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Understanding Food Intolerance: The Difference Between an Enzyme Deficiency and an Immune Reaction

Intolerance to specific food can show up:

  • In the skin as acne, eczema, or skin rashes.
  • In the respiratory tract as nasal congestion, sneezing, cough, or asthma.
  • In the digestive tract as bloating, cramping, diarrhea, constipation, or mouth ulcers.
  • In your emotions and cognitive function, such as poor memory, brain fog, headache, anxiety, depression, and insomnia.
  • As arthritis.
  • As reoccurring ear infections.

An intolerance to certain foods can show up anywhere in the body. This means that food intolerance can manifest in the most superficial layers, such as in the skin, and it can even show up in deepest layers of the body, like within the joints. 

Also, the effect that food has in the body is not confined to the physical body. Food can also affect the mental and emotional aspects of our body. When we remove the offending food, suddenly our skin clears up, our outlook and energy improve, and we no longer have nagging aches and pains.

Figuring Out Which Foods Affect Us and Why

Food intolerance can cause a number of symptoms, like bloating, cramping, constipation, brain fog, headaches, and anxiety.

Many of us who grew up eating the standard American diet were not taught that what we eat could affect our health. Or, if we were educated about food, it was often through “high fiber, low fat” advertising and food packaging. Unfortunately, it turns out that many children and many adults actually have intolerance to foods common to the American diet, such as dairy and many grains.

Intolerance can develop:

  • After the body has an immune response to a food, which is often related to a protein found in a food.
  • Or, intolerance can arise from a deficiency in digestive enzymes.
Food intolerance can develop if we don’t have the right digestive enzymes.

Digestive enzymes break down large food molecules. This takes place in the mouth, stomach, and throughout the small intestine. When large food molecules are broken down into smaller pieces, these smaller pieces can pass through the lining of the gut and nourish the body. There are three macronutrients present in the foods that we eat:

  • Fat
  • Protein
  • Carbohydrate

For example, dairy contains all three macronutrients: fats, proteins, and carbohydrates. In this case, how do we figure out if we have what is called “lactose intolerance”, or if something else is going on?

  • Lactose intolerance is all about the milk sugar called lactose.
  • The enzyme, lactase, is needed to break down the sugar, lactose.
  • If this enzyme is missing, your body will not be able to take apart lactose.
  • This means your gut will not absorb the sugars in lactose.
  • A little tip: Figuring out food labels can be rough! If you are looking out for sugars, keep in mind that most sugars will end in “–ose.” For example, lactose and sucrose.

When enzymes are not present to break down milk sugar, this sugar molecule moves through the gut until resident gut bacteria feast on these milk sugars. What happens if gut bacteria get to lactose before the right digestive enzymes do? Sugars that are fermented by gut bacteria produce gas, bloating, cramping, and even diarrhea or constipation.

3 Ways to Figure Out If You Are Actually Lactose Intolerant

  1. Drink truly raw dairy. Milk naturally comes equipped with the enzymes needed to digest it. Pasteurization and high heat destroy enzymes. When you drink raw milk, you are also drinking the enzyme lactase that will help with the digestion of milk sugar, lactose.
  2. Supplement with enzymes: If you think that your body does not naturally have the enzyme lactase, try taking this enzyme as a supplement before consuming dairy: Body Ecology Assist Dairy & Protein contains lactase.
  3. Eat fermented dairy:Truly fermented dairy does not have lactose in it, or it has very small amounts. This is because the fermenting culture consumes the sugar lactose as food.
    • Common examples of fermented dairy are yogurt and kefir.
    • Did you know that oftentimes homemade fermented dairy is far stronger than a probiotic supplement? When you have the opportunity, try making your own fermented dairy at home. The Body Ecology Kefir Starter Culture makes it easy.
Sometimes food intolerance can develop very early in life.

Intolerance to certain foods can develop from an immune response mounted against a food. This can happen very early in life.

  • This is because babies are born with a permeable gut lining so that they can fully benefit from all the nutrients found in a mother’s breast milk.
  • Oftentimes, if a baby is fed on formula or doesn’t receive all the immune signals and beneficial bacteria found naturally in breast milk, the baby can develop several food sensitivities and have ongoing issues with certain foods.
When intolerance involves the immune system, the body has record of this intolerance.

The immune system can read most any food as a foreign invader, or what is called an “antigen.” This is especially common when the gut is permeable, and when large food molecules are able to pass through the lining of the gut. Once the immune system has a record of an antigen, it will react every time this antigen is found present in the body.

Often times, this immune response also involves what is called “cross-reactivity.” Cross-reactivity is when the immune system is confused. In cross-reactivity:

  • A food protein may be very similar to another different food.
  • The immune system reacts to this food, even though it is not the original offender.
  • This is common in those with sensitivity to the proteins in gluten.
  • Sometimes those with gluten sensitivity will also be sensitive to milk protein or even coffee!
  • Remember, coffee comes from a bean, and this popular beverage contains a protein that the body commonly reads as gluten.

Until you know that you are cross-reactive, treating gluten sensitivity can be futile. So far only one laboratory, called Cyrex Labs, has fully developed a test to check for gluten cross-reactivity.

When we understand why certain foods irritate our digestion or cause reactions in our skin or respiratory tract, we can figure out which other similar foods we may want to also avoid.

What to Remember Most About This Article:

Food intolerance can cause a number of symptoms like skin rashes, respiratory issues, digestive problems, and even emotional problems. Food intolerance will normally develop after the body has an immune response to food or because of a deficiency in digestive enzymes.

To determine if you have a food intolerance to lactose, a milk sugar, drink raw dairy to aid in digestion. It is also important to supplement with enzymes and eat fermented dairy since it contains lactose in very small amounts.

Food intolerances that involve the immune system can become cross-reactive, causing the body to react similarly to another food. This is a very common issue in those who are gluten sensitive. Understanding why certain foods cause irritation can help us know which foods to avoid to protect our health.


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  • http://bodyecology.com/articles/new-findings-on-insomnia-is-this-at-the-root Food Allergies and Insomnia: Is This at the Root? - All Body Ecology Articles

    […] Understanding Food Intolerance: The Difference Between an Enzyme Deficiency and an Immune Reaction… Understanding Food Intolerance: The Difference Between an Enzyme Deficiency and an Immune Reaction […]

  • Nancy

    I'm wondering what's at the root of food intolerance, and am beginning to suspect an underlying immune system challenge that could be from a chronic dental issue, such as dead tissue in the form of root canal teeth / cavitations, which the body cannot deal with effectively (no blood supply), so all the rest of the body is compromised and food intolerance is one of the ways this shows up. Any thoughts on this?

  • sandy

    I can get raw milk in a regular grocery store( Nugget) located near Sacramento. So it's curious why there's so much problems obtaining it.

  • Connie

    I have tried raw cream and don't have immediate reactions but over time, say 2-3 months, my skin becomes drier and I end up with eczema. Would an ALCAT test show this??

  • ali

    Hi Meg R!!

    I am completely fascinated by your post about discovering that quinoa, kale, cucumber and dill align with the wheats and coffee and can cause similar trouble.....
    I've also been having trouble with these exact foods and would love to ask if you'd be open to emailing with me about your experiences and some questions I have about the ALCAT stuff and healing. I'm trying to get healthy and discover my true intolerances with my doctor and it would be so great to get some more perspective. Thanks so much!! ali

  • http://thedetoxspecialist.com/blog Sandy Halliday

    Very interesting and enlightening info about cross reactivity of the coffee bean and gluten. I think that a lot of people would be better off without it.

    Some people who have been labelled IBS have slow diamine oxidase enzyme activity and are better avoiding high histamine foods or foods that induce histamine.

  • Kristin

    Meg R. I am glad you posted your response. I am in the exact same situation...I have been off gluten and dairy for a while trying to help my crohn's, lupus, and hashimoto's thyroiditis,and done well, but I still have "issues" and days where I feel horrible and no energy, etc... exactly what you said. I do a lot of raw veggies and green smoothies - maybe I am eating things that are still bothering me. I wondered who did the ALCAT test for you (I am not sure what kind of doctor to go to for that). Thank you!!

  • Jennifer

    Raw milk is NOT illegal to buy in most states. But, it may be illegal to sell. Typically, it is not illegal to consume raw milk from a cow owners own cow either. For those who do not own their own cows, consider joing a diary co-op (where the buyer is often considered a co-owner of the co-op).

  • http://www.integral-health-guide.com/what-is-chaga/ Tristan

    What is the best test for checking the permeability of the gut lining?

  • Brenda

    Just a note...raw milk is illegal for purchase in Ohio, and most likely other states as well!!

  • Meg R.

    This is a great summary article of what I have been learning and found to be true. Aside from having clear food allergies since my early teens, I recently had been feeling like I was having some kind of delayed response / food intolerance. I had been feeling quite poorly, no energy, muscle and joint aches. Occasionally I would just itch for no reason. And my digestive tract and bowel were not happy either. It felt on some kind of roller coaster ride, feeling ok one day, and lousy the next. After starting to eliminate some foods- dairy, gluten - I began to feel better, but yet would have my ups and downs. Problem was, I had no way to find out what those foods were. I underwent a blood test, ALCAT, which tests the antigen leukocyte cellular antibodies and found that many of the foods I thought were good for me, I had a severe intolerance. Things like quinoa, kale, cucumber, and dill, align with the wheats, and coffee...to name only a very few. With using the enzymes and eliminating the most severe offenders from my diet, I'm starting to feel like a normal person. ... And, my asthma is gone, no more insane itching, digestive track is much better and my energy level is great. I would have never thought it was what I was eating..

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