Food Sensitivities & Autoimmunity: Do Elimination Diets Help? - Enlighten Functional Medicine

Food Sensitivities & Autoimmunity: Do Elimination Diets Help?

Allergies are nothing to sneeze at⸺especially food allergies. Bob eats a peanut; Bob can’t breathe. But, what about food sensitivities? Find out the difference between a food allergy and other food reactions. Plus, discover how an elimination diet may help chronic symptoms and autoimmune diseases, as well.

Food is Medicine or Poison

Food is fuel, information, connection and medicine. Nourishing your body with healing foods could mean fewer symptoms and even halting or reversing the progression of autoimmune disease. However, because we are biologically and epigenetically different, one person’s medicine may be another person’s poison. 

Adverse food reactions hurt you. They may give you headaches, brain fog, joint pain or other unpleasant symptoms. Plus, they contribute to leaky gut and can cause an immune response. Eating foods you are sensitive to contribute to autoimmune diseases.

Some people scratch their heads when their functional medicine doctor asks them to change the foods they eat. “How is this going to help with my Hashimoto’s, my hormones, my IBS?!” They may even stare in disbelief when asked to remove seemingly-healthy foods. 

The truth is, even healthy plants might be a problem for YOU. Take strawberries for an example. Sure, they’re full of folate, vitamin C and phytonutrients. However, if anytime you eat strawberries, you get a headache, there’s a problem. Strawberries may be healthy generally speaking, but not so healthy for you.

Finding out what foods support or hurt your body could be key to your healing journey.

Exactly how do you know if a food is doing more harm than good? First, take a look at some types of negative food responses.

Food Allergies, Food Sensitivities & Food Intolerances

Food allergies:

Food sensitivities and food allergies aren’t the same. The immune system can play a role in both, though. Your immune system keeps you healthy and strong instead of catching the office cold. It sends out armies to attack invaders of bacteria, viruses and other baddies. 

Instead of seeing a glob of peanut butter, it sees an enemy. Attack! Attack! That’s when your skin might get itchy or it could become hard to breathe.  Allergy symptoms are usually immediate, within 15-20 minutes, affecting breathing, digestion or the skin. Usually food allergies involve the production of IgE antibody.

Food sensitivities:

Food sensitivities are a non-allergic, immune response to food. Food sensitivities may be IgG, IgM, IgA and T-cell driven. Sometimes, a blood test can be used to identify these sensitivities. While no food sensitivity test is perfect, Enlighten Functional Medicine often uses a combined IgG, IgA (and IgE) peptide test from Vibrant Wellness. 

Food intolerances:

Food intolerances are non-immunological reactions. They are not driven by antibodies produced against a specific food but instead cause havoc in other ways. A food intolerance is a type of food sensitivity that can result from a lack of an enzyme such as in lactose intolerance or from the body’s inability to properly deal with a component of that particular food. Examples of food intolerances include the inability to handle preservatives or food additives, problems with oxalates, fructose salicylates, histamine responses, non-celiac gluten sensitivity, lactose intolerance and more. 

Symptoms of food sensitivities and food intolerances:

Symptoms of food sensitivities and food intolerances are less severe than allergies. They generally happen within 24 hours, but may take up to 3 days to actually pop up. So that Friday dinner could totally be causing your Monday morning brain fog or headache! 


Types of food reactions. Do elimination diets help? Functional Medicine approach to food sensitivities in Saint Louis.

Food Reactions and Leaky Gut


Food sensitivities can start with your gut. Here, holes in the lining of your intestines cause problems. Now, everyone should have some holes between gut cells. Tight junction cells are suppose to let nutrients into the blood. 

But, the issue is when tight junctions aren’t so tight anymore. More holes in between gut cells lets bigger and bigger things pass through. This is called intestinal permeability or leaky gut.

Think of a fishing net. You need some holes to let the water out. Too big of a hole and your fish plops on out, too!

In the same way, too many holes in your gut is bad. Undigested food particles, viruses and bacteria end up in places they don’t belong! This is bad news for your body. Here, your immune system sends out its armies. Checking for pathogenic invaders is also a key functional diagnostic test your functional medicine provider should be using. Enlighten DNA stool test checks for 31 parasites.

Your unwanted symptoms, and eventually a full blown autoimmune disease, can be the result of this continued food fight. 

After awhile, your body can actually start attacking your own tissues! It’s a complete case of mistaken identity. Through a process called molecular mimicry, your immune system may begin to attack your own body simply because part of the protein structure is of a particular food resembles that of your body. Thyroid attacked? Hello, Hashimoto’s. Joints getting blasted? Here comes rheumatoid arthritis. The list goes on.

Food reactions may or may not involve the immune system. Do elimination diets help? Functional Medicine approach to food sensitivities in Saint Louis.

How bacteria can help with leaky gut

While Mom insisted you wash your hands before dinner, bacteria isn’t always bad. Did you know that you have 3 pounds of bacteria in you? And, it’s completely normal! We have ten times more bacterial cells in us than human cells. 

You see, bacteria has an important job in your gut. It needs to keep the helpful bacteria growing and make sure the disease-promoting bacteria stays away. If your little gut garden is overgrown with bad guys, you are more likely to have big holes in your gut. 

What Can I Do about Food Sensitivities?

So, then what? For a IgE food allergy, you must 100 percent avoid the food all the time. Food allergies usually don’t change. Food sensitivities, on the other hand, have a greater potential to change. 

These are some ways to support your gut when dealing with food sensitivities:

  • Probiotics & fermented foods (like pickles and non-dairy yogurts)
  • Fish & fish oil 
  • Specific nutrients & supplementation
  • Stress-management
  • A food plan to identify food problem foods (a.k.a. elimination diet)

What is an Elimination Diet?

An elimination diet sounds awful, doesn’t it? But really, just think of it as a vacation for your gut and immune system. On vacation you don’t do much work. You may not even makeup your bed! 

It’s the same for your body. Give it the time to have a break from certain foods that are most likely to cause problems. During this food holiday, you’ll be sure to stock up on the things that are relaxing for your gut and immune system: healing foods, stress-management and targeted support to heal up any leaks in your gut.

Benefits of an Elimination Diet

Here are some hallmarks of an eating plan that removes trigger foods:

  • Reduces inflammation
  • Helps identify problem foods (allergies, intolerances & sensitivities)
  • Supports a healthy microbiome
  • Uses phytonutrient-rich foods to help heal the gut
  • Reduces toxic burden by eliminating processed foods, etc.
  • Helps connect the dots between what you eat and how you feel

Elimination Diets Work for More than Just GI Issues

You can have an adverse food reaction that doesn’t involve the classic GI symptoms of constipation, diarrhea or reflux.

Possible symptoms of food sensitivities. Do elimination diets help? Functional Medicine approach to food sensitivities in Saint Louis.

An adverse food reaction may include any of the following, especially if they are chronic symptoms:

  • Asthma
  • Sinus 
  • Depression
  • Mood swings
  • Irritability
  • Joint pain
  • Eczema
  • Low energy

What to Eat and Not Eat on an Elimination Diet?

Okay, so maybe we should say “healing diet” because the word elimination is so harsh. Focus on the good things you can have instead of what you’ll be side-stepping for a bit.

Enjoy these on an elimination diet:

  • Fruits
  • Veggies
  • Protein
  • Healthy Oils
  • Seeds

It may sound like a short list, but really think about the huge variety that each of those includes. So many different colors of fruits and vegetables! Try to eat a rainbow each day.

The biggest food offenders are avoided during an elimination diet—gluten, dairy and soy.

Other foods are often also eliminated for a time to further give the digestive system a break—all grains, legumes, nuts and specific foods that might be a problem based on your personal history.

How To Do an Elimination Diet

An elimination can help identify food sensitivities. Remove potentially problematic foods for at least a month. Systematically, add foods back in and notice any food reactions. Brain fog? Nausea? Headache? Notice it. Record it. Discuss your findings with your functional medicine doctor.

Tips to Make an Elimination Diet Easier

A successful elimination diet takes planning. These tips might help:

  • Read. Look at your food list a few weeks before your start date.
  • Prepare. Give away or eat up any off-plan foods before you begin.
  • Shop. Stock up on foods that are on-plan.
  • Evaluate. Where do you see pitfalls? Where might you be tempted to eat off-plan? What will you eat for breakfast if you favorite food is off-limits for a while? If there are donuts in the breakroom? If you’re invited over for pizza?
  • Support. Functional medicine practitioners are experts at seeing the connection between the foods you eat and your unwanted symptoms. Work one-on-one to get a detailed look at your health history and eating habits. Chart a course for a new health journey together.

Is an Elimination Diet Right for You?

Curious if your nagging symptoms could be food sensitivities? Concerned about autoimmune issues, MTHFR, and how food could play a role in your healing journey? Contact us to setup an appointment. Dr. Emily will take a deep dive into your health history, look at data and get you on your much needed vacation to start healing your body.

Or, get a taste of the good food you can be eating to support your body with Geneius Food Formula. It’s an elimination diet that focuses on superfoods that change how your genes behave. Rewrite your health story. Download a FREE three-day meal plan here.

Free Keto Meal Plan

I Want to Start My Elimination Diet Today!

Super-motivated to make a change now? The Geneius Food Formula has everything you need to start supporting your body with healthy foods. Rather meet with someone one-on-one? We’ll look at your history, your goals and find out if an elimination diet or other support is right for you. Start writing your new health story by making an appointment today. 

About Enlighten Functional Medicine

Known for her successful treatment of mystery illnesses, Dr. Emily Hecker and her team at Enlighten Functional Medicine combine an integrative, functional medicine approach with the appropriate lab testing.

Our unique approach to diagnosing and treating diseases and disorders recognizes that lasting health depends on resolution of the root causes of your disease. Click here to learn more »

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