What is the microbiome diet?

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The microbiome diet was the idea of Dr. Raphael Kellman to encourage beneficial gut bacteria to grow in the digestive tract. Keeping the gut bacteria healthy is essential for human health.
For more research-backed information about the microbiome and how it affects your health, please visit our dedicated hub.
This article looks at how the diet works, what it involves, foods to eat and avoid, and what the research says.
We will also look at the pros and cons of the microbiome diet.
What is the microbiome diet?
Share on PinterestThe microbiome diet focuses on plant-based foods.
The “microbiome” refers to the collection of microorganisms present in a person’s intestines. These microorganisms include bacteria, fungi, and archaea. Having a diverse range of “good” gut flora benefits a person’s health.
However, gut flora can become less diverse and less beneficial for many reasons. The microbiome diet aims to improve the microbiome and overall health, as a result.
Dr. Kellman, who specializes in holistic and functional medicine, developed the microbiome diet. The Kellman Wellness Center website states that looking after the microbiome is important for the following reasons:
• In the right balance, most strains of gut bacteria contribute to human health.
• The microbiome creates short chain fatty acids (SCFAs), which decrease inflammation, boost brain function, and help the immune system.
• Microbes in the gut help regulate a person’s metabolism and mood.
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Diet phases
The microbiome diet has three phases. The first two phases take a total of 7 weeks to complete. The final phase is a long-term maintenance diet.
Phase 1
The first phase of the diet lasts for 3 weeks, and focuses on:
• removing disruptive food, bacteria, pathogens, and toxins
• repairing the gut lining
• replacing stomach acid and pancreatic enzymes
• reinoculating with beneficial bacteria strains
During this phase, Dr. Kellman advises that people avoid the following foods and ingredients:
• gluten
• dairy products, except butter and ghee
• grains
• eggs
• packaged foods
• soy
• fruit juice
• potatoes and corn
• peanuts
• legumes except chickpeas and lentils
• high mercury fish
• deli meat
• artificial sweeteners
• high-fructose corn syrup
• fillers and colors
• trans or hydrogenated fats
• fried foods
Dr. Kellman advises that people focus on plant-based foods that increase microbiome diversity, such as:
• prebiotic foods, such as Jerusalem artichoke, onions, and garlic
• probiotic foods, such as sauerkraut and kimchi
• fruits, such as apples, berries, cherries, grapefruits, kiwi, nectarine, orange, and rhubarb
• healthful fats from fish, avocado, nuts, and seeds
• oils, including flaxseed, sunflower, and olive oil
If a person eats animal proteins, Dr. Kellman recommends focusing on wild fish and grass fed meat.
Phase 2
After phase 1, a person following this diet can start to introduce a wider range of foods over the next 4 weeks, including:
• sheep or goat’s milk dairy and kefir
• organic, free-range eggs
• mangos, melons, peaches, and pears
• gluten-free grains, including amaranth, buckwheat, millet, gluten-free oats, quinoa, brown, basmati, and wild rice
• beans, including, green, black, red, white, and kidney beans
• sweet potatoes and yams
Phase 3
The final phase of the microbiome diet aims to maintain the results of phases 1 and 2. Dr. Kellman advises that people continue avoiding foods that damage gut flora and the gut lining.
Supplements
In addition to dietary changes, the microbiome diet recommends the following supplements during phase 1:
• Antimicrobials: These include berberine, caprylic acid, garlic, grapefruit seed extract, and oregano oil to kill pathogens.
• Acids and enzymes: Supplements containing digestive enzymes, such as protease, lipase, and amylase, to help break down proteins, fats, and carbohydrates in food. The diet also recommends taking apple cider vinegar to stimulate stomach acid production.
• Gut lining supplements: These can include zinc, vitamin D, glutamine, marshmallow, quercetin, and slippery elm, among others, to benefit the intestinal lining.
• Probiotics: These should be products with 50–200 billion bacteria with strains such as Lactobacillus acidophilus, Rhamnosus, Plantarum, bifidobacteria, and Acidophilus reuteri.
Dr. Kellman also recommends that people following the diet:
• use a good quality water filter
• eat organic foods to limit exposure to pesticides and hormones
• switch to natural versions of household and personal products
• avoid the overuse of antibiotics
• avoid nonsteroidal anti-inflammatory drugs, such as ibuprofen
• avoid proton pump inhibitors, which reduce stomach acid production
What the research says
No studies have proven explicitly that the microbiome diet works to improve a person’s microbiome or that it can treat health conditions.
However, the idea that diet can benefit the microbiome and that this, in turn, can benefit human health, does have evidence to support it.
As the microbiome plays a role in immunity and inflammation, a healthy microbiome may reduce the risk of diseases, such asTrusted Source:
• inflammatory bowel disease
• type 2 diabetes
• cardiovascular disease
• cancer
The food a person eats can positively impact the microbiome in the gut.
A 2013 studyTrusted Source showed that dietary changes could rapidly affect the abundance of specific species of bacteria in people’s digestive tracts. As such, switching to a different diet will change the microbiome.
A reviewTrusted Source in 2019 noted, more specifically, that a plant-based diet may promote a healthy diversity of gut flora. As the microbiome diet contains many plant foods, it may have similar benefits.
Another key element of the microbiome diet is probiotics. Research into the potential benefits of probiotics is ongoing. A 2017 reviewTrusted Source found evidence they could help with:
• obesity and insulin resistance
• irritable bowel syndrome (IBS)
• other gastrointestinal conditions
However, scientists are still trying to understand how specific foods and bacterial species affect the microbiome.
A 2019 study found that similar foods could affect people’s gut flora in very different ways, depending on the individual. This suggests that how a diet influences the microbiome is also individualized.
As geneticsTrusted Source have an impact on how changes to the microbiome affect human health, people may need a more personalized approach to nutrition than the microbiome diet. This is especially true if a person has any underlying health conditions.
Overall, scientists need to carry out more research on the ways that specific food choices and probiotic strains impact the microbiome.
Pros and cons
Evidence suggests that a healthy and diverse microbiome is beneficial to human health. The microbiome diet could support this by encouraging people to eat plant-based foods.
Plant-based diets can also benefit people who are overweight to reach a healthier weightTrusted Source.
Some people may notice the benefits of the microbiome diet from its focus on vegetables, fruits, healthful fats, and lean proteins.
However, others may experiences side effects from the restrictions and supplements the microbiome diet recommends. For example, some people experience bloating and gas with a sudden increase in fiber, and when taking probiotics.
These effects typically resolve over time as the body gets used to a higher fiber intake. Probiotic treatment, on the other hand, should be individualized as not everyone benefits from the same strains.
Additionally, it may not be necessary for a person to take antimicrobials and other supplements. Many of the herbal supplements the microbiome diet recommends do not have high quality research to support their use, and they may be expensive and unnecessary.
A person should always consult a doctor before using supplements, particularly if they are pregnant, breastfeeding, take medication, or have a chronic health condition.
It is also a good idea to talk to a dietitian before following a restrictive diet to ensure a person gets the nutrients they need.
If someone is experiencing digestive issues, such as nausea, reflux, bloating, and diarrhea, it is important to consult a doctor for advice before starting a new diet. These symptoms can be a sign of an underlying medical condition that may need immediate attention.
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