Lyme Disease and Leaky Gut: What’s the Connection?

Are you dealing with Lyme disease AND symptoms such as brain fog, joint pain, fatigue, skin irritations, or food sensitivities? Do these symptoms remain persistent, despite having gone through Lyme disease treatment? If you answered “yes” to this question, you may be dealing with leaky gut!

Leaky gut is a condition in which gaps develop between cells that line the intestine, allowing food particles, toxins, and microbes to escape from the gut into the bloodstream.

Once in the bloodstream, these substances trigger an immune response, causing inflammation. The resulting inflammation can provoke many symptoms, including brain fog, joint pain, fatigue, skin irritations such as eczema, and new food sensitivities.

Both Lyme infection itself and Lyme treatment, such as antibiotics, may promote leaky gut, causing inflammatory symptoms. In this article, we’ll discuss the connection between Lyme disease and leaky gut and how to repair leaky gut using nutrition and supplements.

Please note that I am an affiliate for some of the products I’ve linked to in this post. If you click the link here and make a purchase, I may earn a commission at no extra cost to you.

photo of cups of bone broth, which can support recovery from Lyme disease and leaky gut

What is Leaky Gut?

The lining of your intestine contains a layer of cells that are bonded together by various proteins. Think of the cells in the intestinal lining as bricks and the proteins as mortar between the bricks. Normally, the combination of cells and proteins lining the intestine prevents substances from leaking out of the gut into the bloodstream.

However, our modern world is full of factors that interfere with the lining of our guts, causing gaps to develop between intestinal cells.

Once gaps develop between the cells, food particles, toxins, and bacteria can “leak” from the inside of the gut into the bloodstream. In the bloodstream, the immune system recognizes these substances as potential threats, launching an inflammatory attack.

Inflammation provoked by leaky gut can cause a variety of symptoms, including:

  • Brain fog and cognitive dysfunction (1)
  • Anxiety (2)
  • Depression (3)
  • IBS (4)
  • Eczema (5)
  • Acne (6)
  • Food allergies and sensitivities (7, 8)
  • Arthritis and joint pain (9)
  • Fatigue (10)
  • Autoimmunity (11) Lyme disease may also cause autoimmunity; be sure to read my article on this topic!

Note that some of the symptoms of leaky gut overlap with symptoms of Lyme disease; in other words, leaky gut may worsen certain Lyme symptoms! Some of the symptoms of leaky gut are also unique to leaky gut, and may further add to your symptom burden.

Factors that promote leaky gut include:

  • Infections may promote leaky gut by increasing inflammation. Inflammation, in general, is a significant trigger that breaks down the proteins binding our intestinal cells together. While no definitive connection between Lyme disease and leaky gut has been established in the scientific literature, there is a highly plausible connection based on the links between Lyme disease, inflammation, and leaky gut. For example, Lyme disease increases the immune system’s production of inflammatory signaling molecules, such as IL-6, that can subsequently promote leaky gut. (12, 13)
  • Low levels of beneficial gut bacteria, such as Bifidobacteria and Faecalibacterium prausnitzii (14, 15) – Lyme infection and antibiotic treatment may deplete beneficial gut bacteria, increasing the risk of leaky gut
  • Elevated levels of inflammatory gut bacteria, such as Proteobacteria, Yersinia, and Salmonella (16)
  • Exposure to mold and mycotoxins (17)
  • Chronic stress (18) – Lyme disease can be a very stressful illness; prolonged stress related to Lyme disease was predispose you to leaky gut
  • A diet full of processed and refined foods (19)
  • Gluten consumption (20)
  • Antibiotic usage (21) This is very relevant to Lyme disease patients who have been on antibiotics for extended periods of time!
  • Use of non-steroidal anti-inflammatory drugs (NSAIDs), such as ibuprofen. (22)

How is Leaky Gut Diagnosed?

If you ask your typical gastroenterologist to test you for leaky gut, they will most likely tell you that leaky gut doesn’t exist, despite abundant scientific evidence to the contrary. In other words, most gastroenterologists will not be able to help you test for and heal leaky gut.

Even less likely is that your gastroenterologist will understand the crucial connection between Lyme disease and leaky gut.

Fortunately, functional medicine testing can help us figure out whether we’re dealing with leaky gut. For example, the GI MAP stool test includes an optional add-on marker called zonulin. When zonulin is elevated, it indicates leaky gut. I frequently order the GI MAP in my functional nutrition practice.

The Precision Point Diagnostics Advanced Intestinal Barrier Assessment can also be used to test for leaky gut; it is a blood test, rather than a stool test.

Once you’ve tested for leaky gut and determined that it is an issue, you can begin to address the underlying causes of leaky gut using food, supplements, and lifestyle changes.

infographic showing the connection between Lyme disease and leaky gut

How to Repair Leaky Gut Caused by Lyme Disease

Treating Lyme disease is vital for preventing the development of leaky gut and for healing this condition. However, there’s also a lot you can do from a functional medicine perspective to heal your gut and thereby support your Lyme disease recovery.

Address Imbalances in the Gut Microbiome

Since leaky gut is often related to dysbiosis, an imbalance between good and bad bacteria in the gut, treatment should begin by focusing on the gut. If you have already tested positive for leaky gut, chances are you ran a stool test to identify leaky gut. The next step, then, is to address any markers of dysbiosis that appeared on your stool test.

If you suspect leaky gut is an issue but haven’t yet done any gut testing, then I recommend doing a stool test that includes leaky gut markers, such as the GI MAP. In addition, it may be beneficial to test for small intestinal bacterial overgrowth (SIBO), a form of dysbiosis that can cause leaky gut. (23)

I recommend working with an experienced functional medicine provider to test for gut imbalances and put together a personalized protocol to address your unique imbalances and repair leaky gut. Your gut-healing protocol for repairing leaky gut may include probiotics, antimicrobial herbs, and digestive enzyme support.

Manage Stress

Research indicates that stress and depression related to stress can trigger leaky gut. (24) Managing stress in healthy ways is vital for repairing leaky gut and reclaiming your health.

There are many healthy ways to manage stress, including:

  • Meditation
  • Deep breathing
  • Yoga
  • Spending time in nature
  • Exercise
  • Working with a therapist

I recommend selecting 1-2 stress management practices to engage in daily. Schedule these stress management practices into your calendar so that you won’t forget to take this important time for yourself.

Remove Foods That Promote Leaky Gut

Certain foods and ingredients can promote the development of leaky gut in susceptible individuals, including:

  • Gluten (25)
  • Refined carbohydrates, such as flour-based foods and added sugars (26)
  • Industrial seed oils, such as canola, soybean, cottonseed, and safflower oils. These oils are prevalent in processed and packaged foods and in restaurant/takeout food. (27)
  • Emulsifiers, such as polysorbate 80 and carboxymethylcellulose. These are common in processed and packaged foods, including nut milks, creamers, and gluten-free breads and other baked goods. (28)

Avoiding added sugars and refined carbohydrates may also help prevent leaky gut by keeping levels of the intestinal yeast Candida albicans in check .

When Candida albicans overgrows in the intestine, as is common after a round of antibiotic treatment, it can contribute to the development of leaky gut. (29) The GI MAP stool test and an organic acid test (OAT) can be used to identify whether intestinal Candida overgrowth is an issue.

Boost Your Intake of Vitamin A

Vitamin A (comprised of three fat-soluble vitamins – retinol, retinal and retinoic acid) is essential for regulating the lining of the gut. (30) Vitamin A deficiency can promote leaky gut. (31) Vitamin A deficiency is widespread, with at least 43% of American adults not meeting the daily recommended intake of vitamin A. (32)

The best way to replenish vitamin A levels is to consume foods that are rich in vitamin A. Importantly, the form of vitamin A that is necessary for gut health and leaky gut repair is only found in animal foods such as egg yolks, beef liver, and fatty fish including sardines and salmon.

Red, orange, yellow, and green plant foods contain a vitamin A precursor called beta-carotene. While beta-carotene can be converted into true vitamin A inside the body, this conversion process is inefficient and insufficient for raising vitamin A levels in many people.

Therefore, if you’re dealing with leaky gut, it is crucial that you eat foods that contain true vitamin A.

Optimize Your Vitamin D Level

Vitamin D is a fat-soluble vitamin and hormone-like molecule that our bodies can make in response to UVB light exposure from the sun.

Vitamin D deficiency, which is extraordinarily common, promotes leaky gut. (33) On the other hand, optimal vitamin D levels help protect against leaky gut. (34)

For optimal health (including optimal gut health) you should maintain a vitamin D level between 40 and 60 ng/mL. Most people will need to supplement with vitamin D to maintain proper levels of this critical nutrient.

I recommend selecting a vitamin D supplement that also contains vitamin K2; vitamin K2 is another fat-soluble vitamin that supports healthy vitamin D metabolism.

It is crucial to test your vitamin D level at least twice a year to ensure it stays within this range, particularly during the winter months when sun exposure is limited.

Gut issues, including dysbiosis and fat malabsorption, can increase your needs for vitamin D; if you’re supplementing with vitamin D but your blood level isn’t rising, you may need to address gut issues to improve your vitamin D absorption.

Boost Your Zinc Intake

Zinc is a mineral that modifies the proteins that bind our intestinal cells together, helping to prevent leaky gut. (35) In the United States alone, at least 12% of the population is at risk for zinc deficiency. (36)

In my nutrition practice, I’ve found that most of my clients have suboptimal zinc levels, even if they are not frankly deficient in this mineral.

The best dietary sources of zinc are animal foods, including oysters, red meat, poultry, and seafood. Certain plant foods, such as sprouted pumpkin seeds, provide zinc.

However, the form of zinc provided by plant foods isn’t as bioavailable as that provided by animal foods because it’s absorption is inhibited by antinutrients that co-occur in the plant foods, such as phytic acid. (37)

Supplement with Nutraceuticals That Support Leaky Gut Repair

Certain nutrients can help repair the lining of the intestine, including L-glutamine, green tea,


L-glutamine is an amino acid that is an essential fuel for the cells that line the intestine. It also helps maintain the tiny proteins that bind intestinal cells together (the “mortar” between the “bricks” of our intestines). (38)

L-glutamine is rapidly used up by the small intestine, which is the primary site of nutrient absorption in the body, during times of stress.

Prolonged stress (such as the chronic stress many of us with Lyme disease have experienced) necessitates replenishment of L-glutamine through whole foods, such as bone broth and gelatin, and supplements.

Supplemental L-glutamine has been shown to reduce gut inflammation, giving the gut the opportunity to repair itself. (39) By repairing the proteins that bind intestinal cells together, L-glutamine also prevents the leakage of toxins and pathogens from the interior of the gut into the bloodstream. (40)

A supplement that combines L-glutamine with other leaky gut repair ingredients, such as licorice root and arabinogalactan, may be particularly helpful for healing leaky gut. One of my favorite leaky gut repair supplements that I recommend to clients is Leaky Gut Revive.

Green tea

Did you know that green tea can help repair leaky gut? Green tea contains plant compounds called “catechins” that improve the function of the gut lining and reduce gut inflammation. (41)

My preferred brand of green tea is Pique Tea; try their Sun Goddess Matcha or Sencha green teas. Their teas are certified organic, specially processed to optimize their polyphenol contents, and are rigorously screened for harmful heavy metals, pesticide residues, and mycotoxins.

At the very least, buy organic green tea to avoid exposure to pesticide and herbicide residues on conventionally-grown tea leaves.

Licorice Root

Licorice root contains glycyrrhetinic acid (GA), a plant compound that maintains the integrity of the gut lining. (42) Licorice root is also demulcent, meaning it can soothe and coat irritated tissues, such as an inflamed gut lining, offering relief.

Licorice root is often included in leaky gut repair formulas, such as Leaky Gut Revive.

Please note that licorice root can interact with many medications, so it is crucial that you check with your doctor before trying licorice root as a supplement or tea.


Polyphenols are plant compounds found in a variety of vegetables, fruits, nuts, and herbs that increase antioxidant activity in the gut, helping to protect against and repair leaky gut. (43, 44)

Examples of foods rich in polyphenols include:

  • Spices and herbs: Cloves, peppermint, oregano, sage, rosemary
  • Fruits: Blueberries, black currants, plums, cherries, blackberries, black olives, green olives
  • Veggies: Artichokes, red onions, spinach
  • Nuts and seeds: Flaxseed, hazelnuts, pecans, almonds, walnuts
  • Other: Dark chocolate, green tea, black tea, coffee

One of my favorite ways to increase my intake of polyphenol-rich herbs and vegetables is to use Dr. Cowan’s organic vegetable powders in my cooking.

A little bit goes a long way with these concentrated, nutrient-dense veggie powders. Plus, they’re an easy way to increase your total vegetable intake; 1 teaspoon of any powder is equivalent to 1 cup of fresh vegetables. I particularly enjoy the low-oxalate greens and leek powders!

You can check out Dr. Cowan’s Garden vegetable powders here!


Probiotics are live microorganisms, mainly bacteria but also some yeasts, that offer health benefits when consumed. Research shows that certain probiotics, mainly Lactobacillus strains and Akkermansia muciniphila, can help repair leaky gut! (45)

Lactobacillus probiotic strains can be found in both fermented foods, such as sauerkraut and yogurt, and probiotic supplements. Akkermansia can only be supplemented; it is not present in any significant amount in foods.

Pendulum Probiotics sells an Akkermansia probiotic that I often recommend to clients for supporting leaky gut repair. So far, my clients have had good results with it!

Please note that you are only likely to get benefits from specific probiotic strains, such as Akkermansia, if you are actually experiencing low levels of that specific probiotic strain.

Some people with gut inflammation actually have high levels of Akkermansia and are unlikely to experience benefits (and could possibly even feel worse) by supplementing with Akkermansia probiotics.

The best way to figure out what your levels of Akkermansia (and other probiotics) are is to do a functional medicine stool test such as the GI MAP.

The Bottom Line on Lyme Disease and Leaky Gut

Both Lyme infection and the consequences of Lyme disease treatment, including disruptions to the gut microbiome, may cause leaky gut. Leaky gut, in turn, can trigger many symptoms and significantly reduce your quality of life. Healing leaky gut is essential for Lyme disease recovery and for building long-term health.

A comprehensive approach to healing Lyme disease and leaky gut should include:

  1. Addressing imbalances in your gut microbiome
  2. Managing stress
  3. Optimizing your diet
  4. Boost your vitamin A intake
  5. Boost your vitamin D intake
  6. Optimize your zinc intake
  7. Consume foods, herbs, and nutraceuticals that support a healthy and resilient gut lining

By addressing each of these factors, you can “seal and heal” your gut and reclaim your health!

Are you in need of personalized functional healthcare support in your Lyme disease journey? I’d love to work with you one-on-one in my practice! If you’re ready to get started, book your free discovery call to learn more about how I can help!

2 thoughts on “Lyme Disease and Leaky Gut: What’s the Connection?”

  1. Thank you for giving such a clear description of leaking gut, causes and helpful treatment.

    It is a battle to eat well in our faced-paced culture. It really helps to have a clear picture explaining why we need to stay away from certain foods and what we can do to improve leaky gut and it’s debilitating consequences!

    1. Lindsay Christensen, MS, CNS, LDN

      Thank you for your feedback! I’m so glad you found the article helpful. It certainly can feel like an uphill battle trying to eat well in a society where the less health-supportive (and gut-supportive) food options are more readily accessible than whole food-based, nutritious options. I think it is helpful to keep in mind the reasons why we should ideally be avoiding the more processed convenience foods to keep ourselves motivated to stick with more wholesome options!

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