by Jenny Lelwica Buttaccio
Posted 2/3/21

Ever experience gastrointestinal (GI) issues like bloating or cramping after you’ve eaten something? Do foods you used to eat regularly suddenly seem to cause problems? If this sounds all too familiar, you may be dealing with hidden food sensitivities, a digestive condition that typically results from damage to the GI tract.

Though anyone can develop food sensitivities, people with chronic Lyme disease are especially prone because they’ve sustained some gut damage throughout the course of their illness and likely even before. Weeks, months, or years of treatment, especially with synthetic antibiotic use, can really do a number on the GI tract, ushering in conditions like leaky gut syndrome that can lead to food sensitivities you might not even be aware of.

Plus, “There’s a connection between food sensitivities and the consumption of processed foods, which constitute far too much of the modern diet,” says Bill Rawls, MD, Medical Director of RawlsMD and Vital Plan. Both synthetic antibiotics and processed foods can alter the GI tract’s terrain, contributing to an overgrowth of abnormal bacteria or candida in the gut, which wreaks havoc on the intestinal lining.

Let’s take a closer look at food sensitivities and some ways to manage them, improve the health of your gut, and help you feel better.

The Differences Between Food Sensitivities, Allergies, and Intolerances

three glass milk bottles, each with a different color overlay

The words sensitivity, intolerance, and allergy are often used interchangeably, but they aren’t the same. Though many of the symptoms may overlap, they usually arise from a variety of different circumstances. Knowing the disparities can help you track down the chief offenders that might be halting your recovery from Lyme disease.

Food Sensitivities

People with sensitivities have a negative reaction after eating certain foods, food additives, ingredients, or drinks. While the primary symptoms typically occur in the gut, systemic symptoms like fatigue, brain fog, and muscle pain may also develop, says Dr. Rawls.

Symptoms from food sensitivities are typically delayed hours or even days after exposure to the offending foods, so they may sneak up on you without much warning. Food sensitivities often fly under the radar and can be an overlooked contributor to your Lyme disease symptoms.

Food Intolerance

People who experience food intolerances tend to notice if certain foods don’t agree with them. These individuals don’t have the necessary enzymes to digest certain components in the food, so the foods they eat might bother them within a matter of a couple of minutes or a few hours.

Probably the most well-known example of this is lactose, a natural sugar found in dairy products. Lactose intolerance is where an individual has a diminished production of the enzyme lactase, resulting in a host of uncomfortable GI symptoms, including stomach pain, bloating, diarrhea, gas, and nausea. Some people can take an enzyme replacement supplement to improve digestion, while others may need to avoid the food altogether to minimize discomfort.

Food Allergies

Food allergies illicit the most severe and obvious reactions in people. Food allergies occur when the immune system misjudges a food ingredient as a foreign, harmful substance and produces an immune response to defend against it.

Food allergies come on almost immediately after exposure, producing symptoms such as hives, rashes, and swelling. The immune response can also trigger life-threatening, anaphylactic reactions in some people. Unlike food sensitivities, food allergies often take center stage due to the body’s rapid response to the offending food.

Ultimately, because food sensitivities are more covert than intolerances and allergies, they can cause a range of distressing symptoms, which warrants closer examination to help you overcome obstacles that may stand in the way of your healing.

Symptoms of Food Sensitivities

Close up unhappy hopeless mature woman with closed eyes thinking about health or emotional problems alone, lonely older female suffering from headache or migraine, touching head, health trouble

The symptoms of food sensitivities are closely intertwined with Lyme disease symptoms, which can make for a confusing scenario to figure out. However, it’s important to know which symptoms are tied to food sensitivities so that you can make appropriate decisions about removing certain foods from your diet.

Common food sensitivity symptoms include:

  • General: flu-like, inflammation, fatigue, malaise
  • Digestive: gas, bloating, diarrhea, cramping, nausea, stomach pain
  • Musculoskeletal: muscle aches, joint pain
  • Nervous System: headaches, migraines, brain fog
  • Respiratory: nasal congestion
  • Skin: acne, eczema

Common Food Offenders

Notable examples of typical foods associated with sensitivities are wheat (though this is not the same as the autoimmune condition called celiac disease) and dairy products. Although processed food consumption and medications are major irritants that can harm gut integrity, individuals who already have inflammatory conditions such as mast cell activation syndrome (MCAS), fibromyalgia, or ME/CFS (myalgic encephalomyelitis/chronic fatigue syndrome) may be more at risk of developing food sensitivities.

The list of foods that are likely to cause the most problems for people, according to Dr. Rawls, includes:

  • Gluten: Gluten is a plant protein, and it’s present in wheat, rye, barley, and pre-packaged foods that either contain those ingredients or are made in facilities that process those ingredients (in other words, cross-contamination is common). It can irritate the lining of the gut, causing inflammation.
  • Soy: Though an ingredient in many foods, soy is an extremely common allergen. If you’re looking at an ingredient list, soy might be listed by other names: edamame, soybean oil, soy lecithin, and soy protein are some of the aliases you might see mentioned.
  • Lectin: Found in grains, beans, legumes, tree nuts, and nightshade vegetables, lectins are a type of plant protein that can act as an irritant to the gut. They bind to molecules in the cell membranes, which can lead to inflammation and leaky gut syndrome.
  • Mycotoxins: Mycotoxins or mold toxins naturally occur in the environment, but they’re also found in foods like peanuts, processed meats, mushrooms, and most dairy products. When ingested, mycotoxins can induce a host of systemic symptoms like fatigue, brain fog, digestive issues, and pain.

Diagnosing Food Sensitivities

From home test kits and hair mineral analysis to IgG antibody food testing, there’s no shortage of food sensitivity testing on the market. And while the testing may be useful for spotting some of your most problematic foods, it’s certainly not without its limitations.

Immunologist Doing Skin Prick Allergy Test on a Woman’s Arm

Many of the available tests lack well-supported scientific information about their validity and accuracy, suggests an article in The Journal of Allergy and Clinical Immunology. Typically, the tests can’t tell you how much food is required to elicit a reaction. “The degree of reaction is dependent on the amount of exposure,” says Dr. Rawls. “In other words, if you eat a limited amount of an offending food, you’ll probably have a very limited reaction.”

Plus, many patients venture into the world of highly restrictive diets that may not be helpful, sustainable, or cost-effective, and that could put them at risk of developing nutrient deficiencies. So, how can you find out whether or not particular foods might be causing you to feel lousy? A food journal and an elimination diet are two places to start.

tan journal with pen on top. pink background.

#1 Keep a Food Journal.

A food journal involves chronicling what you eat over a period of time; two or three weeks should do the trick. Keep track of the following:

  • The times you eat
  • Each food you consume, including the brand names of the products
  • Oils used to cook
  • Beverages you drink
  • Noticeable adverse reactions
  • The times the adverse reactions occurred

When reviewing your food intake, sometimes a likely suspect will jump out at you. You may be able to avoid that particular food and begin to feel better.

But other times, your food sensitivities may not be so clear cut, and you may need to bring this detailed information to a healthcare provider or a nutritionist who can help identify problematic foods and create a manageable, feasible diet for you to follow. Integrative physicians or nutritionists who specialize in gut health, Lyme disease, or other chronic illnesses may be the best choice to find appropriate help.

empty white dinner plate with silverware to the side. blue background.

#2 Follow an Elimination Diet.

Elimination diets have been used by medical, health, wellness, and dietary professionals for decades to help identify hidden sources of food sensitivities. They require a longer commitment to complete than a food journal — usually five to six weeks.

Foods that are most likely to cause problems or foods you’ve identified as questionable when doing the food journal are removed from your diet. Then, they are reintroduced one at a time as you track your progress, looking for improvements or worsening symptoms. Here’s what a basic food elimination diet might look like:

  • Nix the foods you believe may be creating issues for you, such as the foods mentioned above, for two to three weeks.
  • Note if you experience a reduction in symptoms during this timeframe.
  • Next, reintroduce foods one at a time back into your diet. Wait two to three days between each reintroduction to allow time for any reaction and avoid confusion about which food triggered it.
  • Track the return of any symptoms. If no symptoms return, that food can be brought back into the rotation, and you can move on to the next one.
  • If symptoms return or intensify, you’ll know that food is an issue for you, and you’ll need to eliminate it from your diet for a while and allow your digestive symptom time to reset and heal.
  • Repeat the process with the next food.

If this seems too overwhelming to undertake on your own, a healthcare professional or a nutritionist can help you through the process of weeding out the foods that are causing distress, which will allow inflammation to recede and the gut to heal. Depending on your symptoms, other types of elimination diets (FODMAP, histamine, etc.) may be more suitable for you.

A word of caution: Elimination diets are meant to be used as a short-term tool. Long-term use may increase your risk of developing nutritional deficiencies.

Herbal Therapy Support

three wooden spoons on wooden background. Each spoon holding different colored herbal supplements.

In addition to avoiding or minimizing the offending foods, herbal therapy may be a beneficial way to repair the integrity of the gut. “Herbs and other natural supplements are a simple and effective means to restore gut health,” says Dr. Rawls. “Our bodies recognize and know how to utilize the beneficial plant compounds called phytochemicals to our benefit.”

Dr. Rawls suggests the following herbs to improve gut health:

  • Antimicrobial Herbs: Herbs capable of suppressing the overgrowth of harmful microbes that contribute to gut dysfunction should be the basis of any natural gut restoration protocol. Herbs with the power to rebalance your gut flora include: berberine, andrographis, Japanese knotweed, cat’s claw, and garlic.
  • Mucilage-Containing Herbs: If your gut mucosa has been compromised and you’re experiencing gut discomfort, Dr. Rawls’ preferred herb that contains mucilage is slippery elm bark. The herb creates a protective film in the gut, eases irritation in the mucosal lining, and stops foreign substances from entering the bloodstream.
  • Chlorella: A potent detoxifier, chlorella is a chlorophyll- and nutrient-rich freshwater green algae. It binds to organic-type toxins (herbicides, pesticides, mycotoxins), heavy metals, and plastics in the gut for more efficient waste removal.
  • Digestive Enzymes: A lack of digestive enzyme production may contribute to poor digestion and food sensitivities. Using digestive enzyme supplements can help bridge the gap while you’re restoring your gut health. Enzymes are especially important for breaking down the carbohydrates that feed harmful bacteria. Take an assortment of enzymes (such as protease, amylase, alpha-galactosidase, lipase, and others) for maximum benefit.
  • Bitter Herbs: Herbs like burdock, dandelion, gentian root, fennel seed, and ginger are bitter herbs that activate bitter receptors throughout our GI tract. This releases the saliva, enzymes, and bile we need to break down our food more so they don’t sit in the gut and cause trouble.

The Bottom Line

By keeping tabs on your diet, tracking symptoms, eating nutrient-dense foods, cutting back on your consumption of processed foods, and using herbal therapy to support gut health, you can do a lot to get food sensitivities under control and your digestive system back on track. Soon, you’ll be able to recognize which foods fuel and nourish your body and which ones leave you feeling miserable and drained. Managing food sensitivities can be an integral part of your Lyme disease recovery or jumpstart healing if you’ve hit a treatment plateau.

Dr. Rawls is a physician who overcame Lyme disease through natural herbal therapy. You can learn more about Lyme disease in Dr. Rawls’ new best selling book, Unlocking Lyme.
You can also learn about Dr. Rawls’ personal journey in overcoming Lyme disease and fibromyalgia in his popular blog post, My Chronic Lyme Journey.


1. Food Problems: Is It Allergy or Intolerance? Cleveland Clinic website.
2. Kraneveld AD, Sagar S, Garssen J, Folkerts G. The two faces of mast cells in food allergy and allergic asthma: The possible concept of Yin Yang. Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease. 2012; 1822(1):93-99. doi: 10.1016/j.bbadis.2011.06.013
3. Kelso JM. Unproven Diagnostic Tests for Adverse Reactions to Foods. J Allergy Clin Immunol Pract. 2018 Mar-Apr;6(2):362-365. doi: 10.1016/j.jaip.2017.08.021
4. Lactose Intolerance. National Institute of Diabetes and Digestive and Kidney Diseases website.