The human body is made up of many systems, all working together to keep us healthy. If one system falls out of balance, it can disrupt the others, and our health will start to fail.

To bring back health, we must try to identify what knocked it out of balance in the first place. For many, the initial trigger is an infectious disease and recovery begins by treating the infection(s). But as many Lyme disease patients know, the return to health isn’t always that simple.

In 2020, the world was shaken by the deadly COVID pandemic which impacted nearly every aspect of our lives. As time went on, it became clear that some people had lingering chronic symptoms following their COVID infection, often referred to as long COVID.

While speaking to many patients with chronic Lyme who had then contracted long COVID, I began hearing a common theme: COVID made their gut symptoms worse. Many reported increased diarrhea, constipation, and food sensitivities. Several described a sudden difficulty swallowing, saying pills would get stuck in their throat. That’s something my daughter had complained of after getting COVID in 2023.

The gut: your immune system’s hub

About 70% of your immune system resides in your gut. If the gut is inflamed or out of balance, the immune system may overreact or fail to function properly.

There is increasing evidence that COVID can disrupt the gut microbiome, reducing beneficial bacteria and increasing harmful pathogens.

As I’ve discussed before, the gut is the largest organ connected to the vagus nerve, making it very important for sending and receiving signals in the body. The bacteria in the gut (both good and bad) communicate with the brain through something called the gut-brain axis, with the vagus nerve serving a key role.

A healthy gut lining and blood-brain barrier keep out harmful substances. However, when the gut bacteria are out of balance, it can trigger inflammation that irritates the vagus nerve. It can also weaken the blood-brain barrier, leading to an increase in neurological and psychological symptoms.

This inflammation also weakens the gut barrier, which can lead to a “leaky gut” allowing food and bacteria to enter the bloodstream. All of this can trigger mast cell activation or increase symptoms in those who already have MCAS.

A healthy gut helps absorb vitamins and minerals that your body needs to repair and stay strong. An unhealthy gut can lead to an imbalance (dysbiosis) in the bacteria and other microbes that live in your gut. Dysbiosis can lead to SIBO (small intestinal bacterial overgrowth) and malnutrition.

What helped my daughter heal

While everyone’s experiences differ, here are some things that have worked for my daughter.

1. Stool Testing. There are many options for stool testing to help healthcare practitioners access what may be out of balance in the gut. We went with “GI Effects” by Genova Diagnostics because it adds a broad overview of inflammatory markers while using PCR and stool culture for evaluating the microbiome, acidity, digestive enzymes and more. It also screens for 24 types of bacteria and over 30 parasites. The profile scores the stool on digestion, infection, inflammation, insufficiency and imbalance. The results are easy to read, and they provide a comprehensive guide for interpreting the findings as well as suggested therapeutic support options.
2. Balance the Gut. Once you receive the results of your stool testing, you will have a lot of homework to do. Your healthcare provider may need to treat an infection. You will likely need to increase certain probiotics and prebiotics. My daughter has a limited diet due to food sensitivities. The GI Effects test showed she needed to increase specific probiotics and prebiotics—something I’d never heard of. Prebiotics are not living organisms (like probiotics), but instead are special kinds of fiber that feed good bacteria. The easiest organic foods containing prebiotics for my daughter to add were: baked asparagus, baked apples, brown rice, carrots, green peas, sweet potatoes (the white ones), white beans and zucchini. (Click here for a list of prebiotics)
3. Reduce Inflammation. We followed a low-histamine diet and made lifestyle changes to support MCAS. We also removed triggers like mold, heavy metals, processed foods, sugar, and stress (Learn more about MCAS here.)
4. Eliminate Toxic Chemicals. Besides going with all organic foods, my daughter has worked hard to remove as many toxic chemicals as she can. This includes removing scented laundry detergent, scented personal hygiene products and toxic cleaning products. In our search for toxic chemicals I came across a research paper showing that some dishwasher detergents and rinse aids cause gut epithelial barrier damage. The researchers found that the alcohol ethoxylates present in the detergents and rinse aids cause the epithelial inflammation and gut barrier damage. Following this discovery, we did our own search and found the Clean People fragrance free dishwasher detergent does not contain alcohol ethoxylates. (Other brands are also available, but we were already using Clean People laundry detergent.) We’ve also installed a home water filtration system and use air filters to improve our indoor air quality.
5. Reduce Microplastics. Microplastics are tiny pieces of plastic, smaller than 5 millimeters (about the size of a sesame seed or smaller). They come from things like broken-down plastic bottles, food packaging, synthetic clothing fibers, and even some personal care products. Microplastics carry harmful chemicals on their surfaces which can lead to inflammation and weaken the gut lining. In my house, we have removed all plastic cutting boards, only store food in glass containers, and never microwave plastics.
6. Lymphatic Drainage for Detox. Learning what works for you is important. Whole body lymph drainage massage helps reduce inflammation and remove waste products. It also helps stimulate the immune system and allows the movement of basic hormones needed for rest and healing.
7. Vagus Nerve Stimulation. The vagus nerve, the longest cranial nerve in the body, supports every major organ. Stimulating it can promote healing. (See full description of the vagus nerve here). Here are some of my favorite ways to stimulate the vagus nerve.
   • Humming or singing
   • Massage
   • Cranial sacral therapy
   • Osteopathic manipulative therapy
   • TENS (Transcutaneous Electrical Nerve Stimulation)

Other ways to repair the gut

• Meat Stock Because my daughter was having trouble swallowing, we started making soup with homemade meat stock (a low histamine alternative to traditional bone broth.) To make the meat stock we place one whole organic chicken in the pressure cooker (we use an Instant Pot.) Once it’s done, quickly cool it in fridge, then freeze the liquid into 1-cup glass containers for use as needed. (Freezing the meat stock keeps the histamine levels lower than storing in the refrigerator.) Meat stock is rich in protein, glutamine, fat, minerals, proline, glycine, and other amino acids that help create a healthy gut.
• Olive Oil Polyphenols (oleocanthal and hydroxytyrosol), major components of extra virgin olive oil, also reduce the production of the inflammatory cytokines TNF-α, IL-6 and IL-1B. My husband began producing EVOO with a focus on sustainable farming after our daughter developed severe food allergies due to MCAS. Because Marcum EVOO is 100% pure, certified EVOO and extra high in polyphenols, it has added anti-inflammatory and healing properties. NOTE: Be sure to only use certified EVOO before the “best by” date and NEVER buy oil that is stored in plastic as the acidity of EVOO is high enough to break down plastics.
• Peptides Peptides are short chains of amino acids, which are the tiny building blocks that make up proteins. Think of it this way:  Amino acids = single beads.  Peptides = a short necklace made from a few beads.  Proteins = a really long necklace made from hundreds or thousands of beads. The two peptides my daughter uses are BPC-157 and KPV. (BPC-157 helps repair the gut lining and reduce inflammation. KPV is a fragment of a natural hormone that supports immune balance and mast cell regulation.)

While some peptides are considered experimental treatment, my daughter says she almost immediately felt a difference. I am not an expert in gut healing, but I hope these insights will help you start a conversation with your medical provider.

Resources

LymeSci:

Why Lyme disease treatment sometimes doesn’t work

Are you unknowingly ingesting toxic mold?

How to lift brain fog and boost your immune system

Does having Lyme disease increase the risk for severe COVID?

Do long COVID and long Lyme both activate mast cells?

Post-infectious fatigue and your vagus nerve

12 ways you can help yourself manage chronic pain

Low histamine diet

Dr. Bill Rawls:

Natural remedies for the chronic inflammation of Lyme disease

Comparing herbal therapy to antibiotics for chronic Lyme disease

Dr. Richard Horowitz:

Reducing inflammation can head off serious COVID complications

MEDICAL DETECTIVE #1: An overview of Lyme disease signs and symptoms 

LymeSci is written by Lonnie Marcum, a physical therapist and mother of a daughter with Lyme. She served two terms on a subcommittee of the federal Tick-Borne Disease Working Group. Follow her on X: @LonnieRhea   Email her at: lmarcum@lymedisease.org.

References

Bonaz, B., Bazin, T., & Pellissier, S. (2018). The Vagus Nerve at the Interface of the Microbiota-Gut-Brain Axis. Frontiers in neuroscience, 12, 49. https://doi.org/10.3389/fnins.2018.00049

Gareau MG, Barrett KE. (2023) Role of the microbiota-gut-brain axis in postacute COVID syndrome. Am J Physiol Gastrointest Liver Physiol. Vol. 1;324(4):G322-G328. doi: 10.1152/ajpgi.00293.2022. Epub 2023 Mar 7. PMID: 36880667; PMCID: PMC10042594.