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Heal Your Gut Microbiome With the GAPS Diet

River Yeo was a nursing student when she first recognized red flags in her health including joint pain, constant exhaustion, brain fog, skin irritation, and headaches.

She eliminated gluten from her diet with modest results. Still seeking answers, she came across Dr. Natasha Campbell-McBride’s book “Gut and Psychology Syndrome.” Called the GAPS diet, it’s a strict protocol for those who are serious about healing their guts.

Yeo was compelled to try GAPS because of the science-based explanations offered in the book. Though the protocol itself hasn’t been heavily researched, it relies on findings in the field of microbiology—the study of microorganisms such as bacteria, viruses, and fungi. Yeo was curious about the diet’s ability to reverse dysbiosis—an imbalance of the gut microbiome.

“Even just two weeks into it, I felt a world of difference,” she said. “It flipped my world upside down completely. It’s not just about digestion but the community of microbes in your gut.”

Cultivating the Microbiome

The microbiome, a relatively new frontier in health, refers to any collective of microbes that reside in an area of the body. We have skin, nasal, lung, oral, and other microbiomes. The community living in our gastrointestinal tract—the gut microbiome—is the largest of these collectives. It plays an essential role in digestion, metabolism, immune function, and vitamin synthesis, as well as neurotransmitter production along the gut-brain axis.

The GAPS protocol is an elimination diet that begins by mostly deriving nutrition from bone broth to build back the integrity of the intestinal epithelium—the cells that line the inside of the intestines. As tolerated, more whole foods are added to the diet and the gut is gradually fed prebiotics and probiotics to restore balance to the microbiome. Meat stock, soups, meats and organ meats, eggs, animal fats, seafood, and fermented foods are the staples.

Campbell-McBride’s first book, “Gut and Psychology Syndrome” published in 2004, focused on the brain, including autism, attention-deficit/hyperactivity disorder, schizophrenia, dyslexia, depression, and other neuropsychological or psychiatric problems. In 2020, a second book, that completes the GAP concept—“Gut and Physiology Syndrome”—includes all autoimmune conditions, including celiac disease, chronic fatigue syndrome and fibromyalgia, arthritis, multiple sclerosis, type 1 diabetes, asthma, allergies, and other chronic diseases and infections.

Most people with severe gut issues or other diseased states—including children—can expect to spend 18 months to two years on the plan. It’s recommended that anyone interested begin with the full GAPS diet—described as being similar to the Specific Carbohydrate Diet, ketogenic, paleo, and primal nutritional protocols. Deeper healing may require the GAPS Introduction Diet, which eliminates far more foods and gradually reintroduces them to get to the full GAPS diet.

“It’s the best diet you can be on to restore gut health hands down, but it’s slow. It takes time,” Dr. Armen Nikogosian told The Epoch Times. Nikogosian is board certified in internal medicine and a member of the Institute of Functional Medicine and the Medical Academy of Pediatric Special Needs. He is a  functional medicine provider who specializes in gut issues, immune dysfunction, toxicity, and children and adults with autism. Nikogosian said the children who go on GAPS in his practice typically end up having a growth spurt.

“Dysbiosis seems to be increasing. The younger the generation, the more dysbiosis we see,” Nikogosian said. “The food is different today. A whole lot of our food is genetically modified … what that translates to is food with a whole lot more pesticide.”

How the GAPS Diet Works

The GAPS diet is a six-step plan aimed at the slow and steady work of repairing and rebuilding damaged intestinal lining that plays a role in autoimmune, digestive, and neurological conditions.

The protocol is based on traditional diets found all over the world. Today it is used to calm inflammation by removing food triggers, supporting detoxification, and offering clean nourishment in stages tolerated by the body with home-cooked foods from fresh ingredients. Its main purpose is to correct a compromised intestinal epithelial barrier, called “leaky gut,” that allows bacteria and toxins to migrate out of the gut and into the body, crossing into the bloodstream, and contributing to disease. Research has linked many autoimmune diseases to dysbiosis.

Campbell-McBride, neurologist and nutritionist, first developed the GAPS concept while dealing with autism in her family. Her books have been translated into 26 languages, and she trains practitioners across the world to implement the diet correctly with their patients. The GAPS Science Foundation was also formed to raise money for scientific studies to be conducted and published in peer-reviewed journals.

Many people who try to correct dysbiosis after reading generic advice may feel worse and give up. Campbell-McBride told The Epoch Times that’s because making rapid changes isn’t well tolerated by the body. For instance, adding too much fiber can upset the system. Fiber is a prebiotic food for good bacteria or probiotics. Unlike well-meaning blanket recommendations, GAPS is strategically designed to undo gut damage while educating and empowering patients.

“You have to introduce these sorts of things gradually,” Campbell-McBride said. “You have to be careful with fermented vegetables, especially for someone who hasn’t had them before.”

Who GAPS Works For

GAPS can be an eating approach for anyone, and Yeo said understanding the concepts behind it and incorporating even some elements of it is better than eating the standard American diet.

“Just pulling out processed foods and cooking from scratch, which is much cheaper, makes a huge difference for people,” said Yeo, who has worked as a GAPS coach. “I’m more of an all-or-nothing person, so I just dove in completely.”

Those suffering from food allergies and sensitivities may already have leaky gut. Others with digestive distress may not realize they are reacting to foods until they eliminate them for a period. Yeo suspected dysbiosis because she had to take Benadryl every time she ate cheese, and all dairy made her feel sluggish.

While food like grains and potatoes are not generally recommended on the full GAPS diet, dairy is permitted—eventually—but raw milk is preferred. The protocol is more than a list of foods you can and cannot eat. It emphasizes growing or buying foods that are organic and sustainable, prepared traditionally and sometimes with special equipment, and eaten mindfully.

“There’s a whole community of people who are moving out in the middle of nowhere to be homesteaders for this reason,” Yeo said.

Nikogosian agreed that the protocol is more challenging in metropolitan areas where direct access to farms is rare. “A lot of times patients get hung up on some of the details of it,” he said. “You have to be a little patient with it.”

Some people, Yeo said, even go on GAPS retreats where someone does the cooking for the initial phases of the diet. Others have changed employment or housing due to stress and toxins that contribute to gut damage.

“It’s astronomically more expensive to pay the pharmacy than your farmer in the end,” she said.

Often those drawn to GAPS are people who have run out of options—parents of children with severe health problems who are told there’s nothing that can be done, and people with chronic diseases pronounced: “incurable.” Campbell-McBride said her patients have shown her what is possible.

“There is not one illness that doesn’t respond to this protocol because every chronic illness begins in the gut,” Campbell-McBride said. “The human body is a microbial community—there are far more microbes in you than human cells. Food is the number one medicine for us because food is the most powerful influence on any microbial community in nature.”

Even cancer responds to the GAPS Diet. Certified GAPS practitioner Meme Grant healed her husband from melanoma as described in her book “How We Beat Cancer the Natural Way.”

“Everybody improves to a certain degree. It depends on how much effort someone is prepared to put into their health,” Campbell-McBride said. “There are miracles happening every day.”

The Nuts and Bolts of GAPS

Much of the protocol can be found online, but working with a practitioner or coach can help with customization and accountability. The GAPS books offer full explanations.

The GAPS diet is about 85 percent meat (including organ meat), fish, broth, eggs, vegetables, and fermented dairy if tolerated. Baked goods using nut and seed flours and fruit are allowed in moderation. There are books, tips, recipes, and protocols for dairy intolerant, keto diet, vegan, and others.

The recommended food list is generous, but the restricted food list is much longer. Among some of the suggestions for adopting the full GAPS diet are:

  • Avoid all grains, sugar, potatoes, parsnips, yams, and sweet potatoes.
  • The best foods to eat are eggs, meats, stock, fish, shellfish, fresh vegetables and fruits, nuts, seeds, garlic, and olive oil.
  • Avoid smoked, canned, and processed meats.
  • Fish and shellfish should be fresh or frozen from wild-caught sources.
  • Each meal should have vegetables—which are more alkaline—and meats or fish, which accumulate as acids in the body, to balance pH.
  • Cook with animal fats, coconut oil, or ghee.
  • Plant oils should be cold pressed and organic and consumed raw.
  • Baked goods and fruit should be limited to snacks between meals.
  • Avoid all processed and packaged foods and all artificial ingredients and preservatives.
  • Do not microwave food.

The introduction diet starts with homemade meat or fish stock, which quickly helps regrow cells in the gut lining and has a soothing effect on inflammation. Very small amounts of probiotic foods are introduced gradually in the soups. In stage two, raw organic egg yolks are added, along with stews, casseroles, more probiotic food, and ghee.

Various foods are added to each stage until you reach the sixth stage where apples and other fruits and baked goods can be incorporated. Reactions and digestion are carefully monitored through each stage before moving on.

Preparation Is Key

The biggest hurdle with using GAPS is rarely the foods themselves, but rather the mindset and lack of preparation before starting the protocol.

Jennifer Scribner loves to help her clients in this space. A functional nutritional therapy practitioner certified in GAPS, she’s written the book “From Mac and Cheese to Veggies, Please” and a specialized GAPS journal.

“I would rather have people spend more time making their plan, doing their preparation, and then know they’re ready,” she said. Journaling helps them understand how they are feeling as they record eating and symptoms and even bowel movements. They review it every 30 days and look for patterns like frequent headaches or skin issues. They also record detox baths and how they are feeling afterward.

“They start paying attention because they see these clues or patterns,” she said. “Then when they can’t do it all, they can really double down on the things that are helpful.”

She challenges her clients to think ahead about how they’ll handle the classroom for their children, restaurants for the whole family, social functions, moments of weakness, and how they’ll know whether the protocol is working.

“Don’t just show up and see what happens mentally … for a lot of us that’s how we got sick because we didn’t state our preferences,” Scribner said.

Instead of feeling like their eating habits are bothersome, her clients flip the script and feel empowered to take their food when they need to, make decisions on where to eat out so they can opt for farm-to-table restaurants, and say yes to meeting with friends even if they only order herbal tea.

“A lot of us want to justify our own choices by having them validated by others,” Scribner said. “You have to have your own reasons even if other people don’t understand it.”

Making GAPS Realistic

While medication may offer relief for a lot of these diseases, it only masks symptoms without addressing the underlying root issues. The GAPS protocol is not a quick fix, which is why Scribner said it probably remains on the fringes even after two decades.

In his clinic, Nikogosian speeds up the process by prescribing large doses of herbs, using coconut extracts, colostrum, and putting patients on commercially available probiotics and prebiotics.

“GAPS is one of the modalities we use to heal the gut. In the end, it will probably do the job, but it just takes longer,” he said. “We are doing it from more angles, and it complements what we do very nicely.”

He also pointed out, as GAPS practitioners did, that food isn’t the only reason for dysbiosis. It’s simply the main reason. Other things to consider are toxic products used on the body and in the home, being overworked, stress, and lack of sleep.

Yeo also recommends going barefoot outside, getting plenty of sunlight, and spending time in nature. Besides healing her gut, she said the GAPS diet reversed eight cavities that were found just before starting the protocol.

“I eat all kinds of things now that I couldn’t eat before, and I feel fantastic. I think that’s really important,” she said.

Campbell-McBride added: “I know there’s a big choice in diets out there. GAPS is different because it’s out of the mainstream. It was developed out of love, for love. It works.”

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