Lyme Disease: Patient Guidelines/Outlines 

Lyme Goal #1: Eliminate the Lyme Spirochete:

Lyme Disease is caused from a bacteria name Borrelia Burgdorferi.  It is a specific type of bacteria called a spirochete.  Under normal circumstances this bacteria is difficult to kill because it is one of the fastest bacteria known in existence.  Indeed, it is one of the only bacteria that can actually swim against blood current as it goes through your body.   A basic goal for a Lyme Remedy should surround helping the body get rid of this bacteria.

Borrelia’s Multiform Defense Strategy in Lyme Disease:

Not only can Borrelia exist in is a normal cell wall form, it can also morph into a cell wall deficient form (CWD, L-form or cystic form), and the intracellular form.  This is important because many antibiotics work by targeting a bacteria’s cell wall.  Indeed, if a bacteria has a cell wall, that is the preferred target of destruction.   

Lyme Disease Functional Medicine

Biofilm is like the mote of a castle. It physically prevents or hinders you from even getting to the castle to attack it.

In the CWD form of Lyme, the outer membrane must be the target rather than the cell wall.  Any Lyme remedy that targets a key factor in the bacterial cell wall (as most antibiotics do) will be completely useless against a bacteria in this form.  The body also uses an extracellular matrix of proteins called a “biofilm” in this phase.  This biofilm we think of like the mote of a castle.  t just makes it physically difficult to actually get at the bacteria to attack it.  For this we find several herbal antimicrobials have long-been acting as biofilm busters (such as oregano oil), or enzymes must be added to pnetrate the biofilms and gain access to attack the bacteria.

In the Intracellular form the bacteria has gone inside your own cells similar to a virus.  This is the trickiest form of Lyme because it is trying to use your own body’s cells as a shield.  Penetrating this defense is similar to helping the body eliminate a virus which also employs this strategy to try and hide from the immune system.

Key Point: Any Lyme support strategy must account for Lyme in its 3 different forms and be able to penetrate its biofilm protection 

Bacteria Form  Example Help  Additional Considerations 
Normal Form  Oregano, Thyme, Cloves  Homeopathic 
Cell Wall Deficient Form  Grapefruit Seed Extract  Biofilm + Homeopathic 
Intracellular  Anti-viral strategy  Homeopathic 

 Above is a table illustrating how we might help a patient recover from Lyme.   

Lyme Goal #2: Boost Immune System Function:

Lyme causes damage to the TH1 side of the immune system.  Remember the CD57 test we use to investigate Lyme in patients is a measure of natural killer cells.  These cells are part of the TH1 wing of the immune system.  Thus Lyme disease is a disease of TH1 over-activation but simultaneously ineffectiveness.  Picture flooring the gas pedal in your car while its in park.  You can feel the engine rev, but not being connected to the wheels means the car does not actually go anywhere.  In chronic Lyme the engine is often “red lined” and causing damage, but also not accomplishing the goal of moving the car (in this case not accomplishing the desired effect of eliminating the Lyme and/or the co-infections).   This can lead to a condition known as Chronic Inflammatory Response Syndrome.  This in and of itself is a large box to unpack and we will be outlining it in a future article.  Stay tuned.

Key Point: The end goal for each patient with Lyme disease is the restoration of their immune system’s proper function 

The TH1 immune wing is the hand to hand combat, direct killers of the immune system. It is also called the “cell mediated” immune system. Things that enhance or support the TH1 side of the immune system are: 

TH1 Immune System

We call the TH1 system the “boys” of the immune system. They go in with swords and sticks and whack stuff! However, just like in real life it is dangerous to give boys weapons if they have not been properly trained by a good mother!

    • Echinacea
    • Andrographis ***** – Problably the 2nd most important herb for Dr. Warren’s patients with low CD57 counts
    • Astragalus 
    • Cat’s Claw ***** – Probably the single most important herb for Dr. Warren’s patients with low CD57 counts
    • Maitake Mushrooms
    • Licorice – Dr. Warren’s #1 herb for viral challenges
    • Melatonin 
    • Chlorella 
    • Panax Ginseng 
    • Melissa Officinalis (lemon balm) 
  • Arabinogalactins

Remember the Treg Cells:

A safe approach to enhancing immune system function also involves supporting the TH3 immune modulating cells. If you are doing other reading the TH3 system is made up of T-regulatory cells and we call these cells the “mom” of the immune system. Generally starting with patients to establish healthy Treg function goes smoother than doing only TH1 support alone.  Helping patients with Lyme can be a rocky, up and down road.  Dr. Warren has specifically put pieces of the Lyme protocol in place to get smoother, more consistent results while minimizing the up and down drama as much as possible you may have read many Lyme patients experience.  Support for the TH3 system involves: 

TH3 Immune

The Treg cells are the “mom” of the immune system. They help the boys and girls behave properly.

    1. Glutathione 
    1. Japanese Knotweed
    1. Vitamin D
    1. Vitamin A 
    1. Fish Oils (EPA & DHA)
    1. Short Chain Fatty Acids (from healthy gut bacteria and fiber) 
    1. Opioid Receptors (being happy is helpful!) 
  1. Reishi Mushrooms

Lyme Goal #3: Eliminate Co-infections – Lyme Disease Rarely Comes Alone:

Ticks infected with Lyme are often infected with other tick-born illnesses as well.  The most common are Babesia, Bartonella, Erhlichia/Anaplasma, and Rickettsia.  Other non tick-born co-infections include Epstein Barr Virus, Cytomegalovirus, Powassan Virus, Mycoplasma, Candida, and Mold.  We cover each co-infection and how we go about eliminating it in separate handouts.  For now let’s simply be reminded that most patients with Lyme have multiple, simultaneous microbes that drag their health down.  Doing testing for these various microbes and/or doing programs aimed at helping patients overcome them is part of nearly ALL Lyme protocols.  Dr. Andrew Heyman heads the integrated medicine program at George Washington University and runs a practice in Virginia dealing with Lyme on a regular basis.  As part of his Lyme treatment protocol he assumes a Lyme patient has ALL the co-infections until proven otherwise and will systematically support for each one through a year to 2 years of Lyme treatment.  Dr. Warren highly values Dr. Heyman’s professional opinion and has found co-infections to be one of the trickiest and most diverse part of the puzzle in each Lyme disease case. 

Special Note on Herxing/Detox Reactions – We don’t like them:


Severe detox reactions are avoidable if the program is done with the right balance

Herxing is a detox reaction that happens when you kill off more organism than your detoxification pathways can handle.  Patients get “die off” reactions or a worsening of symptoms when this happens.  It is important to support detoxification pathways during recovery to minimize herxing reactions as they can be unpleasant, uncomfortable and discouraging to patients if they become too severe.  While some believe Herxing or detox reactions may be inevitable, we at RHS disagree.  Detox reactions often mean we are doing the right thing in the wrong way.  Either the dosages of the anti-microbials are wrongly dosed or there is not enough of the correct detox support in place to help clear out these dead organisms, or there is not enough immune support in place etc.  The trick to Lyme is pulling it off simultaneously in balance throughout a moving process. 

RHS Basic Outline for Lyme Support with Comments:

We’ve talked through many pieces of a Lyme Remedy protocol.  Let’s try to conclude by bringing it all together.  Below is an example of an 8-9 month program outline.  The purpose of this picture is not to say exactly what we do!  We do not use this exact protocol!  Each person’s program MUST be customized to yield the best results.  However, this format can dramatically help you understand and keep straight all the moving pieces of recovery from Lyme. 

Lyme Protocol Outline Example

A simplified example of what a support plan for a patient with Lyme might look like.

Phase 1 – Lyme Remedy:

The purpose of Phase 1 is to try and open up detoxification pathways and just begin the process in a slow and gentle way.  Phase 1 really opens up the door to be more aggressive in phase 2 and 3.  Being too aggressive, too early often backfires with severe Herx reactions in most patients.   The fastest way to move forward, is to not move backwards!

Phase 2 – Lyme Remedy:

The purpose of Phase 2 is to amp up support of the immune system.  Simultaneously we start here going after the Lyme and Co-infections more aggressively.   If the detox pathways are clogged when you begin killing Lyme and the co-infections there will be Herx reactions and an exacerbation of symptoms.  If we do this correctly you can feel better during this phase instead of worse.

Phase 3 – Lyme Remedy & Co-infections:

Like Phase 2 here we are supporting continued Lyme support with different co-infection support.  We will continue to cycle through different support every 2-4 months as most patients stagnate and fail to continue their progress unless the plan is altered periodically.  This is likely because of the Lyme bacteria’s incredible ability to adapt to our own system for its own survival.  Having been on glutathione for several solid months helps give patients immune control, detoxification support, and anti-oxidant protection specifically to help the nervous system function without damaging itself.  Think about glutathione as oil in the engine making sure it doesn’t get damaged as it runs.

Phase 4 – Lyme Remedy & Co-infections and “finishing”:

In phase 4 we are winding down as the patient has improved.  ILADS guidelines state we want patients to be basically symptom free for 2 months before really backing off support protocols.  After a patient’s symptoms have shown improvement it can be tempting to pull back protocols too early.  Any veteran Lyme practitioner will be able to tell you stories of patients who quit as soon as they felt better only to have everything return in a few short months.    

Key Point – In order to prevent relapse we want to see 2 months of no symptoms before really pairing down the protocol.

Long-Term Recovery: Phase 5 – Lyme Is Gone, but the Body Is Still Weak.

Depending on how long you’ve been suffering there can be a time of strengthening after Lyme has been eliminated.  Because you have not been able to be active and have healthy habits due to pain or fatigue, your body is now not in good shape!  Replenishing physical fitness, neurological fitness/endurance, and adrenal/stress handling can take time.  However, patients can absolutely get fully recovered after Lyme and go on living a happy, healthy life!  This does not have to linger forever.   For more on Chronic Inflammatory Response Syndrome please stay tuned.Be Strong

Did you read the Part 1 of this blog? Click to learn even more of Lyme Disease from Dr. Warren!

Free Consultation
close slider
  • Please provide your contact information and we will contact you to schedule your free consultation.
  • Restorative Health Solutions
    7701 York Ave S #230
    Edina, Minnesota 55435
  • This field is for validation purposes and should be left unchanged.