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Intestinal Microbiome Function & Protection Strategies in Lyme Disease Treatment
Dr. Marty Ross
Aug. 23, 2022
Intestinal Microbiome Considerations in Lyme Treatment
The exponential growth in research on the activity and importance 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.
As a person considers using antimicrobials to treat Lyme and related infections, they must weigh risks and benefits. There is the risk of harm to the gut microbiome. But 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 RX antibiotics when possible,
- exercise, and
Bricks and Mortar of The Intestinal Microbiome
According to intestinal microbiome expert Gomaa:
- “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 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
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 versus prescription options. For more information see the Infection Treatment Plans chapter 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 that do not exercise regularly. This finding has to be interpreted with some consideration that athletes may also tend to eat healthier as they focus on all aspects of health.
I do recommend exercise to my patients, but at a level that does not flare a person up. In Lyme and tick related illnesses this may mean no exercise is good, or a 5 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.
- 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)
- 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)
- 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. Published 2022 Jul 13. doi:10.3390/nu14142872 (View)