The Microbiome Diet: How and Why to Follow It

The microbiome diet was developed by Dr. Raphael Kellman, a functional medicine physician who specializes in gut health. It's a way of eating that supports a balanced gut microbiome, promoting good gut bacteria and reducing bad ones. It's based on the understanding that a healthy gut microbiome supports overall health and wellbeing. (If you're not sure whether your gut needs the extra support, take our free gut health assessment.) According to Kellman, "as much as 90% of the cells in your body are actually bacteria, not human." Supporting the correct balance of these bacteria is essential for gut health, as well as the health of the immune system (1). Kellman says, "The microbiome diet is the key to safe, sustainable weight loss and a lifetime of good health" (2). Is it too good to be true? Maybe not. Here's everything you need to know about the microbiome diet and whether it's right for you.

What Is the Microbiome Diet and How Do You Follow It?

fresh fruit and a smoothie
The microbiome diet has three phases: The four Rs (remove, repair, replace, reinoculate), the metabolic boost, and the lifetime tune-up.

The First Phase: The Four Rs

The first phase lasts three weeks. This phase is strict, and some people may find adhering to the strict food plan difficult. During this phase, you eliminate foods that feed harmful bacteria and toxins in the gut. You focus on healing prebiotics and probiotics and replacing stomach acid and pancreatic enzymes. This all helps to repair the gut wall. This first phase revolves around the four Rs (1):
  • Remove foods that promote bad gut microbes, pathogens, and toxins. This includes refined carbohydrates, fat, sugar, processed foods, fillers, and artificial coloring.
  • Repair the gut wall by switching to an organic plant-based diet.
  • Replace stomach acid, digestive enzymes, and healthy bacteria by eating foods that increase stomach acid and digestive enzymes, such as apple cider vinegar, fermented veggies, ginger, and spices like cardamom and coriander.
  • Reinoculate your gut microbiome with good bacteria by eating prebiotics and probiotics — known as "microbiome superfoods."
According to Kellerman, you should avoid the following foods for three weeks: packaged foods, gluten, soy, fillers and colors, high-fructose corn syrup, artificial sweeteners, trans fats and hydrogenated fats, potato, corn, deli meat, peanuts, fried foods, high-mercury fish, fruit juice, eggs, grains, dairy (except butter and ghee), and legumes (except chickpeas and lentils)" (1). During this time, follow an organic diet that is mainly plant-based. If you want to eat animal protein, you should find organic, free-range, and cruelty-free options. Focus on increasing your intake of prebiotic foods, like asparagus, garlic, Jerusalem artichoke, jicama, onion, leek, and radish (1). You also want to up your intake of probiotic foods to flood your gut with good bacteria. You can do this by adding in fermented foods like fermented vegetables, kimchi, sauerkraut, and kefir and yogurt made from sheep or goat's milk. Kombucha is a fermented drink you can also enjoy. Eat fruits like apples, berries, cherries, coconut, grapefruit, kiwi, nectarines, oranges, and rhubarb. Get healthy fats from approved animal protein sources — organic, free-range, and cruelty-free — as well as from nuts, seeds, avocado, fish, flaxseed oil, sunflower oil, and olive oil (1). By following the four Rs, you've started to repopulate your gut microbiota with healthy bacteria. By the end of the three weeks, your intestinal health should have improved, allowing you to reintroduce some foods in the second phase.

The Second Phase: The Metabolic Boost

The second phase of the microbiome diet lasts four weeks. This phase is not quite as strict as the first one. You are still avoiding most of the foods listed above but can add the following back into your diet (1):
  • Dairy products
  • Free-range eggs (preferably organic)
  • Fruits and vegetables like mangoes, melons, peaches, pears, sweet potatoes, and yams
  • Gluten-free grains
  • Legumes
By the end of phase two, Kellman says you've likely restored your intestinal health and fully healed the microbiome (1). Phase three is all about maintaining this healthy state.

The Third Phase: The Lifetime Tune-Up

As you may have guessed by the name, phase three lasts your lifetime. It's not so much a strict diet, as it is a way of eating that can be maintained long term. According to Dr. Kellman, "A good rule of thumb is to always try to avoid the damaging foods, listen to your body, and follow your inner guide as to what foods work or don't work for you." (1).

Does the Microbiome Diet Actually Work?

bowls of brown rice and vegetables
Science backs up the notion that diet can impact gut health, in turn promoting overall health or jeopardizing it. It all depends on the state of your gut microbiome. Studies show that many health conditions are associated with changes to the gut microbiota, including "inflammatory bowel disease (IBD), colon cancer, and metabolic syndrome" (3). One reason for this correlation may be inflammation. In a literature review, researchers discovered that gut microbiotas from individuals with metabolic syndrome had fewer species of bacteria than those of healthy individuals (3). In other words, they were less diverse. Researchers also found "high levels of proteobacteria, LPS, and flagellin" in the microbiome of unhealthy individuals, which are all believed to promote inflammation (3). Conversely, the gut microbiotas from healthy individuals had greater species diversity, lower levels of proteobacteria, and higher levels of Bacteroidetes and Bifidobacteria, which may play a key role in metabolism (3). Now you understand how the composition of the gut microbiome can influence overall health. But can diet truly influence the balance of the gut microbiome? Science says it can. In the literature review mentioned above, researchers discovered that "switching from a vegan to an omnivorous diet results in rapid, modest but significant changes in microbiota composition" (3). The specific changes to the microbiome were not detailed. When researchers made mice eat a high-fat diet as opposed to their typical food, their gut microbiota changed quickly, and proteobacteria levels increased — remember, those are the guys that cause inflammation (3). The microbiome diet also promotes the consumption of prebiotics and probiotics, both of which support gut health. Prebiotics stimulate the growth of the beneficial bacteria that make up your gut microflora, serving as food for probiotics. Prebiotic compounds also help balance the harmful bacteria and toxins living in the digestive tract. Research has found that increased intake of foods high in prebiotics can help increase numerous types of beneficial bacteria in the gut, including Lactobacillus rhamnosus GG, L. reuteri, bifidobacteria, and certain strains of L. casei or the L. acidophilus-group (4).

Who Should Follow the Microbiome Diet?

Smiling woman smells a flower
Many different factors can affect your microbiome. When you throw off the balance of good and bad bacteria, you may experience gut dysbiosis. The microbiome diet can restore the balance, promoting gut health and overall wellbeing. Here are some signs you're suffering from gut dysbiosis and may benefit from the microbiome diet:
  • You've taken antibiotics recently.
  • You're experiencing chronic stress.
  • You feel constipated, bloated, or gassy.
  • You have bad breath.
  • You have food allergies or sensitivities.
  • You're feeling depressed or anxious.
  • Your joints are sore.
  • You eat a Standard American Diet that's high in processed foods, refined sugar, gluten, and dairy products.
  • You have a chronic degenerative disease such as inflammatory bowel disease, irritable bowel syndrome (IBS), celiac disease, allergies, asthma, metabolic syndrome, cardiovascular disease, or obesity.
This list is not exhaustive. If you're struggling with gastrointestinal issues, always consult your healthcare provider. We recommend talking to your doctor or nutritionist before starting the microbiome diet.

Support Your Gut Health With the Microbiome Diet

Smiling woman during golden hour
The microbiome diet is a science-backed method to lose weight and promote overall health by rebalancing gut microbiota. The diet involves the elimination of foods that promote "bad" bacteria like refined carbohydrates, fat, sugar, processed foods, coloring, and fillers. Then you increase foods that promote "good bacteria" such as prebiotics, probiotics, and healthy fats. Some people may find this diet too restrictive and hard to adhere to. You're required to eliminate many foods for a short time before reintroducing some foods. Then you'll need to maintain this way of eating over your lifetime. But this healthy lifestyle change can have a lot of benefits. If you're ready to restore your gut health, sign up for our email list and receive exclusive health tips we don't share with the public. As a friendly reminder, we're not doctors and this information does not constitute medical advice. Always consult your healthcare provider before starting a new diet.

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