How to Treat Gastrointestinal Lyme Disease

Lyme disease isn’t classically associated with gastrointestinal symptoms, at least not in the early stages of infection.

However, many people with Lyme disease report gastrointestinal symptoms, including abdominal pain, bloating, gut paralysis (such as gastroparesis), diarrhea, and constipation. So what’s the connection between Lyme disease and gastrointestinal issues?

In this article, we’ll look at the fascinating connection between Lyme disease and the gut and how to treat gastrointestinal Lyme disease using functional medicine and nutrition strategies.

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.

gastrointestinal Lyme disease

How Does Lyme Disease Affect the Gut?

When we think about Lyme disease, gastrointestinal symptoms are typically not the first thing that comes to mind. However, research shows that gastrointestinal symptoms are actually extraordinarily common in people with Lyme disease!

A study of 314 patients with acute Lyme disease found that a significant number of the patients were experiencing gastrointestinal symptoms. (1) For example:

  • 23% of patients suffered from anorexia, or loss of appetite (this is different from anorexia nervosa, the eating disorder)
  • 17% experienced nausea
  • 10% experienced vomiting
  • 8% had abdominal pain
  • 2% had diarrhea

These are some significant numbers!

Next, let’s discuss a few of the ways in which Lyme disease can affect the gut.

Lyme Disease Challenges the Immune System in the Gut

70-80 percent of your immune system is located in your gastrointestinal tract. (2)

Lyme disease profoundly challenges the immune system, heightening inflammation while also depressing other aspects of immune function; these immune system changes caused by Lyme disease may make the gut inflamed and susceptible to infection. (3)

In some people, Lyme disease may activate mast cells, immune cells that release histamine and other inflammatory substances. (4) The gut is full of mast cells.

Lyme disease-induced activation of these mast cells may trigger gut inflammation and other symptoms of mast cell activation syndrome (MCAS). MCAS can cause bloating, abdominal pain, changes in bowel movements, histamine sensitivity, and other food sensitivities.

If you’re dealing with MCAS, be sure to check out my article “The Definitive Guide to the Mast Cell Activation Syndrome Diet.”

Lyme Disease May Affect the Nerves That Innervate the Gut

Lyme disease affects nerves throughout the body, causing symptoms such as Bells Palsy and neuropathy. It follows that Lyme disease may also affect nerves that innervate the gut, regulating intestinal contractility and motility.

Small intestinal bacterial overgrowth (SIBO) is a condition in which excessive bacteria and other microorganisms grow in the small intestine, which should normally only house a small population of microbes. SIBO symptoms include gas, bloating, diarrhea, chronic constipation, and fatigue.

Scientists and medical professionals agree that impaired gut motility, which is regulated in part by the nerves innervating the gut, is a significant underlying cause of SIBO.

By harming the nerves that regulate gut motility, Lyme disease may predispose people to SIBO. (5) Therefore, treatment for Lyme disease and other tickborne infections may be crucial for helping some people recover from SIBO.

Lyme Disease and Lyme Treatment Alter the Gut Microbiota

Furthermore, both Lyme infection itself and antibiotic treatment can disrupt the gut microbiota, the collection of microorganisms that lives in your gut. Disruptions to the gut microbiota can cause symptoms such as bloating and diarrhea, as well as compromise immune function.

Preliminary research indicates that people with Lyme disease experience distinct changes in their gut microbiota, including “dysbiosis,” an imbalance between beneficial and harmful microorganisms in the gut. (6) These changes may be caused by Lyme infection itself and antibiotic treatment, which is known to throw off the gut microbiota.

In addition, specific pathogens transmitted alongside Borrelia burgdorferi, including bacteria called Bartonella henselae, can trigger gut inflammation and may compound symptoms of gastrointestinal Lyme disease. (7)

Don’t ignore your gut health if you’re dealing with Lyme disease!

Left unaddressed, gut health problems may reduce your immune system’s ability to fight Lyme disease, render you more susceptible to other infections, and cause symptoms that significantly reduce your quality of life. Addressing gut health is crucial for Lyme disease recovery.

Furthermore, the healthier your gut is before and during Lyme treatment, the better you’ll tend to tolerate necessary treatments. ⁠

In other words, addressing gut health is crucial for Lyme disease recovery!⁠

Next, let’s discuss some of the symptoms of gastrointestinal Lyme disease and how to support gut healing as part of your Lyme disease recovery process.

Symptoms of Gastrointestinal Lyme Disease

Gastrointestinal Lyme disease symptoms run the gamut. Here are several of the most common gut-related symptoms of Lyme:

  • Nausea: Chronic nausea and nausea after eating are common in Lyme disease. Nausea may stem from dysfunction of the autonomic nervous system, the branch of the nervous system responsible for controlling involuntary bodily functions, such as the heartbeat and digestive process. Borrelia burgdorferi is known to trigger autonomic nervous system dysfunction. (8) In some individuals with Lyme, nausea may also be accompanied by vomiting.
  • Gut paralysis: Lyme-induced gut paralysis may occur in the stomach, a condition referred to as “gastroparesis.” (9) It may also occur in the small intestine, contributing to small intestinal bacterial overgrowth or SIBO. While the pathogenesis of dysmotility (impairment of the digestive tract muscles) in Lyme disease is not entirely understood, it may stem from nerve inflammation caused by direct invasion of Borrelia burgdorferi into nerve cells.
  • Diarrhea: Diarrhea in Lyme disease may stem from antibiotic treatment or from the infection itself. Interestingly, the incidence of diarrhea is higher in people with vector-borne infections other than Lyme disease, including ehrlichiosis, tick-borne relapsing fever, and Rocky Mountain spotted fever.
  • Constipation: Constipation may stem from Lyme disease gut paralysis or from shifts in the gut microbiota that occur due to antibiotic treatment for the disease.
  • Abdominal pain: Lyme disease is known to cause abdominal pain, possibly through the effects of the infection on the nerves that innervate the gut. Hepatomegaly (enlargement of the liver) and splenomegaly (enlargement of the spleen) can also occur in Lyme disease and cause abdominal pain.
  • Food allergies and food sensitivities: New-onset food allergies and sensitivities are something I routinely see in my clinical nutrition practice amongst my clients with Lyme disease. These allergies and sensitivities may emerge from Lyme-induced immune dysfunction or from gut imbalances triggered by infection and antibiotic treatment. Research indicates that imbalances in the gut can contribute to both food allergies and food sensitivities, indicating that gut healing may be crucial for resolving food reactions. (10, 11)

Clearly, Lyme disease can have a major impact on the gut and on your quality of life! Next, let’s talk about how to treat gastrointestinal Lyme disease using functional medicine and nutrition approaches.

How to Treat Gastrointestinal Lyme Disease

Treating Lyme infection and co-infections is vital for recovering from gastrointestinal Lyme disease. However, gut healing doesn’t end there! Optimizing your diet, addressing Candida overgrowth, and testing for gut imbalances are essential steps to take for healing your gut.

In the infographic below, you can see a preview of my approach to helping clients heal from gastrointestinal Lyme disease:

infographic showing an example approach for how to treat gastrointestinal Lyme disease

Optimize Your Diet

The first step to alleviate gastrointestinal Lyme disease symptoms is to optimize your diet. You can optimize your diet by removing foods that irritate the gut and eating nutritious foods that reduce gut inflammation and support healing.

In my nutrition practice, one way that I help my clients identify foods that may be irritating their guts is by having them complete several days of food tracking in an app called Cronometer before we meet for their initial consultation.

Remove Foods That Irritate the Gut

Foods that irritate and inflame the gut and should be avoided include:

  • Gluten: Gluten is a common trigger for gut inflammation and can play a role in chronic bloating, diarrhea, constipation, abdominal pain, and IBS, among other gastrointestinal symptoms. (12) I have found that many of my clients with Lyme disease feel their best avoiding gluten, especially if they have gut issues.
  • Conventional dairy products: Dairy products contain two proteins, casein, and whey, that resemble gluten. A body that is sensitive to gluten can thus react to dairy products, triggering gut inflammation. I find that many of my clients with Lyme disease do best avoiding conventional industrially-raised dairy products. However, some do well with goat or sheep milk dairy products.
  • Industrial seed oils, including corn, canola, cottonseed, grapeseed, soybean, safflower, and sunflower oils. These oils contain oxidized lipid byproducts that disrupt the gut microbiota and inflame the gut. (13)
  • Refined carbohydrates and added sugars: Refined carbohydrates and added sugars fuel the growth of inflammatory gut bacteria and yeast, which can cause gastrointestinal symptoms such as pain and bloating. (14, 15) Examples of refined carbohydrates include food made with flour, such as bread, pasta, and cereal. Examples of added sugars include cane sugar, brown sugar, high-fructose corn syrup, agave syrup, and glucose syrup.
  • Grains and legumes: Some people with Lyme disease will feel best limiting their intake of grains and legumes. Grains and legumes contain high levels of antinutrients, compounds made by plants to defend themselves against pests and predators. While antinutrients are beneficial for plants, they are (generally speaking) not beneficial for our bodies. When we consume large amounts of antinutrients, these compounds interfere with our ability to absorb essential nutrients, such as calcium and magnesium. Certain antinutrients, such as saponins, may also cause leaky gut. If you are already dealing with gut issues caused by Lyme disease, eating foods rich in antinutrients may further irritate your gut, so you may feel better limiting your grain and legume intake until your gut has healed.

Eat Anti-Inflammatory, Nutrient-Dense Foods That Support Gut Health

A gut-healing diet for Lyme disease should focus on:

  • Animal protein: Examples of high-quality animal proteins to focus on include beef, bison, chicken, turkey, pork, eggs, and wild-caught seafood. Try to emphasize quality as much as possible by purchasing grass-fed, pastured, and organic animal proteins; these types of animal protein tend to be lower in toxins, such as synthetic hormones and antibiotic residues, and richer in nutrients than factory-farmed beef, poultry, and eggs.
  • Non-starchy vegetables: Vegetables provide dietary fiber, vitamins, and minerals that support the gut. Most people are not eating enough vegetables for optimal gut function. I recommend eating at least three servings (approximately 3 cups) of non-starchy vegetables each day. Non-starchy vegetables are vegetables that don’t taste sweet. Examples of non-starchy vegetables include broccoli, cauliflower, kale, brussels sprouts, lettuce, spinach, onion, mushrooms, celery, spaghetti squash, and zucchini.
  • Whole fruits: Examples of fruits to choose from include blueberries, blackberries, raspberries, strawberries, kiwi, avocado, apples, peaches, and citrus fruits. If you’re struggling with Candida overgrowth, you may be better off focusing on low-sugar fruits, particularly berries and avocado.
  • Starchy vegetables: Starchy vegetables are an excellent source of gut-friendly carbohydrates. Examples of starchy vegetables include sweet potato, white potatoes, winter squashes, root vegetables, plantains, and cassava.
  • Healthy fats: Choose healthy fats, such as extra virgin olive oil, avocado oil, ghee, pastured butter, coconut oil, and pastured animal fats such as tallow, lard, and duck fat. Avocado, olives, nuts, and seeds are also healthy fat-containing foods that you should include in your gut-healing diet.

Specific functional foods can provide further support for your gut health when you’re recovering from Lyme disease:

  • Fermented foods: Fermented foods contain probiotics, beneficial bacteria that can support healthy gut function. Examples of fermented foods include sauerkraut, kimchi, beet kvass, water kefir, and coconut yogurt. If you tolerate dairy products, grass-fed organic yogurt and kefir are also excellent sources of probiotics. When purchasing fermented foods, be sure to select them from the refrigerated section, NOT the condiments aisle. Fermented foods with live, active probiotic cultures must be refrigerated to maintain the viability of the probiotics. For example, the sauerkraut in the unrefrigerated condiments aisle is not a fermented product but is cured in vinegar and doesn’t contain live probiotic cultures.
  • Prebiotic foods: Prebiotics are substances that support the growth of beneficial gut bacteria. Examples of prebiotic foods include garlic, onion, leeks, chicory root, dandelion greens, berries, and green tea.
  • Bone broth, collagen, and gelatin: Bone broth, collagen, and gelatin are rich in amino acids that help maintain a healthy gut lining, protecting against leaky gut. (16) You can easily make bone broth at home using whole chicken or beef bones purchased from the meat counter at your local grocery store. You can also supplement with collagen peptides or make gelatin gummies with grass-fed gelatin.

Address Candida Overgrowth

If you’ve ever taken antibiotics for Lyme disease, it’s likely that your doctor either prescribed an antifungal drug, such as Nystatin, or a probiotic at the same time. These items are added to antibiotic protocols to reduce the risk of Candida overgrowth, which is a common occurrence when taking antibiotics.

Candida albicans (referred to as “Candida” for short) is an opportunistic yeast that normally lives at low levels in your gut. However, when you take an antibiotic, the antibiotic knocks down helpful bacteria that normally keep Candida in check.

Reduced levels of beneficial bacteria subsequently allow Candida to proliferate, taking up far more “real estate” in your gut than it normally should. (17)

It is crucial that you take measures to prevent Candida overgrowth, or treat it if you’re already experiencing it, because excess Candida can worsen gut inflammation and hinder healthy immune function. (18, 19)

Candida overgrowth may be obvious; for example, it can cause a white filmy coating to develop on your tongue or cause vaginal yeast infections in women. However, Candida overgrowth can also cause subtler, non-specific symptoms such as bloating, constipation, and food sensitivities.

If you’re experiencing any of the following symptoms, you may be dealing with Candida overgrowth:

  • A white coating on the tongue or in patches elsewhere in the mouth, also known as oral thrush
  • Vaginal yeast infections
  • Low tolerance for dietary carbohydrates, including grains, legumes, fruits, and starchy vegetables
  • Chronic bloating
  • Food sensitivities
  • Skin conditions, such as dry, scaly skin, psoriasis, and fungal toenails
  • Oxalate sensitivity: Oxalates are substances found in various plant foods, including spinach and beets. Interestingly, fungal microorganisms, like Candida, can produce oxalates. Therefore, fungal overgrowth in the gut can increase oxalate levels in the body and potentially trigger reactions to to oxalate-containing foods. If you struggle with oxalate sensitivity, it is important that you test for Candida overgrowth and treat it, if necessary.

So, what can you do if you’re struggling with Candida overgrowth caused by Lyme disease antibiotic treatment? There are several impactful steps you can take:

  1. Reduce your intake of refined carbohydrates and added sugars. Candida loves to eat refined carbohydrates, so consuming lots of refined carbohydrates in the form of grains, foods made with grain-based flours (bread, pasta, cereal, etc.), and added sugars will fuel Candida growth. (20) Limiting your intake of refined carbohydrates is essential for treating Candida overgrowth and restoring a healthier balance to your gut microbiota.
  2. Take Saccharomyces boulardii. Saccharomyces boulardii is a probiotic yeast that can help prevent Candida overgrowth during Lyme disease antibiotic treatment. It prevents Candida from adhering to the gut lining and creating biofilms, which are sticky layers of proteins and sugars that protect Candida from antifungal agents, making it more difficult to treat. (21)
  3. Incorporate antifungal herbs and probiotics. Many herbs and probiotics offer antifungal properties and can help control Candida populations in the gut. For example, the probiotic Lactobacillus acidophilus helps control Candida growth while oregano oil (derived from the culinary herb oregano) has direct antifungal activity against Candida. (22, 23)

Test for Gut Imbalances

For many people, improving their diet can significantly improve gastrointestinal Lyme disease symptoms. However, some people continue to struggle with gut issues despite making dietary changes. In this case, the next step is to pursue gut testing to identify gastrointestinal imbalances.

There are two main types of gut test: Stool tests and small intestinal bacterial overgrowth (SIBO) tests.

Functional medicine stools tests, such as the GI MAP, look at levels of beneficial and harmful microorganisms in the gut, including bacteria, yeast, viruses, and parasites. This type of gut test also assesses markers of gut inflammation, digestion, and leaky gut, providing a truly comprehensive assessment of gut health.

I frequently run functional medicine stool tests, including the GI MAP stool test and SIBO tests, in my nutrition practice.

SIBO tests assess for the presence of small intestinal bacterial overgrowth, an overgrowth of bacteria (and, sometimes, other microbes) in the small intestine.

If you’re experiencing chronic bloating, diarrhea, constipation, gas, abdominal pain, or other gut issues and haven’t found relief through diet alone, I strongly recommend testing for SIBO with the help of a functional medicine practitioner.

Implement a Personalized Protocol to Improve Your Gut Health

Once testing has been used to identify gut imbalances, specific treatments can be incorporated to address your unique gut imbalances. For example, if your stool test shows signs of leaky gut, then you may benefit from supplementing with a leaky gut repair formula, such as Leaky Gut Revive.

If your test shows low levels of beneficial bacteria, then probiotic and prebiotic supplements may be warranted. If there are signs of digestive insufficiency, you may need stomach acid and digestive enzyme support.

If you test positive for SIBO, you’ll need to either go through antimicrobial herbal treatment or antibiotic treatment to clear up the bacterial overgrowth. Rifaximin and Neomycin are two antibiotics often used for SIBO treatment. However, herbal protocols can be equally effective at clearing SIBO. (24)

If you’re dealing with SIBO, you may also need to incorporate herbs and nutrients that support gut motility; proper gut motility is essential for overcoming SIBO and preventing a recurrence. Parasym Plus is one of my favorite supplements for supporting proper gut motility.

I strongly recommend working with a functional health care provider to test your gut and create a gut protocol to address your unique issues, rather than taking the DIY approach. Getting professional help for resolving gut issues tends to be far more efficient, saving you time and money in the long run!

The Bottom Line on How to Treat Gastrointestinal Lyme Disease

Gastrointestinal Lyme disease symptoms such as bloating, diarrhea, and constipation aren’t just a nuisance; these are signs of important underlying changes happening in your gut that could hinder your Lyme disease recovery.

An unhealthy gut can compromise immune function, worsen inflammation, and impair your ability to absorb nutrients, thereby hindering your Lyme recovery and your long-term health. Conversely, taking steps to improve your gut health can alleviate gastrointestinal Lyme disease symptoms and vastly improve your quality of life.

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 “How to Treat Gastrointestinal Lyme Disease”

  1. My daughter had multiple tick diseases from a bite in 2014. She just confided in me that she has many of the symptoms you describe. she was on multiple repeat doses of oral antibiotics over several months. Is a gastroenterologist a good place to start? Do they recognize the correlation and will they check for these problems.

    1. Hi Diane,

      Honestly, most gastroenterologists aren’t familiar with the impact of Lyme disease and other tick-borne infections on the gastrointestinal system. However, if a person is experiencing gastrointestinal symptoms, it’s always wise to get checked out by a gastroenterologist to rule out more serious symptoms before pursuing a functional medicine-oriented treatment.

      In health,
      Lindsay Christensen

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