notebook; otherwise, a computer is OK.

Connect/reconnect: Think of something that makes you feel purposeful, meaningful, and connected. It could be a way of "giving back"—volunteering at an organization, doing a favor for someone else, teaching someone a skill or concept that you’re good at. It could be a form of self-expression—writing, painting, composing, building, repairing, or renovating. It could be something extremely personal—your own special activity. Find half an hour each week to engage in this activity.

Breakfast, Day 3: Grapefruit and orange sections, avocado and kiwi slices

Snack, Day 3: Roasted carrots, Brussels sprouts, and asparagus

Lunch, Day 3: Mexican Fish Salad With Jicama, Black Beans, Avocado, and Lime

Jicama and tomatoes are microbiome superfoods that nourish your gut bacteria, as do the black beans. The healthy fat in the fish, avocado, and Lemon Vinaigrette helps keep your cell walls strong, which is especially important for brain health. This is a wonderful meal for a satisfying, protein-rich lunch, giving you the wherewithal to get through your afternoon energized and alert.


  • ¾ cup flaked, cooked firm-fleshed white, low-mercury fish, such as cod or halibut
  • 2 tablespoons peeled and diced jicama
  • ¼ teaspoon ground cumin
  • ½ teaspoon snipped fresh cilantro
  • Salt and freshly ground black pepper
  • 4 slices peeled and diced avocado
  • ¼ teaspoon finely chopped jalapeño pepper, or more to taste
  • 2 tablespoons diced tomato
  • 1 tablespoon peeled, seeded, and diced cucumber
  • 1 scant cup cooked organic black beans (if canned, drain and rinse)
  • 2 cups salad greens

For garnish

  • 4 thin slices avocado
  • 4 thin slices tomato
  • 1 sprig cilantro
  • ¼ lime


  1. Mix the fish in a small bowl with the jicama, 1 tablespoon of the vinaigrette, and the cumin and cilantro. Add salt and black pepper to taste.
  2. In a second small bowl, combine the avocado, jalapeño, tomato, and cucumber with 1 teaspoon of the vinaigrette.
  3. In a third small bowl, combine the black beans with 1 tablespoon of the vinaigrette.
  4. Heap the greens on a plate and arrange the fish in the center surrounded by the avocado mixture and the black beans. Garnish with the avocado and tomato slices, cilantro, and a lime wedge.

Snack, Day 3: Apple slices with almond butter

Dinner, Day 3: Chicken Stew With Fennel, Turnip, and Portobello Mushroom With Roasted Potato Salad and Garlic-Sautéed Kale

Prepare this savory chicken dish for one dinner and refrigerate or freeze the second portion for another dinner. You’ll love the full flavors from the tangy marinade and the variety of textures from the different vegetables. Your brain will love the fiber in the fennel and turnip and the healthy fats in the olive oil.


  • 2 boneless chicken breasts or 4 chicken thighs
  • 2 tablespoons white vinegar
  • ½ cup turnip, peeled and cut into ½-inch pieces
  • ½ cup fennel, cut into ½-inch pieces
  • 2 tablespoons olive oil
  • 1 cup portobello mushroom, cut into ½-inch pieces
  • ½ teaspoon minced garlic
  • 1 tablespoon roughly chopped fresh tarragon, plus 1 teaspoon, for garnish
  • ½ cup freshly squeezed orange juice


  1. Marinate the chicken in the vinegar in a nonreactive bowl for 15 minutes.
  2. Meanwhile, preheat the oven to 375°F.
  3. In a saucepan, sauté the turnip and fennel in 1 tablespoon of the olive oil. After about 10 minutes, when the turnip begins to soften, add the mushroom and garlic. Cook over medium heat for about 5 minutes.
  4. Add the tablespoon of chopped tarragon and the orange juice. Remove from the heat and set aside.
  5. Drain the vinegar from the chicken. Dry with paper towels.
  6. Heat the remaining teaspoon of olive oil in a baking dish and add the chicken. Brown on the stovetop over medium heat for 2 to 3 minutes on each side. Cover the chicken with the vegetable mixture.
  7. Cover the dish with foil and bake for 25 minutes.
  8. Garnish with the remaining teaspoon of chopped tarragon. This dish may be baked ahead of time and refrigerated for 3 days or frozen.

Good luck with this reboot! I know I’ve given you a lot of information and asked a lot of you in just three days. Take your time, follow my suggestions, and soon enough you will start to notice that your microbiome—and your overall health and vibrancy—is back to its optimal function.

These sneaky things are damaging your microbiome.

Frank Lipman, M.D.

This 3-Day Microbiome Cleanse Will Eliminate Bloat, Improve D
Frank Lipman, M.D.

Related Posts

The Weird Food Supermodel

Dr. Charles Passler is the man responsible for keeping supermodels like Bella Hadid, Adriana Lima, and Amber Valletta fee…

Read More Loading next article...

Your article and new folder have been saved!