On Wednesday, March 8, Dr. Sunjya Schweig and his wife, Lia Gaertner, together gave a deeply affecting and informative presentation sharing their personal and professional experiences with Lyme disease. The talk was part of the ongoing Distinguished Speaker Series. What follows is a synopsis of some of the highlights.

Lia Gaertner sharing her story with a full room at the speaker series event in Berkeley, CA.

Lia Gaertner, a member of the Bay Area Lyme Foundation Science Committee, and Dr. Schweig, who is on the foundation’s Advisory Board, bring a wealth of professional expertise and knowledge to the table. But their story starts on a personal note, for it was just one month after Dr. Schweig started working in private practice that Lia — after 10 years of battling serious illness, unexplained symptoms, and debilitating physical and mental challenges — was finally diagnosed with Lyme disease. Together, the couple took what they describe wryly as a “rapid descent together down a rabbit hole” – a deep dive into Lyme, trying to learn as much as possible for their survival.

The Case for Functional Medicine

How is functional medicine different than regular “allopathic” medicine? Dr. Schweig explained using an analogy of a tree. In the allopathic model there are specialized medical fields like cardiology, immunology, gastroenterology, pulmonology, etc. These are important disciplines, but ultimately fall on the outer leaves and branches of the tree, working to manage and control the final manifestations of disease and symptoms. The “roots” and “trunk” of the tree are the foundation or what determines patient health outcomes and includes factors like sleep, exercise, nutrition, stress, relationships, community, trauma, micro-organisms, environmental pollutants, genetic predispositions, experiences, attitudes, mental and emotional and spiritual influences, and the strength or vulnerability of the immune system. Functional medicine thus attempts to address all of these factors in an integrative approach to treating disease. This approach gives the practitioner a much broader toolkit,  particularly important when addressing complicated chronic illness such as Lyme disease.

Dr. Sunjya Schweig making his case.

Lyme disease is caused by Borrelia burgdorferi, a type of bacteria known as a spirochete. Another bacteria in the same family is Treponema pallidum, which causes Syphilis. Like Lyme disease, Syphilis has multiple stages: an acute phase, an intermediate phase, and a chronic phase. The symptoms of Syphilis can become more severe over time and include neurological symptoms as well as impacts on many different body systems and organs. Syphilis has long been known as “The Great Masquerader” because the symptoms are similar to so many other diseases and therefore very hard to diagnose. Dr. William Osler (1849-1919), was quoted as saying, “He who knows Syphilis, knows medicine,” in reference to its virulence, evasiveness, and ability to cause so many different problems. Dr. Schweig maintains that Lyme is the Syphilis and ‘Great Masquerader’ of today.” However, Dr. Schweig also explained that the Lyme-causing spirochete may well be significantly more complicated.

Dr. Schweig then spent some time explaining that in a functional medicine model, the goal is to optimize the holistic functioning of the human organism and to take an enlightened approach to patients with chronic illnesses and vector-borne diseases. Doctors focus on all three “eyes” of disease: inflammation, immune response, and, of course, the causative infection itself, especially important for an illness like Lyme that has symptoms across so many different body systems.

Resetting the Baseline

Eradicating the bacteria is extremely important, but that may not be the right first step for most patients. In functional medicine, the initial focus is on controlling the inflammation, decreasing immune dysregulation, and reducing auto-immune activation. Once the body has been “re-set” to a new baseline, doctors can then address the physical impacts of the infection. Once the triggers are removed, the immune system is also often able to re-establish its proper functioning and will be more effective at eradicating the bacteria on its own, allowing for fewer or shorter duration treatment protocols and fewer side effects. (Of course, if a patient presents with a new infection/tick-bite or is acutely ill, doctors will then need to be very aggressive to contain and eradicate the infection.)

Working through the Gut

Part of resetting the baseline involves the gastro-intestinal balance. Over 70% of the human immune system is located in the gut, which makes sense when you think about the amount of information that our immune system has to process in our gastro-intestinal tract every single day just dealing with all the different foods and drink we ingest. Your body is constantly deciding what do I do with this new input? Do I break it down? Do I keep it out? Do I bring it in? A healthy gut is a very, very important interface at the frontline of fighting any kind of infection.

There are lots of things that we can do to promote gut health. Boosting the right kinds of gut bacteria can be achieved by moving away from the typical high fat-high carb-refined sugars Western diet. Western diets often put us at risk for increased inflammation and lowered ability to fight infection when exposed. Also, Western diets tend to cause confusion in the autoimmune responses of the body — signals get crossed and the body cannot work to optimize its primary function which is survival.

The intestinal tract needs to have tight junctions within the gut to “keep the outside world at bay” and fight intruders like bacteria, viruses, mold, fungal infections, yeast infections (Candida), toxins, food allergies, stress, etc. The condition of having a “leaky gut” — a gut that cannot work optimally as an effective barrier – puts our bodies at risk.

Eating fiber, complex starch, vegetables, lean meats, and prebiotics (to feed the good bacteria in our gut through fermentation) promotes tight junctions within the gut and provides an optimal environment for anti-inflammatory response. It also improves mood and hormonal balance and cognitive function so that everything works better. Probiotics (through food sources or through supplements) are also important to boost the immune system, decrease inflammation, and reset the body’s ability to handle a threat like Borrelia burgdoferi or any kind of bacterial infection.


Antibiotics are an important tool in the arsenal that can be deployed to fight infection, and many, many patients respond positively to antibiotics. But of course, functional medicine doctors are just as acutely aware as allopathic doctors about the risks of over prescribing antibiotics and the need to use them judiciously on a case-by-case basis. As a result, they are constantly weighing the pluses and minuses of deploying antibiotics depending where each Lyme patient is in the treatment stage. When antibiotics are used, it is important to also focus aggressively on gut support in order to protect and later rebuild and reestablish a healthy gut flora.

Often, after the initial treatment and the anti-inflammatory diet is adopted, there is a lessening of symptoms. Joint pain improves, headaches subside, the classic “brain fog” described by Lyme patients can lift. It is important to realize that these gains cannot be achieved with antibiotics alone, it comes by working holistically. This response has been noted not just with respect to Lyme patients. There are many chronic diseases where patients have experienced an easing of symptoms by adopting an anti-inflammatory diet including rheumatoid arthritis, Lupus, multiple sclerosis, chronic fatigue syndrome (CFS), fibromyalgia, irritable bowel syndrome (IBS), and Crohn’s Disease.


Ultimately, we are still trying to understand the auto-immune responses of the body. Typically, patients are given drugs to suppress and turn down these auto-immune responses and that can work for a while, but over time, the treatments can cease to be effective. Symptoms re-emerge and side-effects can impact patients negatively – which is not what anyone wants. We also know that if a patient has one auto-immune disease, the chances of getting a second or third is much higher. There is a snowballing effect as the whole system becomes “on fire.”

We are now learning that chronic infections are at the root of many auto-immune disorders and diseases, and there’s a hypothesis that we will look back 30-50 years from now and have a lot more answers about this connection. Lyme disease and its related co-infections are big triggers for auto-immune disease due to the inflammation and immune disruption they cause. Dr. Schweig argued that this is partly due to the fact that these bacteria are able to persist in the body; a fact that is at the heart of some of the most significant debates about Lyme disease and a source of division between those who believe in persistent Lyme infections and those who don’t.

Closing the Case for Integrative Holistic Medicine

Dr. Schweig finished up his presentation by recommending two books to the audience: The Last Best Cure by Donna Jackson Nakamura, and When the Body Says No – The Cost of Hidden Stress by Gabor Mate, MD. Both of these books are tremendous resources for people looking to understand the path to optimizing health through a combination of approaches.

In short, using a functional and integrative medicine approach can help move Lyme patients back to health by deploying all of the tools at our disposal. And, yes, that includes antibiotics in many cases, but antibiotics are not the singular “silver bullet cure” to fighting this ancient and wily bacteria.

For more information about other upcoming Speaker Series events, click here.

2 Comments on “Treating Lyme Disease: A Functional and Integrative Medicine Approach

    1. Thank you for the question. You would best consult your doctor for specific recommendations regarding other conditions like RA. Best wishes.

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