Intestinal Microbiome Function & Protection Strategies in Lyme Disease Treatment

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Updated: 1/31/23

Intestinal Microbiome Considerations in Lyme Treatment

The exponential growth in research on the activity and significance of the intestinal microbiome indicates the important role the bacteria, viruses, yeast, and parasites living in our intestines play in health. This is especially true in chronic illnesses like Lyme disease and tick-related infections.

When considering using antimicrobials to treat Lyme and related infections, one must weigh risks and benefits. One risk of harm is to the gut microbiome. However, for most people the benefit of using antimicrobials is a return to a quality life that makes this risk worthwhile.

In this article, I describe the role of the microbiome. I also layout strategies to protect the gut microbiome using

  • herbal antibiotics rather than prescription antibiotics, when possible,
  • diet,
  • exercise, and
  • probiotics.

Marty Ross MD Discusses Intestinal Microbiome Health 

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Bricks and Mortar of The Intestinal Microbiome

Gomaa(1) makes the following points:

  • “The intestinal microbiota consists of more than 1500 species, distributed in more than 50 different phyla.”
  • “As a result of their abundance in the digestive tract, bacterial species make up to 60% of the feces dry mass. Fungi, protists, archaea, and viruses are also present in the gut flora; however, less is known about their activities.”

The Institute for Functional Medicine also teaches that 90 percent of the genetic material in human bodies comes from the viruses, bacteria, yeast, and parasites that make up the microbiome.

Key Functions of the Intestinal Microbiome

A well-balanced microbiome

  • supports a healthy immune system,
  • decreases inflammation,
  • protects against intestinal infections,
  • promotes cell growth and proliferation,
  • supports the blood vessels,
  • regulates the hormonal systems,
  • provides brain and nerve signaling,
  • supports and regulates mental health,
  • promotes bone density,
  • provides energy to the body,
  • makes key vitamins and metabolic chemicals,
  • makes neurotransmitters,
  • eliminates toxins,
  • eliminates allergens, and
  • more.

How to Protect the Microbiome in Lyme Disease

Use Herbal or Prescription Antibiotics Only if You Have Symptoms

If someone tests positive for an infection like Lyme, but has no symptoms, I do not recommend herbal or prescription antibiotics. First, the test could be a false positive. Second, even if the test is true, I do not want to disrupt the microbiome and potentially cause more long-term harm down the road.

When Possible, Choose Herbal Over Prescription Antibiotics

In my experience, herbal antibiotics cause less disruption of the gut microbiome. I say this because I rarely see intestinal yeast overgrowth infections when someone is on herbal antibiotics. I see intestinal yeast overgrowth infections much more frequently when someone is using prescription antibiotics. The presence of intestinal yeast overgrowth means the microbiome is out of balance.

Unfortunately, I am not able to find any research that supports the idea that herbal antibiotics are less harmful to the gut microbiome—but clinically they seem to be.

In each of my articles on how to treat Lyme and related infections, I provide herbal antibiotic options with a description of the relative chances the herbs will help compared to prescription options. For more information see the Infection Treatment Plans section on this site.

Emphasize Plant-Based Food

Fiber in plant-based diets supports a healthy microbiome much better than foods found in the SAD (Standard American Diet). Types of diets rich in plant-based foods include Mediterranean style diets and plant-forward paleo type diets. And obviously, vegetarian diets do this, too!

Exercise for Microbiome Health

Athletes tend to have healthier intestinal microbiomes than those who do not exercise regularly. This finding must be interpreted with some consideration that athletes may also tend to eat healthier since they tend to focus on all aspects of health.

I do recommend exercise to my patients, but at a level that does not create flare-ups. In Lyme and tick-related illnesses, this may mean no exercise, a five-minute walk, or even long-distance running if a person can tolerate it.

Use Probiotics During Treatment

Probiotics are shown to protect and maintain microbiome health. There are a variety of probiotics, including:

  • human strains like Lactobacillus acidophilus;
  • spore-forming soil-based strains like Bacteroides; and
  • healthy yeast like Saccharomyces boulardii.

For my patients, I recommend they take human and spore-forming strains together. At times, I also recommend adding Saccharomyces boulardii.

For an extensive article on how to use probiotics during treatment and which products I recommend, see Probiotic Strategies in Lyme Disease Treatment.


The ideas and recommendations on this website and in this article are for informational purposes only. For more information about this, see the site-wide Terms & Conditions.


View Citations

  1. Gomaa EZ. Human gut microbiota/microbiome in health and diseases: A review. Antonie Van Leeuwenhoek. 2020;113(12):2019-2040. doi:10.1007/s10482-020-01474-7 (View)
  2. Lynch SV, Pedersen O. The human intestinal microbiome in health and disease. N Engl J Med. 2016;375(24):2369-2379. doi:10.1056/NEJMra1600266 (View)
  3. Sharon I, Quijada NM, Pasolli E, et al. The core human microbiome: Does it exist and how can we find it? A critical review of the concept. Nutrients. 2022;14(14):2872. doi:10.3390/nu14142872 (View)
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About The Author

Marty Ross, MD is a passionate Lyme disease educator and clinical expert. He helps Lyme sufferers and their physicians see what really works based on his review of the science and extensive real-world experience. Dr. Ross is licensed to practice medicine in Washington State (License: MD00033296) where he has treated thousands of Lyme disease patients in his Seattle practice.

Marty Ross, MD is a graduate of Indiana University School of Medicine and Georgetown University Family Medicine Residency. He is a member of the International Lyme and Associated Disease Society (ILADS) and The Institute for Functional Medicine.

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