Microbiome Diet: How Healing Your Gut Can Help You Lose Weight

The Microbiome diet rolls two of my favorite topics into one: gut health and weight loss!

This new diet focuses on helping you lose weight and keep it off in the long term by improving your gut health.

Focusing on improving your gut health should be a no-brainer because your gut health is connected to so many other aspects of your overall health.

Mediterranean salad and swordfish on a white plate - a good example of a microbiome diet meal.

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What is the Microbiome Diet?

The Microbiome Diet is a three-phase food program that focuses on helping you lose weight by improving and restoring your gut health.

The diet was developed by Dr. Raphael Kellman, an internal medicine doctor who is also a pioneer in functional medicine.

Functional medicine focuses on the whole patient, including the complex interaction of all the systems in your body, including your metabolism, hormones, genetics, environment and more.

Functional medicine makes so much sense to me – why would you just want to slap a bandaid on a problem (the way standard medicine does with pharmaceuticals), when you should also be working on the root cause of your issues?

Besides running a center for integrative and functional medicine, Dr. Kellman wrote a book called (no surprise), The Microbiome Diet.

The Microbiome Diet is a flexible plan that can work with many other styles of eating and diets: paleo, keto, vegan, raw, kosher, low-carb, and more.

This plan may be new, but it is NOT a fad diet. It’s an easy to follow eating plan that gradually changes your lifestyle and food choices to one that is healthier for you in the long term.

Why the Microbiome Diet?

If you’ve read any of my other posts on gut health, you know that I am passionate about improving gut health because it is connected to so many other aspects of our health.

And again, it’s gut health for the win! Cutting edge science has shown that our gut microbiome (the name for all of the microflora living in your entire digestive system) is hugely responsible for our ability to lose weight and maintain a healthy weight.

The approach outlined in the microbiome diet works both now for immediate weight loss AND later by changing your gut microbiome long term so you can maintain your weight loss.

The diet is based on eating the right foods that keep your gut microbiome healthy, which can help boost your metabolism, eliminate cravings and help you drop those unwanted pounds.

Tomato and olive salad with basil.

How To Do the Microbiome Diet

The Microbiome Diet is divided into three different phases, each designed to help improve your gut health, which in turn will help you lose weight and keep it off.

Phase 1: 4 R’s To Improve Your Gut Flora

This first phase is the strictest of the three phases.

During this 21-day phase, you will concentrate on removing the unhealthy bacteria that has been accumulating in your gut, and adding probiotics and prebiotics.

  1. Remove foods that interfere with a healthy gut microbiome like bad bacteria, pathogens, and toxins. This step also involves cutting out foods that can cause inflammation, foods that include pesticides, hormones, antibiotics, and some medications.
  2. Repair your gut wall by focusing on eating plant foods and supplements that are gut healing and support your gut microbiome.
  3. Replace your stomach acid and pancreatic enzymes by eating recommended herbs, spices, and digestive enzymes to improve the balance of good bacteria in your gut.
  4. Reinoculate your gut with large amounts of healing, probiotic and prebiotic rich foods and supplements.

In Phase 1 of the microbiome diet, you are required to avoid foods that are high in refined carbohydrates and processed foods. Also foods high in fat, sugar, fillers, artificial colorings, flavoring, and sweeteners.

Foods to avoid during this phase include all grains, eggs, dairy, most legumes as well as starchy vegetables and fruits.

The foods to be avoided have been proven to allow the overgrowth of bad bacteria. By removing these foods for the first phase, it allows the gut to begin to change for the better.

You are encouraged to eat a an organic (to make sure you’re not ingesting extra toxins), plant-based diet rich in prebiotic foods like onions, garlic, leeks, and asparagus.

Probiotic foods are also important because they contain large amounts of beneficial bacteria. Fermented vegetables, kimchi, sauerkraut are examples of the probiotic foods recommended during this phase.

Recommended supplements include zinc, Vitamin D, and probiotics.

Phase 2: The Metabolic Boost Phase

By the time you’ve completed the three-week phase 1, your intestine has begun to heal, inflammation is down, your gut is already stronger

Phase 2 of the microbiome diet lasts 28 days and is not nearly as strict as phase 1.

While you continue to eliminate gut-damaging foods, because of your gut’s improved health, you are allowed to add some of phase 1 forbidden foods.

Additional Phase 2 Foods include:

  • Organic, free-range eggs
  • Some fruits: melon, mango, peaches, pears
  • Gluten-free grains: amaranth, buckwheat, millet, oats, quinoa, brown rice, basmati rice, wild rice
  • Dairy: goat and sheep’s milk yogurt, cheese and milk.
  • Legumes: green beans, and all other types of beans
  • Sweet potatoes and yams

Phase 3: Lifetime Tune-up

At this point, your gut is either completely healed, or is well on its way, so this is considered the maintenance phase.

Phase 3 of the microbiome diet is meant to be followed until you reach your weight loss goals. Even after you meet your goals, phase three is perfect to help you maintain your weight loss long term.

During this phase, you should continue to avoid the trouble-making foods, but you can eat them 30% of the time – or about at one meal a day.

For maintenance purposes and good gut health, it’s recommended to avoid processed foods and added sugar as much as possible.

What To Expect With the Microbiome Diet

As you progress through the plan, you can count on feelings of satiety and lower, less ravenous hunger. This will make it much easier to make healthy choices and to avoid overeating.

People also report having more energy, better sleep and a general increase in feelings of well being.

Be prepared to be a bit gassier as your body adjusts to all the new fiber, probiotics, and prebiotic foods.

Recommended Supplements

Along with probiotic and prebiotic foods, the Microbiome diet recommends various supplements as a way to strengthen your gut, reduce inflammation and help rid your gut of unhealthy bacteria.

The microbiome diet relies rather heavily on supplements as you can see from the list below. Aside from being expensive, most of these supplements don’t have a ton of scientific research backing up their efficacy.

Dr. Kellman recommends these supplements, especially during the first phase:

Foods to Eat

These foods can be enjoyed and are encouraged for all phases of the microbiome diet:

  • Grass-fed meat
  • Wild salmon
  • Good fats from nuts, seeds, nut butter (not from peanuts), avocados, flaxseed, sunflower and olive oil.
  • Chickpeas and lentils
  • Fermented vegetables: sauerkraut, kimchi, pickles
  • Non starchy prebiotic vegetables: Garlic, onions, artichokes, leeks, asparagus, radish
  • Non-starchy fruits: apples, berries, cherries, coconut, citrus, rhubarb, kiwi
  • Spices and herbs like cinnamon and turmeric.
  • Phase 2 foods: See phase 2 list above

Foods to Avoid

All the foods recommended to either eat or avoid on the microbiome diet are meant to help improve the health of your gut and microbiome.

For phase 1, these are to be completely avoided:

  • Packaged/fried/processed foods
  • All grains containing gluten
  • Soy
  • Fillers/colors/artificial sweeteners
  • Sugar and high-fructose corn syrup – basically an added sugar detox
  • Starchy fruits and vegetables: Corn, potatoes, peas, bananas
  • Trans fats and hydrogenated fats
  • Deli meat and lunch meat
  • Peanuts, legumes (with the exception of chickpeas and lentils)
  • Dairy (except butter/ghee)
  • Eggs
  • Fried Foods
  • Fish with high mercury content
  • Fruit juice and dried fruit

Drugs to Avoid

Certain drugs can disrupt the gut microbiome and should be avoided if at all possible.

Before discontinuing any recommended medications, be sure to get your doctor’s approval.

These drugs can disrupt the balance of good gut bacteria:

  • Antibiotics
  • Non-steroidal anti-inflammatory drugs (NSAIDS) .
  • Proton Pump Inhibitors (like Prilosec, Prevacid)

More Rules To Improve your Microbiome

One foundation of the Microbiome Diet is to avoid toxins, pesticides, hormones and chemicals by eating cleaner organic foods and avoiding certain foods, to help heal your gut.

  • By choosing organic foods, you can eliminate the hormones and pesticides found in and on conventionally grown and raised foods.
  • The author of the diet also recommends using a good water filter when you drink tap water.
  • Limiting the chemicals you’re exposed to by choosing household cleaners and personal care products made with safer ingredients.

The Takeaway

The Microbiome Diet aids gut health and weight loss by limiting gut harming foods like sugar, processed foods, fried foods, and other generally unhealthy foods.

These troublesome foods are replaced with fresh vegetables and fruits, lean proteins, healthy fats and probiotic and prebiotic foods.

It is restrictive at first, but as you move through the diet and your gut begins to improve, you can add more of the restricted foods back in limited doses.

The Microbiome diet is a plan that slowly changes your dietary lifestyle to one that is healthier in terms of weight control and gut health.

By the time you complete the three-phase program, you will have healed your gut. Because of your improved gut health, your hunger and cravings for unhealthy foods will have decreased, and you will have naturally lost weight by eating healthy foods.

For more complete information including the detailed 3-phase plan and recipes, read The Microbiome Diet by Raphael Kellman, MD.

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Breakfast smoothie bowl for gut health.