The Lyme Disease Treatment Order of Operations: Why Results Depend on Sequencing
When attempting to heal from late-stage/ chronic Lyme disease, many people fall into a vicious cycle of achieving temporary relief followed by an inevitable relapse of symptoms.
Others experience such an intensification of symptoms once they start treatment that they either can’t complete their protocols or they end up effectively disabled trying to white-knuckle through it. This leaves people at the end of the road, time and time again, always left unsure where to turn next.
People can spend years, sometimes decades, stuck in this cycle; spending all their time treading water and all their energy trying to reach the surface again when each new wave pulls them under.
This is unsustainable - physically, mentally, and financially.
This pattern of treatment failure - in my experience and observations - usually boils down to two things:
Failing to follow a strategic sequence - an order of operations - at the biochemical level; and
Failing to establish a strong foundation at the biophysical level, which can be considered a prerequisite for the body’s ability to heal and handle treatment
At the biochemical level, I’m talking about examining life at the level of molecular interactions. This has to do with medicinal treatment, whether via herbal or pharmaceutical means.
When I reference the biophysical level, I’m talking about a deeper examination of biology at the atomic and subatomic levels. This is more foundational because physics underlays chemistry. It has do with photons, electrons, protons, magnetism - upstream subatomic particle interactions that drive downstream chemical behaviors.
When these two factors are ignored (when a strong biophysical foundation isn’t in place and when strategic sequencing is ignored during biochemical treatment) Lyme patients are at a much greater risk of failing to achieve sustained improvements and face a higher likelihood of getting trapped in the chronic illness vortex.
This article lays out 4 steps to consider when evaluating and addressing chronic tick-borne infections - a biophysics-based prerequisite followed by a three-step biochemical order of operations:
Building a strong biophysical foundation - focusing on increasing redox potential and improving mitochondrial function. Without doing this, the body’s natural detoxification abilities are impaired and it can lack sufficient charge to heal effectively.
Dissolving biofilms (after clearing acute infection). By ignoring biofilms, you’re more likely to face persistent infection and experience relapsing symptoms when treatment ends.
Targeted treatment, in proper sequence. Some treatment options indiscriminately decimate the microbiome and mitochondria that your immune function and long-term health are dependent upon in the first place. Coinfections and other cofactors are also often not addressed in an effective sequence.
Bind & eliminate toxins and inflammatory debris. When detoxification is impaired, the risk of feeling more sick after initiating treatment is increased. When the wrong binders are taken they will be ineffective, and when the right binders are taken at the wrong time they can be a hindrance.
Before diving into these steps, some important context is needed.
Context & Disclaimer
This article is educational, not prescriptive. The information presented here is intended to help you better understand the mechanisms behind chronic Lyme disease and the logic of treatment sequencing. It is not a specific protocol and should not be treated as medical advice. Every case of tick-borne illness is different, and any changes to your treatment approach should be discussed with a qualified healthcare provider who understands your unique circumstances.
With that said, some important context:
First, the ideas in this article are specifically addressing late-disseminated Lyme disease, or chronic Lyme, and not early infection. Early-onset infection with tick-borne pathogens can often be cleared swiftly with a short course of antibiotics, but that is not the case for late-disseminated disease where the infection has had the opportunity to penetrate deeper into the body.
Second, there is really no one such thing as Lyme disease. The label of “Lyme” itself is associated with the bacterium Borrelia burgdorferi; however, there are numerous other subspecies of Borrelia which can also be pathogenic. Vectors like ticks also spread a variety of coinfections together with Lyme, including other bacteria like Bartonella and parasites like Babesia. Each individual case of Lyme disease is likely dealing with a unique mix of pathogens and exposures, each presenting different symptoms.
For clarity’s sake—when I refer to Lyme disease in this article, I am referring to a disease complex which can include an array of various coinfections in addition to the actual Lyme bacterium.
Since no two cases of Lyme disease are necessarily the same, treatment recommendations need to be tailored to the individual and their unique circumstances. This bioindividuality is why working with a knowledgeable practitioner is essential—someone who can assess your specific pathogen load, coinfections, genetic factors, and overall health status. At the biochemical level, there is no one-size-fits-all protocol; however, the general sequencing principles I discuss apply broadly. At the biophysical level, many interventions do apply across the board, which helps simplify things.
Alright—with that context established, let’s dive into the importance of sequencing when it comes to treatment.
Since the biochemical level is more widely familiar, we'll start there. However, it's critical to understand that the following biochemical steps should only be the focus once the biophysical foundation is in place. For many people stuck in the chronic illness cycle, jumping straight into antimicrobial protocols without first addressing redox potential, circadian function, and detoxification capacity is precisely why treatment feels overwhelming or fails to produce lasting results. If you've tried protocols before and crashed hard or relapsed repeatedly, consider skipping ahead to "The Biophysical Prerequisite" section—that may be the missing piece
The Biochemical Order of Operations
Successful treatment after previous failed attempts often requires strategic sequencing:
Dissolve Biofilms
Treat
Bind & Eliminate
Getting this order wrong or skipping steps increases the likelihood that the treatment will fail or yield only temporary results. We’ll explore the reasons for this below.
Important note before diving in: These steps assume two things. First, that you've already focused on fixing circadian rhythms and increasing redox potential—the biophysical prerequisite. Second, that acute, active infection has already been addressed with an initial round of antimicrobials. The focus here is on chronic illness.
Step 1: Dissolve Biofilms
Lyme and other tick-borne infections take strategic advantage of biofilms in the body.
Biofilms are slimy, protective layers of extracellular polymeric substances (or EPS - primarily composed of polysaccharides, proteins, DNA, and lipids) that are secreted by colonies of microorganisms. Biofilms themselves are neither good nor bad. Beneficial biofilms line the gut and are crucial for digestion and immune defense, while those on the skin provide a natural protective barrier. But when the internal environment is out of balance, opportunistic pathogens can fill the gap and form detrimental biofilm fortresses that house and protect disease-causing microbes. As the biofilms expand, they periodically bubble up and disperse organisms for further colonization.
Pathogens nested within biofilm layers are typically protected from antibiotic treatment. This means even when you clear out active infection that is openly vulnerable in the bloodstream, if you do not address biofilms, more pathogens will continue to be released into the system once treatment is halted. Without assessing and addressing biofilms, the patient is at high risk of relapsing symptoms.
This is why dissolving biofilms is a first step at the biochemical level for chronic cases when people have experienced prior failed treatments. While this is listed first in the biochemical order, it is commonplace for an initial round of antimicrobial therapy to precede this to address acute infection. In chronic illness states, patients have typically already undergone initial antimicrobial treatment—often multiple rounds—without sustained improvement. It's at this stage that biofilm dissolution becomes a priority, as unaddressed biofilms are often the reason prior treatments failed.
If and when an individual is ready to address this step, dissolving biofilms must be done carefully and gently. Dissolving biofilms is like peeling away layers of an onion. You don't want to release too much at once and overwhelm the system.
There are numerous biofilm dissolvers, and which ones you take really depends on your unique circumstances, overall health profile, and considerations of any drug interactions. In general, some of my favorite choices include nattokinase, lumbrokinase, and cistus incanus tea.
Once you have initiated the dissolving of biofilms, you then need to be prepared to treat what is released and openly vulnerable.
Step 2: Treat
When it comes to Lyme treatment, antibiotics are often first to mind. They are appropriate in some cases. However, caution with antibiotic use is advised. Unlike with early-stage infection, antibiotic use in chronic stages tends to be ineffective and often counterproductive. Here are five reasons why.
Tissue Penetration. The Lyme bacterium is a very motile spirochete, shaped like a corkscrew that can swim from the bloodstream and literally drill its way into your tissues. Many antibiotics are effective for bloodstream infections, but lack tissue penetration capabilities. This is why lipophilic drugs like the tetracyclines (doxycycline, minocycline) are chosen above the hydrophilic beta-lactams (amoxicillin, penicillin). So the fact that Lyme drills into tissues does not rule out antibiotic use, but it complicates things, especially in consideration with the subsequent points.
Biofilm Resistance. The presence of biofilms that are anchored to tissue surfaces significantly increases antibiotic resistance for numerous reasons: the matrix of film layers creates a physical shield; biofilm communities contain slow-growing or dormant organisms which are naturally resistant to antibiotics that target rapidly-dividing bacteria; biofilm communities have high genetic exchange to increase antibiotic resistance; and enzymes are secreted within the film which break the antibiotics down.
Persister Forms. The Lyme spirochete is intelligent. When it detects a threatening antibiotic, it will shapeshift and change its physical form into a round body - a dormant, protected cyst that is impervious to antibiotics. Once antibiotic treatment stops, the cysts awaken. Not properly addressing the persister forms of Lyme is a common reason (in addition to not addressing biofilms) why many people experience relapsing symptoms once treatment is paused.
Microbiome Destruction. Your overall immune health is dependent upon the strength and diversity of your microbiome. Antibiotics are a largely non-selective, nuclear option that wipe out beneficial bacteria as much as the ones you are trying to target. There are numerous second and third-order effects of a decimating the internal environment, leaving you less resilient and with greater susceptibility to antibiotic-resistant bacterial strains.
Mitochondrial Toxicity. Antibiotics tend to be mitochondrial toxins. This is a huge issue, as the overall state of your health is ultimately dependent on the health and function of your mitochondria. By impairing mitochondrial energy production (oxidative phosphorylation), we shift cellular metabolism toward glycolysis. This is a less energy-efficient pathway that also creates favorable conditions for Lyme (as well as other diseases like cancer).
Antibiotics are undoubtedly a miracle of modern medicine. But they have become overprescribed at the expense of other effective therapies, like heliotherapy. Antibiotics will certainly still be required for some cases, but any chosen treatment should consider its effects on the body as an integrated whole system, rather than on isolated mechanistic parts.
As an alternative, there are various herbal remedies for Lyme that have demonstrated efficacy for late-stage cases. In contrast with antibiotics, herbal remedies do not breed antibiotic resistance with long-term use, are highly selective and do not decimate the gut microbiome, have much weaker signaling for Lyme to change into its persister form, and generally do not harm the mitochondria (and in some instances actually offer mitochondrial protection).
Like with biofilm dissolvers, choosing the right herbal protocol is dependent on the individual’s unique circumstances. Most of the research points to the effectiveness of herbs like Japanese knotweed, cat’s claw, cryptolepis, and Chinese skullcap. Herbal treatment is a marathon, not a sprint, and this approach requires consistency. The herbs you select should also be determined by which coinfections are present.
The coinfection factor leads to a microcosm of the order of operations principle: with severe cases of Lyme disease complex, there is often a sequence to follow when addressing coinfections. Babesia, for example, suppresses the immune system and in a sense can protect the Lyme. It often makes sense to target Babesia first to alleviate this immune pressure, so that your immune system can work in your favor when then addressing the Borrelia. This can speed things up. In my experience, Bartonella - which has been implicated with many cases of long-Covid - tends to rear its head and even show up on testing toward the later stages of treatment.
The good news is that some herbal remedies have cross-reactivity for multiple coinfections, to varying degrees. While strategic prioritization should be implemented (like working from macro-to-micro with regards to organism size), throughout an herbal protocol you can often be addressing multiple infections at the same time.
Step 3: Bind & Eliminate
As pathogens are killed, they release inflammatory compounds—lipoproteins and cell wall fragments from Borrelia, hemolysis byproducts from Babesia, and endotoxins from Bartonella. If your body’s detoxification pathways are inhibited - if you can’t eliminate waste as fast as you’re producing it - you’ll be more likely to experience a flare of symptoms. This is known as a Jarisch-Herxheimer reaction: a worsening of symptoms in response to treatment, common with Lyme, and often severe enough that people become debilitated or have to abandon their protocols entirely.
This is where binding helps. Binders are compounds that grab onto toxins—either electrostatically, due to opposite charge, or structurally, due to molecular shape—so they can be escorted out of the body rather than recirculated. Different binders have different affinities: some are more effective for heavy metals, others for chemical pollutants, others for bacterial debris and mycotoxins. It's often wise to rotate binders selectively based on what you're trying to clear.
The electrical charge of a binder is an often overlooked factor when it comes to binder selection. Many toxins like heavy metals and chemicals pollutants have a positive charge. So negatively charged binders will attach to them and help remove them from the body. Biotoxins like those from Lyme and mold, however, are negatively charged. They are often more effectively removed using a positively charged binder or neutral porous binders.
Timing also matters with binders. They should be taken with enough spacing from your treatment so it has time to work without being bound up and inhibited itself. The same principle applies to food, supplements, and medications—but binder selection does make a difference. Some binders are indiscriminate and may bind to minerals and nutrients along with toxins. Others are more selective—binding to low-molecular-weight toxins while leaving larger nutrient compounds intact.
Some examples of commonly used binders include enterosgel, activated charcoal, chlorella, modified citrus pectin, and cholestyramine. Which binders you use, and when, depends on what you're targeting (e.g., mold mycotoxins, heavy metals, Borrelia lipoproteins, Bartonella endotoxins, etc.).
For some individuals, the bind & eliminate step is especially critical. Approximately 25% of the population carries HLA-DR genetic variants that impair the immune system’s ability to recognize and clear biotoxins. In these individuals, biotoxins bind to bile in the liver, which is sent to the gastrointestinal tract for excretion—but during enterohepatic circulation, the bile is reabsorbed in the small intestine and returned to the liver, bringing the toxins with it. The result is a recycling loop: persistent symptoms even after the source of exposure is addressed. This often explains why some individuals can remain sick for weeks to years after mold exposure, while others seem fine. Binders can help interrupt this cycle and eliminate the toxins from the system.
To be clear, these three biochemical steps are typically done concurrently within the same day, not as separate multi-week phases. A typical daily protocol might look like: biofilm dissolver in the morning, antimicrobial treatment 30-60 minutes later, then binders approximately two hours after that. This cycle repeats daily over the course of treatment.
For many people, reorganizing their treatment protocols in this way can help them see improvement in treatment efficacy. Others, however, have tried this and it still feels unsustainable and overwhelming. The vast majority of these cases have not completed the biophysics prerequisite for biochemical treatment, and that is what I’ll introduce below.
The Biophysical Prerequisite
The physics of biology and the emerging field of quantum biology explores the ways in which light and electromagnetism regulate our biology and impact our health.
For those who are chronically ill, failing to address this foundation means they will quite literally lack the energetic capacity—the charge—for their bodies to heal, promote healthy internal flow, and remain resilient. They’ll feel stagnant, backed-up, foggy, and inflamed. These people likely need to focus on increasing their redox potential before they’re ready to dive into a treatment protocol.
For some individuals—particularly those with milder cases or strong constitutional health—focusing on the biophysical foundation alone can lead to significant symptom resolution without any aggressive antimicrobial treatment. The body, when given adequate charge, flow, and circadian coherence, can often manage low-grade infections on its own. This is another reason why I consider biophysics a prerequisite: it's not just preparation for treatment—it may reduce or even eliminate the need for intensive treatment altogether.
Increasing Redox Potential
Redox (reduction-oxidation) reactions involve the exchange of electrons between atoms or molecules. When a molecule loses an electron (or becomes oxidized), it can become a free radical that will steal electrons from neighboring molecules, triggering an inflammatory cascade. When a free radical gains an electron (or is reduced), it becomes neutralized and the inflammation is quelled.
Note that free radicals are not a negative thing - they are critical for immune function, biophoton signaling, and intercellular communication. However, there needs to be balance.
The more electrons you are capable of storing in the body, the more will be available to participate in redox reactions to regulate healthy levels of inflammation, increasing your body’s innate capacity to heal.
Coherent Domains: Electron Reservoirs
One way to increase the body’s redox potential (think of this like electron storage capacity), is to support the development of coherent domains, or Exclusion Zone (EZ) water inside and around your cells.
EZ water is a gel-like substance with a layered, regularly repeating lattice or liquid crystalline structure. As this tightly woven liquid crystalline structure develops, it excludes solutes and nothing larger than a proton is capable of passing through it when it’s intact. This has important detoxification and cellular protection implications, helping to push toxins out of a cell while also serving like a veritable forcefield around it. This is very relevant for Lyme disease since Borrelia scavenges lipids from cell membranes to cloak themselves from immune detection.
In addition to its exclusion property, EZ water is charge-separated. EZ water will form from liquid water when it interfaces a hydrophilic material, such as proteins and cell membranes. As it is constructed, the EZ layer develops a negative charge due to an abundance of electrons, while positively charged protons will be ejected into the neighboring liquid water from which it is forming.
This charge separation creates potential energy that acts like a biological battery. This promotes flow and supports detoxification. When negatively charged EZ layers line the inside of a biological tube (like blood and lymph vessels), positively charged liquid water will be forced into the center. Since like charges repel, the protons will generate electrostatic flow independent of a mechanical pumping mechanism.
Too little EZ water in the body means less cellular energy, less cellular protection, and impaired drainage and detoxification capacity - all critical for healing from chronic Lyme disease.
So how to build it? We’ll focus on just three factors - infrared light, grounding, and improving mitochondrial function.
Infrared Light
Long-wavelength, invisible infrared light penetrates through the body and powers the construction and expansion of EZ water. It is also absorbed by mitochondria, fueling their production of ATP and metabolic water. Mitochondrial water production is essential as this produces EZ water as soon as it interfaces with the biological matter inside your cells.
Sunlight is approximately 50% infrared, but most people spend limited time outdoors. We’ve also removed most infrared sources from our homes by swapping incandescents for LEDs.
The result is a widespread infrared deficiency that also leads to chronic intracellular dehydration, undermining redox potential at the most fundamental level.
Grounding
When two conductive surfaces touch, electrons flow from the area of greatest concentration toward the least. The Earth’s surface is an infinite repository of electrons due to such things as solar radiation and lightning strikes, and is therefore negatively charged. When we physically touch the surface of the Earth, electrons flow into our bodies and support the development and storage capacity of the EZ water networks in the body. This EZ lines all the connective tissue and fascia in the body, which means the electrons become available to participate in redox reactions essentially anywhere throughout the body they are needed.
In addition to a widespread infrared deficiency, the argument could be made that we face a widespread electron deficiency in modern society due to our disconnection from nature. We then become overly reliant on receiving all of our electrons from the metabolism of food.
Supporting Mitochondrial Function: Circadian Rhythmicity and Environmental Inputs
Mitochondria are electromagnetic environmental sensors responsible not only for ATP and metabolic water production, but also hormone regulation, ROS and biophoton emission, thermogenesis, and much more.
A first step in improving mitochondrial function is fixing your circadian rhythms. Because we evolved on a planet with regular cycles of light and darkness, our cells evolved clock genes to determine the time of day to know when to up-regulate or down-regulate their activity (think of the inverse relationship between cortisol and pineal melatonin).
As the Sun travels across the sky, the proportion of wavelengths dynamically shifts throughout the day, and this electromagnetic/light information is directly fed to a master clock in the brain - the suprachiasmatic nucleus - to distribute throughout the body so its many parts can operate together cohesively.
A lack of morning sunlight exposure coupled with overexposure to artificial blue light at night fuels chronic illness at a massive scale by causing biological decoherence. The wavelengths of light present at and just after sunrise, for example, stimulate pregnenolone and cortisol production while increasing serotonin and dopamine levels in the brain. Darkness at night, meanwhile, initiates melatonin release which is a potent antioxidant that regulates cellular repair (autophagy) and removal of irreparably damaged cells (apoptosis) to allow for healthy regeneration.
Since this is a critical, foundational topic, I’ve written a comprehensive Circadian Optimization Guide to help people integrate the findings of circadian biology.
This guide provides in-depth explanations, actionable steps, and valuable tools to help you improve sleep, boost energy, and enhance overall health.
I highly recommend checking this out if you or someone you know is struggling with chronic fatigue, mental health struggles, or chronic illness.
In addition to the foundational importance of our daily circadian rhythms, our bodies are adapted to seasonal infradian rhythms due to the axial angle of our planet as we orbit the Sun. Seasonal variation in light has environmental impacts, and would traditionally invoke cycles in mTOR vs. AMPK metabolic dominance, promoting periods of growth vs. repair. We have largely interrupted this natural cycle due to imported, out-of-season food availability, artificial light, and temperature modulation. One way to support this cycle is by eating a local, seasonal diet, which offers the benefits of periodic ketosis and deuterium depletion.
This is important for Lyme disease because Borrelia depend on glucose and lactate to survive—they have no mitochondria and cannot run on ketones. We can. By restoring mitochondrial health and strategically shifting into ketosis during lower-light months, we deplete deuterium, reduce glucose intake, reduce lactate production, and cut off the bacteria’s fuel supply.
I explore this metabolic angle in depth here:
Starving Lyme: How to Exploit Borrelia’s Metabolic Weakness
In line with the theme of sequencing and there being a proper order to things, the mechanisms of action that are explored in the above article suggest that initiating treatment after a period of targeted/seasonal ketosis may be the most strategic timing to promote its effectiveness.
There’s much more to explore when it comes to establishing a strong biophysical foundation—circadian biology, light exposure, cellular hydration, electromagnetic environment, seasonal eating, deuterium depletion, and more. This is what I largely focus on in my work, so feel free to follow @regenerint on social media or visit www.regenerint.com as I continue these explorations.
The good news is that most of these interventions are completely accessible and affordable (if not entirely free). Get out in morning sunlight. Block artificial blue light after sunset. Ground with the Earth. Eat a local and seasonal diet. Mitigate excess non-native electromagnetic exposure. These aren’t expensive supplements or complex protocols—they’re a return to the basics our biology expects.
The answer to Lyme disease is not to fear being outside in nature. It is our very disconnection from nature—its light, cycles, rhythms, frequencies, and charge—that has created our susceptibility to Lyme and other tick-borne diseases in the first place.
Recap - The Full Order of Operations
To recap, the Lyme disease treatment order of operations is:
Increase Redox Potential. This involves fixing circadian rhythms, focusing on mitochondrial health, and increasing EZ water production.
Dissolve Biofilms. Gently and layer by layer, followed by antimicrobial treatment approximately 30 to 60 minutes later.
Treat. Herbal remedies offer a number of advantages for chronic cases - so look into those.
Bind and Eliminate Toxins and Inflammatory Debris. Take approximately two hours after treatment. Do not take around other medication or supplement use (generally, certain types are ok).
Following this order of operations can help address the root causes of persistent Lyme disease while supporting your body’s natural resilience—reducing the likelihood of severe crashes, brutal herxes, and recurring relapses. Often times, failing to approach things in the right order can inhibit progress and stall improvement. Get this right, and all your hard work and efforts can actually start working in your favor and paying off.
If you or someone you’ve known has been trapped in the vortex of chronic illness and repeated treatment failures, this framework may offer a way through it. It’s not another protocol to white-knuckle through, but information to guide your decision-making when it comes to how you shape your environment, your lifestyle, and your approach to medicine.
Looking for Support?
This framework comes from my own experience navigating chronic Lyme, my clinical work with clients, and years of research into tick-borne illness, circadian biology, and quantum biology.
If you’re struggling and want one-on-one guidance—help building your biophysical foundation, sequencing your treatment, and addressing your unique circumstances—I offer consultations as well as a Lyme & Biotoxin Illness Recovery coaching program.
Learn more at REGENERINT.com
If you found this article helpful or insightful, consider sharing it with someone else who might be struggling with Lyme disease and related tick-borne illness. The more information we have, the better informed our decisions can be.
Thank you for reading!
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