by Stephanie Eckelkamp
Posted 7/21/22

Lyme disease is known to cause a range of neurological, cognitive, and emotional symptoms in certain individuals, manifesting as sleep disorders, brain fog, poor focus, and even mood disorders like depression and anxiety. For some people, these symptoms could result from Lyme-causing borrelia bacteria directly invading and infecting brain cells (around 15% of people have neurological Lyme disease). But in other cases, the Lyme-brain connection may be triggered by disturbances to the gut microbiome — the collection of trillions of microorganisms that live in your intestinal tract.

In recent years, researchers have begun to understand how the gut and brain communicate back and forth via the gut-brain axis — a two-way communication network between the gastrointestinal tract (and its many microorganisms) and the central nervous system. The problem: Lyme disease can trigger significant gastrointestinal dysfunction in some individuals, which may lead to gut microbiome alterations that influence your cognition, attention, and emotions, according to Dr. Bill Rawls, MD, Medical Director of RawlsMD and Vital Plan

The good news: There are things you can do to support the health of your microbiome during Lyme disease recovery, which may ease the burden on your brain.

Below, we’ll break down:

  • How Lyme disease impacts the gut microbiome
  • How these changes to the gut can affect your brain and mental health
  • How to support your gut health during Lyme recovery

How Lyme Disease Impacts the Gut Microbiome

Everything in your body happens as a result of well-coordinated cellular activities. But when borrelia enters the scene, it invades all types of cells (heart, joint, brain, intestinal, etc.) to gain nutrition and resources to survive and multiply. “Lyme disease is an assault on the cells of the body,” says Dr. Rawls, and this assault compromises cellular function, leading to widespread symptoms.

image split in half between borrelia and woman holding stomach in pain

Lyme’s invasion of your cells ends up being a major physiological stressor on the body — and this stress, coupled with the heightened emotional stress that many people with Lyme experience, can be a recipe for gastrointestinal dysfunction. Why, exactly? “When cells are stressed, they release chemical substances that activate nerves, and these nerves send distress signals to the brain saying there’s a crisis on board and that resources should be reallocated toward defense and away from routine activities like digestion,” says Dr. Rawls. “This causes intestinal motility, or the movement of food waste through the intestines, to slow way down.”

Food waste sluggishly moving through the intestines not only sets you up for constipation, but it can result in an overgrowth of pathogenic bacteria in the gut — leading to an imbalanced state called gut dysbiosis. Some Lyme treatments, including antibiotics, can further exacerbate gut dysbiosis by killing off beneficial gut flora and allowing problematic microbes to thrive. This bacterial overgrowth gives rise to a number of problems, one being that it strips away the protective mucosal layer of the intestinal membrane, contributing to a “leaky gut” and allowing bacteria and other harmful pathogens to enter the bloodstream when they shouldn’t.

Additionally, the bacteria in your gut are responsible for producing many of the body’s neurotransmitters, so gut dysbiosis can alter your body’s normal balance of these mood-regulating chemical messengers. Both of these factors can impact your cognitive and emotional health, as you’ll learn shortly.

How Lyme-Induced Gut Problems Impact the Brain

As mentioned above, Lyme disease can contribute to gut dysbiosis, which has been associated with anxiety and depression, sleep disorders, ME/CFS (myalgic encephalomyelitis/chronic fatigue syndrome), and more. But what’s the connection between the gut and these cognitive and emotional issues? Let’s explore some potential mechanisms.

Human intestines, mucous membrane, intestinal villi under a microscope 3D illustration

First, under normal conditions, your intestines are selectively permeable, allowing only certain microscopic substances such as nutrients and neurotransmitters to pass through to the bloodstream, while maintaining a barrier that prevents larger, potentially harmful substances from entering circulation. However, when you have a leaky gut, a steady stream of larger bacteria, bacterial endotoxins such as lipopolysaccharides (LPS), and toxic digestive metabolites break through.

Then, these substances hitch a ride on your red blood cells, which carry them throughout the body, including to the brain, explains Dr. Rawls. However, when your immune system spots these intruders where they don’t belong, it launches an attack and tries to neutralize them by sending in white blood cells, generating the release of chemical messengers called cytokines. Over time, this immune response can contribute to widespread chronic inflammation, including neuroinflammation — and that’s a problem.

Inflammation is a potential contributor to many chronic health conditions; several studies have found an association between markers of inflammation (like C-reactive protein and pro-inflammatory cytokines) and depression, schizophrenia, and bipolar disorder. Research suggests that pro-inflammatory cytokines can change mood and cognition by reducing levels of monoamine neurotransmitters (e.g., serotonin, dopamine, adrenaline, noradrenaline) in the brain. They can also increase the excitatory neurotransmitter glutamate, which can cause anxiety, restlessness, and impaired brain plasticity, which is the ability to create and reorganize neural pathways after new experiences, a primary key to learning.

senior man covering his face with his hands.vintage tone

Studies have also shown that patients with major depressive disorder (MDD) have higher LPS antibody levels (the bacterial endotoxin implicated in leaky gut) — supporting the theory that a leaky gut drives the inflammation that drives depression. Inflammation in the body caused by circulating LPS has also been shown to disrupt the integrity of the blood-brain barrier (BBB) — the network of blood vessels and tissue that protects the brain from harmful substances — which may further compromise cognitive and mental health.

Beyond leaky gut and its downstream consequences, gut dysbiosis can also shift the types of neurotransmitters and other chemical messengers your gut bacteria produce to communicate with each other and your cells. Pathogenic bacteria can tip the scales from favorable, mood-elevating neurotransmitters to ones that activate the fight-or-flight response and cause agitation, says Dr. Rawls.

How to Support Your Gut and Your Brain During Lyme Treatment

So, what can you do while treating Lyme to bolster gut microbiome health and thereby lessen its potentially negative effects on your brain, cognition, and emotional wellbeing? Quite a bit, fortunately. Your best bet is a multi-pronged approach involving stress reduction, healing existing gut damage, and consuming foods and supplements that support intestinal motility and foster the growth of good bacteria while suppressing the bad, says Dr. Rawls.

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1. Eat Foods that Support Motility and Microbial Diversity.

“Eating lots of vegetables and plant foods and cutting back on refined carbohydrates and meat, which can feed bad bacteria, is a good place to start,” says Dr. Rawls. Plant foods, such as vegetables, nuts, seeds, fruits (especially berries), legumes, and whole grains, naturally contain fiber, which helps move food through the digestive tract and feeds and fosters the growth of good gut bacteria.

Be sure to load up on colorful plants, too. Deeply pigmented plant foods, such as purple cabbage, berries, tea, dark chocolate, and herbs and spices, contain beneficial polyphenol compounds known to cultivate the growth of good gut bacteria and suppress the growth of gut pathogens, helping restore gut microbiome balance.

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2. Move Your Body Every Day.

Regular physical activity has been shown to help ease constipation by speeding up intestinal motility — which can help offset the motility issues triggered by Lyme disease and chronic stress. Additionally, research has found that exercise improves the diversity and abundance of certain beneficial bacterial species in the gut microbiome, which could help reverse the gut dysbiosis associated with impaired motility and constipation.

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3. Take Steps to Reduce Stress.

Anything you can do to curb stress in your life may help limit its negative effects on your gut microbiome. Meditation, breathing exercises, walking, limiting caffeine intake, prioritizing sleep, spending time with people (or pets) you love, or performing a hobby you enjoy are some of Dr. Rawls’ favorite strategies for lowering your stress load and supporting mind-body balance.

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4. Consider These Herbs and Supplements.

To heal a Damaged Gut:

Herbs that are considered demulcents, such as slippery elm, can help soothe irritation, rebuild the mucosal layer of your intestinal lining, and keep foreign substances out of the bloodstream, according to Dr. Rawls. Supplements containing slippery elm bark have also been shown to improve bowel movement frequency in people with constipation-predominant irritable bowel syndrome (IBS). The amino acid L-glutamine, which can be found in bone broth and in supplement form, has also been shown to preserve gut barrier function and prevent permeability to toxins.

To Suppress Bacterial Overgrowth:

Berberine is an antimicrobial compound found in the stems, bark, roots, and rhizomes of various herbs — it can be found in isolated supplements or from berberine-containing herbs such as goldenseal and coptis. It’s beneficial for balancing the gut microbiome by suppressing pathogenic bacteria and other harmful microbes.

To Promote Calm and Counter Stress:

Because Lyme disease is a major stressor on the body — both physiologically and emotionally — taking calming herbs is often beneficial. Lemon balm, passionflower, chamomile, and even CBD oil (derived from hemp) can promote calm during the day and help improve sleep at night. Adaptogenic herbs like ashwagandha can help normalize stress hormones like cortisol and improve stress tolerance, says Dr. Rawls.

To Repopulate Your Gut with Good Bacteria:

If antibiotics are a part of your Lyme treatment protocol, you should consider taking a probiotic (that contains both lactobacillus and bifidobacteria species) to help replenish some of the good gut bacteria that gets destroyed. But keep in mind, probiotics won’t do much to support intestinal motility, says Dr. Rawls, so you’ll still want to eat a good diet, get regular physical activity, and implement stress-reducing practices. Fermented foods, which naturally contain fiber and probiotic bacteria, may be a more supportive strategy for long-term gut health.

​​Bottom Line

Lyme disease can be incredibly stressful on your body’s cells — and this stress can slow intestinal motility and lead to gut microbiome imbalances, triggering subsequent processes that negatively influence your cognitive and emotional health. Fortunately, making strategic changes to your diet, lifestyle, and supplement routine during your Lyme treatment and recovery can help support your gut and ease the burden on your brain.

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.


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