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Dealing with autoimmune diseases and digestive problems

Gut shield

Autoimmune diseases and digestive related problems (Crohn’s disease, Celiac disease, ulcerative colitis, IBD, IBS, lupus, rheumatoid arthritis, interstitial cystitis, multiple sclerosis) can be very debilitating and can take over your whole life. We think that eating a Paleo diet has the potential to cure a good part of those conditions that are quite new to us. However, for those dealing with problems like that, it might take more time and dedication to be successful and finally heal, but this dedication will pay off at least a thousand-fold.

Even though some more perseverance is involved on your part, we think that you’ll agree with us that if you’re dealing with any of those problems, you’d be willing to go through anything to regain your health and stamina.

I myself have been dealing with intestinal flora imbalances and leaky gut for a good while now and I’ve been able to learn lots of things about how to deal with it properly. For me, it has mostly been a journey of trial and error.

It’s funny because I almost discovered Paleo this way. My digestive system became so fragile that the only things I could stomach where meats, fats and well-cooked vegetables. I was then easily able to come to the conclusion that the foods that we digest the most easily are meat, fat and cooked vegetables and that focusing on those foods is a good idea for anybody.

Dealing with leaky gut

Leaky gut is a condition where your intestines become permeable and larger particles are able to enter the bloodstream. Our body then sees that those particles are foreign and attacks them while attacking regular healthy cells at the same time and compromising the immune system. This leaky gut situation also causes digestive and intestinal problems. Candida overgrowth, Celiac disease, irritable bowel syndrome (IBS), inflammable bowel disease (IBS), allergies, malabsorption and loads of other autoimmune diseases are all associated with a leaky gut.

I think that dealing with leaky gut is the way to also deal with the other problems that are linked to it. Heal your gut and the rest will follow.

Some of the worst offenders that contribute to the development of a leaky gut in the first place are gluten and grains in general, NSAIDs (non-steroidal anti-inflammatory drugs: Advil, Motrin, ibuprofen), dairy products and plain general inflammation, chronic stress and lack of sleep. Never consume grains, dairy, vegetable oils, legumes, sugar, yeast or NSAIDs when trying to heal your gut.

Upset StomachAlso try to limit the amount of fruit you eat. Ideally, you’d want to eat no fruits at all. It feeds Candida and if you have a leaky gut, you automatically have Candida problems. Don’t worry, you don’t really need fruits in your diet and vegetables as your only source of carbs will do just fine. If you want to take things even further, maybe try staying just out of ketosis, which means about 60g of carbs per day or more. You’ll see that it doesn’t take many vegetables to reach that 60g. Make sure your vegetables are well-cooked and soft. It makes them much easier to digest. Eat lots of leafy green vegetables. Your body needs the precious nutrients in them.

Here are other foods that we would recommend eliminating from your diet until you’re 100% healed:

Nuts and seeds

We personally believe that most people would do better without them. They can be somewhat gut irritating and contain small amounts of antinutrients. Our personal opinion on nuts is that they’re not supposed to be eaten frequently or in huge quantities. We also read about a lot of people feeling better without them.


This sounds like the name of an underground street fighting group, but it’s really the name of a family of vegetables. Nightshades are a family that includes vegetables that are quite new to human consumption and that contain chemicals that are irritating. Night shades include bell peppers, hot peppers, tomatoes, eggplants and potatoes. Eliminate them when dealing with an autoimmune problem.


Most living organisms develop ways to protect themselves from being eaten. Animals, for instance, can run or attack, but eggs have to find another way to protect themselves from foreign intruders. Egg whites contain anti-bacterial compounds and have the property to bind to biotin and some other nutrients. Some people will argue that they’re fine when cooked, but my experience tells me otherwise. Of course, if you decide to only have the yolks, you can do so without restrictions, yolks are perfectly fine.

But yolks are full of cholesterol and fat, you might say. Your body needs both of those. Cholesterol is a  crucial hormone and if you don’t get it in food, your body produces some by itself. It’s a high carb diet that leads to high levels of the wrong type of cholesterol.

Sticking to the diet

Let me reiterate that it’s really important that you stick to this more strict version of the diet 100% because only one little intruder will tend to mess everything.

Also make sure to get the most sleep you can possibly get and reduce the stress in your life. If you exercise, do it lightly.

If you find the diet to be too restrictive to be followed for any period of time, have a look at any Paleo food list and you’ll see that you still have plenty of choices when it comes to meat, fats and vegetables. You can enjoy delicious salads, soups, stews, stir-fries, curries and whatever your imagination can think off.

A good thing to integrate in big quantities is fresh homemade bone stock. Use it in soups and stews. Preparing stock will extract gelatin, collagen and glucosamine from the bones, which are all greatly needed by a healing gut. It will also keep you very well hydrated.

A word on supplements

The main thing you’ll want to do is introduce good bacteria (lots of them), reduce inflammation and make sure not to become deficient in any nutrient.

Probiotic sauerkrautWhen it comes to probiotics, the subject is a bit tricky. We found that most of them won’t do any good if your problem is advanced. The good bacteria, no matter what quantity you take, will either die in your stomach because of the acid or it will be too weak to form colonies in your intestines against the other opportunistic bacteria and yeast. The only thing that we have found that works for severe cases are soil based organisms, which are spore forming and will easily resist much harder environments.

You’ll probably hear a lot of hype around prebiotics, a type of indigestible fiber that’s supposed to feed the good bacteria, but we found that if your flora is disturbed enough, bad bacteria will start to feed on it.

To reduce inflammation and soothe your whole digestive system, try taking a DGL supplement with either Slippery Elm or marshmallow extract You can also incorporate a glutamine supplement, which is really food to rebuild the intestinal wall.

Finally, we would recommend you take in 4,000 IU of Vitamin D3 every day and a good fish oil. The only mineral that we would consider supplementing is magnesium, because most people are already deficient in magnesium and food sources of it are limited. Halibut is a great source of magnesium if you can have it fresh in season.

In summary, I’m sure that anyone still dealing with autoimmune challenges and digestive problems even when following a 100% Paleo diet will finally find great relief by following this protocol. Also stay reassured that by following a Paleo diet in the first place you’re already doing 90% of the work for a perfectly healthy version of you and those little tweaks will finally get you there.

Photo of Ashley Noël

Hi I’m Ashley, I’m an ADAPT Certified Functional Health Coach

Get coaching around:

  • transitioning to a Paleo diet
  • reaching your fitness goals
  • getting through those hurdles
    • limiting sugar, gluten, carbs
    • eating out
  • overall life satisfaction

I can’t wait to help you make lasting lifestyle changes