The spirochete that causes Lyme disease – Borrelia burgdorferi – and the associated tickborne infections such as Bartonella and Babesia can directly affect any organ system in the body, including the gastrointestinal tract. About 80% of the immune system is located around the digestive tract, so digestive health influences the immune response.

Rarely does acute Lyme disease cause gastrointestinal symptoms, but occasionally nausea, vomiting, heartburn, and abdominal pain can occur. More commonly, digestive symptoms such as constipation, gas/bloating, and abdominal discomfort occur in chronic or late-stage Lyme disease. Lyme bacteria can directly infect the gastrointestinal tract causing inflammation that creates digestive symptoms. In turn, digestive issues can cause immune dysregulation increasing susceptibility to chronic infections. Whether digestive problems are a result of Lyme disease or increase the susceptibility to chronic infections, it is essential to address the underlying issues to restore health more quickly and effectively.
Lyme Disease and Leaky Gut Syndrome
Small intestine inflammation – more commonly known as leaky gut syndrome – is a condition where the spaces between the cells that line the small intestine become enlarged. This allows bacteria and food particles to enter the bloodstream triggering the immune system to respond by releasing inflammatory cytokines. The outer layer of bacteria that enters the bloodstream contains a fat and a carbohydrate called lipopolysaccharide (LPS) that the immune system reacts to. Food allergies, alcoholism, stress, infections (including SIBO), toxicants, certain medications, and mast cell activation syndrome (MCAS) are some of the causes of increased intestinal permeability. Paradoxically, leaky gut syndrome also leads to an increase in food allergies since food proteins pass through the inflamed small intestine into the bloodstream creating an antibody response.
Leaky gut syndrome can lead to systemic inflammation which contributes to fatigue, headaches, joint pain, ADHD, and brain fog. Research has demonstrated leaky gut syndrome can contribute to autoimmune conditions. Since many of the symptoms related to Lyme disease are caused by inflammation, successfully treating leaky gut syndrome (if present) is crucial to reducing the systemic inflammatory burden.
Diagnosing intestinal hyperpermeability can be accomplished with a simple blood test. Cyrex Labs has a panel called Array 2 that tests for antibodies against LPS and the proteins between the small intestine cells called zonulin and occludin. Cyrex produced a great video illustrating leaky gut pathophysiology. Zonulin can also be tested in the GI Map stool test. Inflammation in the gut is a dynamic state which can change depending on current exposure such as food allergens, alcohol, bacteria, etc.
The goal of treating leaky gut is first to remove whatever is contributing to gut inflammation. Nutrients such as zinc carnosine and L-glutamine can also help heal the intestinal lining. Oral immunoglobulins help to neutralizes the LPS, which in turn reduces systemic inflammation.
Constipation in Lyme Disease
It is estimated that up to 25% of the world’s population struggles with constipation. Not only is constipation uncomfortable and can affect daily activities, but it can also predispose individuals to develop more severe health issues. What about people who are doing “all the right things” to prevent constipation – drinking plenty of water, eating plenty of fiber, and exercising regularly – but still constipated?
With Lyme disease, people can experience what has been referred to as “Bell’s palsy of the gut.” Just like the facial paralysis that can occur in Lyme disease, the nerves that innervate the intestines can be affected causing a decrease in the muscular wave of contractions that usually move the contents of the intestines downstream. Chronic constipation ensues, and people end up taking magnesium, Dulcolax or other laxative medications for long periods because the underlying cause of their constipation was never addressed. Nerve dysfunction can occur elsewhere in the gastrointestinal tract, including the esophagus, which leads to difficulty swallowing.
When constipation or difficulty swallowing is related to nervous system dysfunction from Lyme disease, treating the infection helps to improve nerve transmission. Prescription and herbal motility medications can also support the function of the migrating motor complex to help normalize bowel function.
Small Intestine Bacterial Overgrowth (SIBO)
Likely the most common gastrointestinal disorder associated with Lyme disease and other tickborne infections is small intestinal bacterial overgrowth (SIBO). It is estimated 60-70% of people with Lyme disease have SIBO. The incidence of SIBO was as high as 81% in one gastrointestinal practice that screened patients for Lyme disease. Research has confirmed that SIBO causes 60-70% of IBS. This is promising because SIBO can be successfully treated leading to the resolution of IBS.
The incidence of SIBO was as high as 81% in one gastrointestinal practice that screened patients for Lyme disease!
In a normal state, the small intestine has very few bacteria. However, in SIBO there is an overgrowth of bacteria in the small intestine causing a host of symptoms. Bacteria can enter the small intestine either orally or can migrate from the large intestine into the small intestine. At the junction between the small and large intestine, the ileocecal valve keeps the contents in the large intestine from entering the small intestine. Ileocecal valve dysfunction allows bacteria to move into the small intestine. Antibiotics and excessive sugar consumption can also cause bacterial overgrowth in the small intestine.
The most common symptoms of SIBO are IBS-like symptoms of gas/bloating, abdominal discomfort, and diarrhea or constipation, or both. In SIBO, excessive bacteria in the small intestine ferment food that is consumed then produce gases leading to these symptoms. Bacteria overgrowth in the small intestine also leads to poor absorption of nutrients, which can contribute to fatigue, low iron, and low vitamin B12. Because SIBO causes inflammation in the small intestine, it can lead to leaky gut syndrome and its associated symptoms.
A lactulose breath test (LBT) measures gas collected from the breath every 20 minutes over 3 hours after consuming lactulose. If there are excessive levels of bacteria in the small intestine from SIBO, the bacteria will digest the lactulose and produce methane and/or hydrogen. A rise of either, or both, gases in the small intestine indicates SIBO.
SIBO is treated with antibiotics or herbal regimens that have proven to be effective against the hydrogen or methane-producing bacteria. Probiotics, special diets, and motility agents are also used in the treatment of SIBO. However, SIBO – especially caused by methane predominant bacteria – can be more difficult to treat in someone with Lyme disease.
Digestive Symptoms Related to Mast Cell Activation Syndrome (MCAS)
Bacterial overgrowth in the small intestine, in conjunction with the inflammation caused by leaky gut, primes the immune system that surrounds the digestive tract. Mast cells are part of the immune system and tend to be located where the “outside world” interfaces with the inside of the body. The skin, lungs and gastrointestinal tract are examples of these locations. When mast cells are triggered by a variety of stimuli, they release histamine and other chemical mediators. In MCAS, mast cells are more prone to releasing their contents leading to a myriad of symptoms. The most common digestive symptoms experienced in MCAS are nausea and heartburn, but abdominal pain, diarrhea, and constipation also be present. MCAS also contributes to systemic symptoms and digestive dysfunction needs to be addressed if it is driving MCAS.
Other Digestive Issues That May Be Associated with Lyme Disease
Other digestive signs that give clues there may be an underlying infection like Lyme disease are candida (yeast) and parasite infections that are difficult to treat. Infection with Borrelia causes immune dysfunction, making it challenging to treat yeast or parasitic infections until Lyme is successfully treated.
The Lyme Disease and Digestive Symptom Connection
Since Lyme disease is a systemic infection, the bacteria can affect any organ or tissue in the body. The bacteria that cause Lyme disease and its associated infections can directly damage the digestive tract and can create immune-mediated inflammation that causes gastrointestinal symptoms or disorders. These digestive symptoms or conditions may occur in isolation, but if systemic symptoms are present or the digestive disorders are challenging to treat, a proper Lyme disease test should be performed. Also, treating these digestive disorders helps improve the outcome in treating Lyme disease.
Great informative information.
Thank you Sharon!
Almost 10-12 years ago I was told by a doctor in London that I had had lime disease. But that was all.No treatment was offered and that was that. However I have suffered many setbacks since then, including fantastic weight loss and mobility problems. Is it too late to do anything about it as it is becoming a real handicap?
Many thanks
David Minett
Hi David,
I am sorry to hear about what you have gone through. I believe it is never too late begin to heal. Find a Lyme-literate physician who can help you identify and treat the causes(s) of your symptoms!
In health,
Todd Maderis, ND
I think I may have MCAS and am waiting on test results as I have many of the symptoms and am completely miserable. I am in my 30’s now but years ago as a teenager I was treated for Lymes. I’ve never had a problem with it since but could dormant Lymes still cause MCAS? Also, I have recurrently had yeast infections. Could I likely have leaky gut and most importantly, could the treatment of leaky gut cure or reduce the MCAS?
Hi Sabrina,
Persistent infections like Lyme disease can contribute to MCAS. It’s hard to say of you have leaky gut, but I strongly recommend getting properly tested. Too often I see patients who are told they have leaky gut but have never been tested. If someone is positive, I like to re-test after a few months of treatment to see if treatment was successful so a patient can stop the treatment. Yes, leaky gut syndrome can contribute to MCAS.
In health,
Todd Maderis, ND
I was diagnosed with lyme disease on 11/23/2020. I have fast heart rate, high blood pressure, arm numbness, burping, brain fog, anxiety, panic attacks. It is a nightmare. Im getting treated for it, 21 days on doxycycline 100 h daily. I think i had lyme disease for a long time because i also have IBS symptoms and acid reflux, recurrent yeast and awful back pain when i lay down on my back for a long time. Does it get better after the antibiotic treatment?
Hi Vianca,
I am sorry to hear about you have been suffering with symptoms for so long. Yes, it does get better after successful treatment. Unfortunately, three weeks of doxycycline is often not effective for chronic Lyme disease. Read the articles I have written about proper testing for all Lyme co-infections and other possible associated conditions such as mold illness. Also, find a Lyme-literate physician to help you. It can be a journey, but it does get better!
In Health,
Todd Maderis, ND