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

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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

  • Vegetables: Asparagus; leeks; radishes; carrots; onions; garlic; jicama; sweet potatoes; yams; sauerkraut, kimchi, and other fermented vegetables
  • Fruits: Avocados; rhubarb; apples; tomatoes; oranges; nectarines; kiwi; grapefruit; cherries; pears; peaches; mangoes; melons; berries; coconut
  • Dairy: Kefir; yogurt (or coconut yogurt for a nondairy option)
  • Grains: Amaranth; buckwheat; millet; gluten-free oats; brown rice; basmati rice; wild rice
  • Fats: Nut and seed butter; beans; flaxseed, sunflower, and olive oils
  • Protein: Organic, free-range, cruelty-free animal proteins; organic free-range eggs; fish
  • Spices: Cinnamon; turmeric

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

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