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.

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

  1. How can one prevent tick bites if you are susceptible to them and mosquito bites. Bitten 4 times now. Is there a way to change your body scent?

  2. I have been feeling ill for the past three years and had no idea what was causing it. I went to Chicago and was treated by a Functional Medicine doctor who gave me over a dozen supplements. I have followed this routine without ever skipping a day, only to keep getting worse and worse. Brain fog, lack of balance (must walk assisted) only to develop gastric reflux, leaky gut, migraine headaches, hearing loss, lately vision loss. Fortunately, on October 9 last year, I went to an appointment at the Cleveland Clinic´s Functional Medicine Department at which I was told that I probably had Lyme. My blood exam came as “highly positive for Lyme, Babesia, and a host of other neurological problems. Now, I am looking for a clinic that might be able to cure me. I really do not have a life anymore. I feel so awful that I have isolated myself and no longer go out of my house.

    1. Sandra, we are so terribly sorry to hear of your suffering. Accurate diagnosis is an important part of the solution (and one not easily achieved in many cases, like yours). Unfortunately, that is only part of the battle, however, and you will need the care of a knowledgeable Lyme-literate doctor as well as a good support network.

      The first place to start might be the Physician Referral service offered by the International Lyme and Associated Diseases Society (ILADS) which can help you navigate to care providers in your area.

      The RAWLS MD Lyme Support Group Directory is a curated database of local Lymel support groups throughout the US that can provide additional support and resources.

      We wish you strength to persevere and days of good health ahead.

    2. Sandra – there is hope! Did you find someone to help you? I went through something very similar last year and discovered Lyme. Please email me and I will share what doctors/supplements have helped me. I have done the Cowden Protocol and it has worked wonders.

    3. I, too, am just finding out about having Lyme disease. I live in Franklin, Tenn. And am going to a functional medicine doctor … Sanctuary medical. Google them, they maybe can refer you to someone in your area. Insomnia has been debilitating…among other things. Too tired to move but life, work, and sick in-laws…no time to rest.

    4. Hello Sandra, I just wondering if you have found a good doctor as of yet? I’m curious to know why the Cleveland Clinic Functional Medicine couldn’t help you?? I was going to schedule there and I’m having second thoughts.

  3. Six years ago I removed a large adult female deer tick from my side. It had not been attached for 48 hours so I wasn’t worried but in five days I had a fever and stiff neck. After antibiotics, I felt better but then flare ups started. A doctor with an interest in Lyme disease diagnosed Bartonella infection. (burning feet, shin pain, enhanced sense of smell, night sweats), I continue to have these symptoms – most often at full moon. The doctor said I would never test positive for Lyme or Bartonella because I took antibiotics before my body could build up antibodies.

    Since then, I have become aware that I have a genetic mutation with the down stream effect of prevention of normal manufacture of glutathione in the liver. One in ten (1 in 10) caucasians are thought to be homozygous for MethyleneTetraHydroFolateReductase c677t and two in ten (2 in 10) have one copy (the rate is higher in Asians and Hispanics). Glutathione is the body’s primary detox agent. It is interesting to me that ten percent (1 in 10) of people infected by ticks continue to have persistent Lyme symptoms. Could there be an overlap of MTHFR mutations leading to the lack of the body’s ability to manufacture adequate Glutathione and the body’s ability to shake off Lyme and coinfections?

    I recently learned, after being given IV tylenol in a hospital procedure, that tylenol depletes Glutathione and a process that is degrading to liver cells can ensue (The same pathways as Tylenol overdose). Could Glutathione, or lack thereof, be the key to recovery of Lyme or persistent post Lyme/coinfection symptoms?

    1. Apologies for the belated response. We wanted to get Dr. Schweig’s expert opinion. Here is his response:

      “Interesting thoughts but not a clear cut answer: There are MANY SNPs (single nucleotide plolymorphisms/genetic variatipns) and it is becoming popular to use 23andme or other genetic data to generate long reports of these. But it is not clear what the clinical significance of these variations are. Many people want to equate a SNP like MTHFR (or others for glutathione, like GST, GSTP) with a certain clinical outcome or phenotype like low glutathione or greater need for B vitamins but it is hard to find clinical research that supports these correlations.

      “In our practice, we see some patients who have either one or two copies of each MTHFR SNP but we also see patients who are sick and have no abnormal variations in this SNP. More research is needed.

      “Also, with glutathione, there is some research that suggests one needs to be careful about boosting levels or taking it as a supplement when taking antibiotics as this might blunt the efficacy of the antibiotics.”

  4. The following was received by a reader offering another resource regarding Lupus and Lupus-like symptoms, some of which resemble Lyme and many of which can be successfully treated with the integrative approaches referenced by Dr. Schweig.

    My name is John Hawthorne …I recently wrote an article on lupus and it symptoms, causes and treatments. My article can be found here 10-common-symptoms-of-lupus. I was wondering if you would like to use my article as another reference regarding Lupus on your site.

    Thank you,

    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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