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Lyme disease patients can develop gastrointestinal issues from the prolonged use of antibiotics and the infection itself. 

When patients consider taking long-term antibiotics for persistent Lyme disease, they need to weigh risks and benefits of treatment. Gastrointestinal risks can include the possibility of a C.diff infection, or candida overgrowth, which is a yeast infection that occurs not just in typical places you imagine but also in the gut. A good Lyme Literate Medical Doctor (LLMD) will put a patient on probiotics and a specific diet to mediate these risks, or may decide to go the intravenous route to take pressure off the gut.

Medication is not the only way that the gut can be impacted by Lyme disease; the infection itself can cause gastrointestinal issues. In his book How Can I Get Better? An Action Plan for Treating Resistant Lyme & Chronic Disease, Richard I. Horowitz, MD notes that Lyme and co-infections can cause inflammation leading to issues such as abdominal pain, nausea, gas, bloating, constipation, diarrhea, or reflux disease, with occasional vomiting. He writes, “…a review of gastrointestinal and liver problems associated with tick-borne diseases found that in 5 percent to 23 percent of those with early Lyme borreliosis, patients presented with varied gastrointestinal symptoms, such as nausea, vomiting, abdominal pain, anorexia with loss of appetite, and hepatitis, and some even had symptoms of an enlarged spleen and liver.”[i] And that’s just in early Lyme—in later stages of the disease, spirochetes (Lyme bacteria) can burrow deeper into the gastrointestinal tract, causing more damage. Other tick-borne diseases can also cause their own gastrointestinal issues, often overlapping with Lyme symptoms when the patient is co-infected.

Because every case of tick-borne illness is different, some Lyme patients may not experience any gastrointestinal symptoms. When I was at my sickest with Lyme disease, babesiosis, ehrlichiosis, possible bartonella, and chronic active Epstein-Barr virus, I used to joke, “Well, at least my stomach feels okay.” Because I wasn’t experiencing abdominal pain or vomiting, I figured my stomach was the one part of my body that had gotten off easy.

In fact, many of the symptoms I experienced in other parts of my body, including joint and muscle pain, migraine headaches, fever, and fatigue, were directly related to weakness in my gut caused by disease. Unbeknownst to many people—myself included before I got sick—the gut is a major player in the immune system. Dr. Horowitz writes that the “GI tract houses 80 percent of our immune system and 70 percent of our lymphocytes, making it the first line of defense against infections.” He goes on to explain that “…the gut can hold as many as 100 trillion microbes, referred to as the microbiome.” The bacteria in each person’s unique microbiome “help to supply essential vitamins; fight dangerous pathogens; keep the immune system in balance and modulate autoimmune disease (like MS and rheumatoid arthritis); modulate hormones, appetite, weight, glucose metabolism, and diabetes; modulate cardiovascular risk, neurological and psychiatric diseases (like Parkinson’s and schizophrenia); affect epigenetics, modulate cancer risk and affect inflammatory reactions in the body, including allergies, asthma, Crohn’s disease, and colitis.”i

An imbalanced microbiome can lead to intestinal permeability, commonly called “leaky gut syndrome.” This can allow toxins pass into the gut, causing inflammation and changes in flora; it’s similar to what happens when the blood-brain barrier is compromised. A 2020 study done by researchers at Johns Hopkins University School of Medicine, Northeastern University, and University of California San Diego found that the gut microbiome of post treatment Lyme disease patients was distinctly different than the gut microbiome of healthy subjects.

Whether Lyme patients experience gastrointestinal symptoms or not, their microbiome is impacted by their infection(s), their medications, and their diet. A weakened microbiome means a weakened ability to heal. As Lyme patients, we can help strengthen our microbiome by taking probiotics to replace good bacteria that are killed by antibiotics (some patients also take an anti-fungal medication, which can have anti-spirochetal effects, too), and by sticking to “The Lyme Diet.” Gluten and sugar are particular menaces to the microbiome, and your doctor may also recommend other dietary changes or nutritional supplements to help you maintain gut health. As I’ve come to learn, it is central to overall health!


[i] Horowitz, Richard I., MD. How Can I Get Better? An Action Plan for Treating Resistant Lyme & Chronic Disease. New York: St. Martin’s Griffin, 2017 (327, 328-9).

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Jennifer Crystal


Opinions expressed by contributors are their own. Jennifer Crystal is a writer and educator in Boston. Her work has appeared in local and national publications including Harvard Health Publishing and The Boston Globe. As a GLA columnist for over six years, her work on GLA.org has received mention in publications such as The New Yorker, weatherchannel.com, CQ Researcher, and ProHealth.com. Jennifer is a patient advocate who has dealt with chronic illness, including Lyme and other tick-borne infections. Her memoir, One Tick Stopped the Clock, is forthcoming from Legacy Book Press in September 2024. Ten percent of proceeds from the book will go to Global Lyme Alliance. Contact her via email below.

Email: lymewarriorjennifercrystal@gmail.com