Autoimmune Protocol Diet ~ To Heal The Gut Biome

The link between the health of the gut biome, and the immune system is central to our overall health. Whether the immune system is over reactive and erratic, as it is with autoimmune disorders, or weak, leaving us prone to colds and various infections, the gut biome is key.

There is no overnight cure, or probiotic in a pill form that you can take for instant results. The process of healing the gut takes months, not a few days of taking supplements, or eating dandelion greens.

Many things can alter or destroy the gut biome. One of the worst offenders is antibiotics, especially the chronic overuse of antibiotics. 

Those who have chronic yeast infections, can be pretty sure something is off kilter with their gut biome. In fact, just like recurrent autoimmune flare ups, recurrent infections of any kind, are indicators of a gut biome disruption. People tend to focus on the specific body part that is affected, such as chronic bladder infections, by taking antibiotics, and drinking cranberry juice. 

The gut biome is not only about the intestine, it is also about the liver, pancreas, gall bladder, and neurochemistry. In fact immune related health problems are systemic, not localized. 

Years ago, my eye doctor told me that as time goes on, I will likely have more systemic autoimmune inflammatory disorders. 

All medication affects the gut biome, just as all the food we ingest affects the health of our gut. There are trillions of bacteria in the gut, most of which contribute to a healthy gut. But there also has to be balance.

Where to begin? It is not a matter of adding one thing, and deleting another. Often we think we are eating a healthy diet, but it may not be as healthy as we think, especially if we are reacting to the proteins in dairy or gluten. For some people, these proteins are not a problem, but for others, there is an inflammatory response.

Having been plagued by an autoimmune eye condition for many years, I have tried a variety of things without much success. When I started researching the AIP diet, it seemed like it might be the answer.

The idea with the AIP diet is that you eliminate entire food groups for a period of six months. After six months, you decide what you are going to reintroduce into your diet, and what you will leave out. That way you can assess the response or physical reaction to each food you add.

I started the AIP diet at the end of January. It took a couple of weeks to eliminate what is on the list. Coffee seemed to be the worst as far as withdrawal, and changing habits. But after a week or two, it was no big deal.

To give a brief outline of what must be eliminated: Gluten and all grains, milk, eggs, and all dairy, all legumes, seeds, and nuts, all nightshade vegetables. Nightshade includes potatoes, eggplant, goji berries, tomatoes, bell peppers, and all spices made from peppers. You are also supposed to avoid processed food, sulphites, additives, and sugar. Alcohol is also to be avoided, which is not a problem because I gave up alcohol more than twenty years ago. 

Like everything else, for some people, alcohol is not a problem in general. But for others, it is best to avoid it all together, especially if there is a genetic predisposition, or a background of early childhood trauma. 

Though it sounds very restrictive, there are still many things you can eat. You can eat most fresh vegetables and fruit. Although regular potatoes are off limits, sweet potatoes and yams are okay. You can also eat most fish, chicken, lean pork, beef, etc.

Another key addition to the diet is to consume a certain amount of fermented foods. This includes olives (check for sulphites), sauerkraut (again, check the label to avoid additives), kombucha, kefir, and many others. If something is made in a vinegar brine, it may not be fermented, so it takes a bit of time to figure out what is actually fermented.

The most radical change is in what you can eat for breakfast. In the past I would eat an egg, sunflower flax toast, coffee, and a few cherry tomatoes. I thought it was a nutritious breakfast. However, once I started the AIP diet, there was not one thing I could keep as part of that breakfast routine.

Nor can you eat oatmeal, or any kind of cooked breakfast cereal, granola, etc. It brings clarity to how much we rely on various grains in our diet. I tend to avoid gluten free processed food, as it is often loaded with sugar, and other additives. 

For breakfast, I started eating sardines or salmon to get the protein. Added to that, is fresh cucumber with chives or herbs, maybe an avocado, a couple tablespoons of sauerkraut, and a few olives.

I now drink a couple ounces of kombucha first thing in the morning, followed by oolong, or another type of loose leaf tea mix. Then I have a cup of Matcha, which is a Japanese powdered green tea.

Matcha is an interesting type of tea, supposedly with many antioxidants, and health benefits. But you have to be mindful that more is not better. I stick to one teaspoon a day. There are many items you can buy, like Matcha tea sets that cost $40-$50 dollars. But you don’t really need most of that.

I did buy a bamboo whisk, but realize now that any small whisk will do. You can drink it out of a bowl if you want, but I drink it out of a wide mug. You can also buy a flat bamboo spoon and strainer. Any small strainer will do, and you can use a teaspoon to flatten out the lumps.

You just place the strainer over the wide mug, add a teaspoon of Matcha, and press it through the strainer. After that you add an ounce or two of hot water and whisk it. Then you add the rest of the hot water.

Some people use a frother to make Matcha latte, but I have not tried the latte yet. It is a fairly mild tasting tea compared to some of the stronger tasting green teas, and if you add honey, you don’t need much, maybe a half a teaspoon.

The evening meal is not as much of a change as the breakfast is, because you can make chicken, fish, pork etc. and any vegetables you want to eat.

As far as results, one of the most notable changes was a reduction in shoulder and hip pain. I thought I had torn the rotator cuff in my left shoulder from lifting things. But it was all inflammations, because within two weeks on the diet, the shoulder pain was much better. Now, I hardly notice it.

It has now been three months, and the positive changes are well worth it. The only things I did not eliminate, are chia seeds, and flax added to smoothies with frozen berries.

After the six month period of time, I think I will reintroduce eggs and legumes. But I am pretty sure I will continue to avoid gluten and dairy.

Overall, I think the diet has many similarities to the Paleo diet, but with a few more restrictions during the six month gut healing phase.

As an additional note, you are also supposed to avoid OTC medications, to include all NSAIDs. In fact, any kind of medication can dramatically alter the gut biome. The only thing I take is a teaspoon of cod liver oil once a day, which is quite revolting because they added a lemon flavour to it, which in my opinion makes it worse. It is a far cry from those little bubble-like gel caps of cod liver oil. Apparently those are not good, because who knows how old they are? Plus cod liver oil is supposed to be refrigerated, and has a shelf life of just three months.

Although it is still to early to tell what the overall effects of this diet will be, I am glad to have discovered a comprehensive guideline to make these changes. I have already noticed some positive results, so it has been well worth it.

Once the gut health has significantly improved, obviously it is important to avoid falling back into old patterns. I love tomatoes, but I think I will continue to avoid them.

Our reactions to foods, and micronutrients is highly individual. Therefore, one person may react to tomatoes, when 80% of people do not.

The entire exercise of healing, and promoting a healthy gut, requires patience, and bodily awareness. I think the changes help increase energy, and better sleep.

Time will tell, as I am only half way through the six month elimination phase. For those with autoimmune disorders, or chronic inflammation – so far, I would recommend this diet. I only wish I had researched, and known about this diet sooner.

It seems like finally there is a solution, or a partial solution, to the complex autoimmune disruption. I feel very fortunate that the autoimmune problems I have experienced, are not totally debilitating.

But I know full well that out of the eighty or more autoimmune disorders adversely affecting the health of millions of people, some of those diseases are extremely debilitating. A few examples – giant cell myocarditis, MS, lupus, type 1 diabetes, and many others…