Comprehensive Guide to Treating Chronic Lyme Disease and Co-infections in Minnesota: Evidence-Based Herbal Protocols

Dr. Kyle Warren, Functional Medicine
Lyme Testing Update: 
The Critical Importance of Multi-Species Detection
Hidden Lyme: Why Traditional Testing Misses Multiple Borrelia Species
Are you suffering from unexplained chronic fatigue,  joint pain, neurological symptoms, or cognitive issues despite being told your Lyme test was negative? In this groundbreaking educational video, Dr. Warren reveals critical information about Borrelia infections and Lyme disease diagnosis that most conventional physicians are not aware of— information that could be the missing key to your health struggles!

Watch the video below to learn more:

A Personal Message from Dr. Warren:

"Just this morning, we identified a patient with strongly positive results for Borrelia bavariensis who had previously tested negative for Borrelia burgdorferi. Without comprehensive species testing, this patient would have remained undiagnosed and untreated. If you're struggling with unexplained symptoms despite negative Lyme disease tests, you're not alone. After years of treating complex Lyme cases, I've discovered that standard testing for only Borrelia burgdorferi misses numerous infections caused by the other 17+ Borrelia species that cause Lyme disease. In our clinic, we regularly identify patients with Borrelia mayoni, Borrelia bavariensis, and other species that conventional tests completely miss. Research by Dr. Leona Gilbert confirms these species travel globally, making geographic restrictions outdated. Furthermore, Lyme bacteria transform from antibiotic-susceptible spiral forms to resistant round bodies after 4-60 days, explaining why delayed treatment often fails. If you've been told "it's not Lyme" but continue suffering, I encourage you to seek comprehensive testing for all Borrelia species and explore our multi-faceted treatment approach that targets all forms of the bacteria, supports immune function, and restores health to damaged systems—because finding the true cause of your symptoms is the first step toward genuine recovery. Thanks"

Dr. Kyle Warren, DC, CFMP, Lyme Specialist

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The Fundamental Problems with Standard Lyme Disease Testing Your Doctor Never Mentioned

1: Multiple Borrelia Species Cause Lyme Disease But Most Tests Only Check For One

The outdated approach of testing solely for Borrelia burgdorferi (the first discovered Lyme-causing bacteria) misses numerous infections. Our specialized clinic tests for 18 different Borrelia species, including Borrelia mayoni (discovered at Mayo Clinic in 2013), Borrelia bavariensis (which can cause more neurological symptoms), Borrelia californiensis, Borrelia garinii, and Borrelia spielmanii—all of which can cause Lyme disease symptoms but won't show up on standard tests.
*Infographic comparing outdated single-species Lyme testing (Borrelia burgdorferi only) with comprehensive testing for multiple species including B. mayoni, B. bavariensis, B. spielmani, B. californiensis, and B. garinii.

2: Understand That Lyme Disease Can Be Contracted Anywhere

Cutting-edge research by Dr. Leona Gilbert Ph.D. and her team has conclusively demonstrated that different Lyme-causing Borrelia species now appear globally. The conventional belief that specific Borrelia variants only exist in certain regions is scientifically inaccurate. Tick vectors travel extensively via birds and other carriers, and patients can contract any Borrelia species regardless of geographic location. This outdated regional thinking leads to countless missed diagnoses and unnecessary suffering.

*Infographic showing how different Borrelia species travel globally rather than staying in specific regions, based on Dr. Leona Gilbert's research on worldwide tick migration patterns.

3: The Critical Time Window for Effective Antibiotic Treatment

Most physicians don't realize that Borrelia bacteria undergo morphological changes within the body, transitioning from a spiral form (highly susceptible to antibiotics) to resistant round body forms and protective biofilm colonies. Antibiotics are approximately 80-90% effective when administered within the first 4-60 days of infection. Dr. Myriah Hinchey's research suggests the most optimal window may be even shorter—within the first four days. Beyond this period, the bacteria transform, rendering standard antibiotic protocols increasingly ineffective. This explains why patients treated months or years after infection often fail to improve with conventional two-week antibiotic regimens.
*Infographic:  Timeline infographic showing how Lyme bacteria change form over time from antibiotic-sensitive spiral forms to resistant round body and biofilm forms, reducing treatment effectiveness from 80-90% to 10-20%.
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4: The Comprehensive Approach Required for Chronic Lyme Disease

At our specialized clinic, we understand the complex nature of tick-borne infections and recognize that Lyme disease is not a one-size-fits-all condition. Our diagnostic approach includes comprehensive testing for multiple Borrelia species and common co-infections, along with detailed assessment of immune function and inflammatory markers. 

For patients with confirmed infections, we develop individualized treatment protocols that address all aspects of chronic Lyme disease, including the various forms of the bacteria, immune dysfunction, neurological involvement, and systemic inflammation. Our integrated approach has helped thousands of patients recover their health when traditional medical approaches failed to identify or adequately treat their condition. For patients with persistent Lyme infections, especially those affecting the nervous system, cardiovascular system, and joints, our multi-faceted protocol addresses:
  • Targeted therapy for all morphological forms of Borrelia (spiral, round body, and biofilm colonies)
  • Identification and treatment of common co-infections (Babesia, Bartonella, Ehrlichia, Anaplasma, and others) that frequently accompany Lyme and complicate recovery
  • Immune system modulation and support to counter Borrelia's sophisticated immune-circumventing properties
  • ​Systematic restoration of cellular function in tissues damaged by chronic infection
  • ​Detoxification support to address the inflammatory burden of long-term infection
  • ​Neurological rehabilitation for cognitive symptoms and nervous system inflammation
Infographic:  Four-pillar approach from Dr. Kyle Warren at Restorative Health Solutions: infographic for treating chronic Lyme disease: targeting multiple bacterial forms, supporting immune function, addressing co-infections like Babesia and Bartonella, and implementing body-wide rebuilding.

Have you experienced the frustration of being told "your test is negative, so it can't be Lyme" while your symptoms persist or worsen?

This experience is unfortunately common, as standard testing may miss your infection entirely. Many of our patients have previously consulted with multiple specialists, undergone countless tests, received conflicting diagnoses, or been told their symptoms are psychosomatic—only to discover they've had Lyme disease caused by a Borrelia species not included in conventional testing panels.
Get a second opinion today!
Click below to book a free consultation with Dr. Kyle Warren, DC, CFMP, Restorative Health Solutions.
At our specialized clinic, we understand the complex nature of tick-borne infections and recognize that Lyme disease is not a one-size-fits-all condition. Our diagnostic approach includes comprehensive testing for multiple Borrelia species and common co-infections, along with detailed assessment of immune function and inflammatory markers. 

For patients with confirmed infections, we develop individualized protocols that address all aspects of chronic Lyme disease, including the various forms of the bacteria, immune dysfunction, neurological involvement, and systemic inflammation. Our comprehensive approach has helped hundreds of patients recover their health when traditional medical approaches failed to identify or adequately help their condition.

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Frequently Asked Questions
Q: I was treated for Lyme disease and feel better, but now I feel ill again. Do you think I still have Lyme disease? 
A: Yes! If you are not 100% better after your course of standard Lyme meds, go back to your doctor immediately and get another course. Being aggressive in trying to eliminate Lyme in the acute phase (1-3 months) is the best approach!

Q: Are Antibiotics the best treatment for Lyme disease or Chronic Lyme disease?
A: For acute Lyme, antibiotics are 100% the undisputed best remedy. Even most of my natural minded colleagues will encourage standard meds as first round of care.  But please understand, research suggests a few percentage 6-21% still go on to develop what the CDC calls Post Treatment Lyme disease.

Q: I have Chronic Lyme: I am currently receiving treatment for it. Why do I go from feeling very good one day to very bad another, on the same treatment?
A: That depends on the type of treatment and how it is all balanced. It is possible to heal from Chronic Lyme and regain your health, but if a person does the right things in the wrong balance it can be a terrible roller coaster of ups and downs.

Q: I have Chronic Lyme. What’s the best approach?
A: Unfortunately that is not simple answer. We believe the best answer has 4-6 major steps. We have to help the immune system be restored, detox, kill the Lyme bacteria, kill co-infections, help the mitochondria to be healthier, and then exercise/stimulate the nervous system. These all must be done in the right order and in the right balance or patients will not get better or not be able to tolerate the protocol.

Q: I had Lyme, was treated for it, but I feel like it hasn’t gone away. Should I take more meds?
A: If you are past the 3 month mark from the tick bite you are entering a phase of the disease where antibiotics alone are less likely to resolve the issue. We need to understand why your body is not able to fight off this bug, like it has fought off so many bugs, so many times before! It is highly likely you will need a more comprehensive approach.

Q: I had a positive Lyme test in the past…would you still go through testing me for Lyme or do you do things a little differently?
A: If you’ve already been diagnosed with Lyme, we will do things a little different…we already know you had it at one point and the question now becomes, is it gone, are you over it, or is this still causing your problems? The answer in your unique case could be Yes, or a No, but it is very important to not make assumptions! We have many questions we ask you to help understand if you are truly over the Lyme, or we need to address the Lyme again. We can’t go on blaming Lyme everything, but if it is truly causing symptoms again we don’t want to miss it either.

Q: What is some of the feedback that the MDs have given you in terms of your Protocol combined with theirs?
A: They are surprised it goes smoother for their patients! They aren’t getting some of the negative reactions with some of these drugs that they are used to seeing in patients. Our functional medicine and functional neurology Lyme protocol can complement an MD's treatment beautifully.

Q: I’ve heard of the term “Lyme literate MD.” Who is a Lyme literate MD and what has been your experience with them?
A: Who we consider a “Lyme literate MD” is a medical doctor who recognizes there are some flaws in the Lyme testing and understands that Lyme can go chronic. In our experience, a Lyme literate MD will typically have a more aggressive protocols. They are usually using high-dose, longer duration treatment for 6-18 months…now that’s aggressive, but usually what you are getting. Some Lyme literate MDs will add in other support protocols…and while a patient is on these meds, there are some downsides to taking meds for this length of time, but necessary for some people. So it’s our role to help support the patient during this time to help round out the protocol, help it go smoother, support the restoration of the immune system and the detox systems with that.

Q: Is Chronic Lyme the same as Post-treatment Lyme disease Syndrome?
A: People argue over this term. The CDC refers to chronic lyme as “ Post-treatment Lyme disease Syndrome.” The way to think about it is - In 10%-20% of patients, Lyme disease does not resolve easily. In my experience this is usually when the patient also is dealing with co-infections such as Bartonella, Babesia and Anaplasma. We refer to this minority population as Chronic Lyme Patients.

Q: Do you work with me alone or will you be able to work with my MD?
A: The answer is “Sometimes.” We have a few different great MDs that we can refer people to. If you are not seeing results at some of our checkpoints by 3 or 6 months, we are going to start to have you also work with an MD! We also have MDs that ask us to just handle the detox part or the immune regulation part, and the MD will prescribe you meds to help kill the Lyme. So, we do believe in a team effort, as needed. Every Lyme patient is unique, with their own immune system, their own mix of Lyme, co-infections, bacteria, yeast, etc., etc.

Q: What is your current success rate in working with Chronic Lyme Patients?
A: Close to an 80% success rate of getting rid of Chronic Lyme…and it has taken several years to get the results we are now getting with patients! (**Please note, Individual results might vary!**)

Q: How soon can I start feeling better once on your protocol?
A: Great Question! If you’re not starting to see Significant Improvement in 3-6 months that you are happy with…we are going to start working with additional referral partners; adding an MD, or an acupuncturist for example…so my first checkpoint, is between 3-6 months. Then people ask… “Okay, but when am I going to be done!?” I tell people, Lyme is one of the longest things we have to deal with. It often takes 12-18 months to be done. Now that doesn’t mean you have to wait 12-18 months to improve and start feeling better! Patients typically feel better during the Lyme protocol. Slow and steady wins the race, but you will not have to wait too long to start feeling better!

Q: I have been getting treated for Chronic Lyme, but I don't think I’m getting better. Should I get a second opinion?
A: I was taught by a mentor that people are looking for “measurable results in a reasonable timeframe.” If you are currently working with someone, ask yourself what are my expectations for results and what is the timeframe we are expecting them.

Q: How does the treatment from one doctor to the next differ for Chronic Lyme?
A: A comprehensive look at various approaches would take too much time for this format. The most common pitfalls I find when reviewing other doctors work is #1 getting over-focused on meds and killing Lyme and undervaluing the other necessary parts of support the body needs, or #2 chasing symptoms with no clear purpose for really healing the body at a core level.

Q: I was diagnosed with depression before being diagnosed with Chronic Lyme. Do you think they are related?
A: Abnormal neurological symptoms, anxiety, depression, PODS can all be possible from Lyme. Lyme creates a massive neuro-inflammatory response and neuro-inflammation is the most highly researched pathway for causing depression.

Q: I have Arthritis-type symptoms. Should I get tested from Chronic Lyme?
A: Absolutely!! Symptoms from Lyme that are prevalent: it frequently causes pain, that can be headaches, migraines, arthritis-type joint pain, muscle pain, and even chronic fatigue.

Q: How long and how often do I see Dr. Kyle when working with RHS for Lyme?
A: We most typically follow up with patients every 4-8 weeks depending on which part of the protocol you are working through.We try to give patients enough support to work through problems, keep pushing forward, and be successful.

Q: Is there any follow up testing?
A: I really like the idea of running a test, doing a therapy, then re-checking that test to monitor progress. We try to follow this formula whenever it is possible.  Follow up testing is often less expensive than the initial battery of tests, because it is only a subset of the initial labs.


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