Adjunct Supports and Therapies for CIRS
Chronic Inflammatory Response Syndrome (CIRS) is one of the most complex conditions for various reasons. Its multi-system effects are rarely addressed by a single therapy alone, which is why complementary adjunct supports and therapies often become essential for lasting recovery. While we believe a personalized Shoemaker Protocol should remain the foundation of CIRS treatment, the reality is that many patients benefit from additional layers of support.
Adjunct therapies can optimize the Shoemaker Protocol by easing the burden on inflamed systems, supporting detoxification pathways, and addressing neurological or hormonal imbalances. At the same time, complementary supports can be typically necessary because it’s rarely just CIRS. The immune dysregulation at the heart of this illness commonly sets the stage for other issues such as chronic infections, vector-borne illnesses, mast cell activation, and various comorbidities.
For this reason, identifying and implementing the right adjunct supports can be crucial for symptom management and achieving root-cause healing. These therapies can help patients better tolerate the Shoemaker Protocol and also address the many downstream effects of CIRS, creating a more complete and sustainable path toward recovery.
Let’s take a closer look at troubleshooting roadblocks, adjunct supports and therapies, and the importance of proper timing.
Key Takeaways
- CIRS is a complex, multi-system illness that often requires adjunct supports alongside the Shoemaker Protocol for sustainable healing.
- Core therapies address biotoxin-driven immune dysfunction, while adjunct therapies support tolerance, resilience, and individualized recovery.
- Nervous system regulation and mind-body work are foundational for improving treatment tolerance and long-term outcomes in CIRS.
- Gut healing is essential in CIRS due to low MSH, leaky gut, and common co-infections such as SIBO and SIFO.
- Supporting detox and drainage pathways helps reduce Herxheimer reactions and improves binder tolerability.
- Sleep optimization plays a critical role in immune regulation, detoxification, and tissue repair in CIRS.
- Gentle, personalized movement supports lymphatic flow, neurogenesis, and overall recovery despite exercise intolerance.
- MCAS and histamine intolerance are common in CIRS and often require temporary symptom support during root-cause treatment.
- Advanced adjunct therapies may be helpful for individuals who plateau or experience persistent roadblocks in healing.
- Even when progress feels stalled, additional layers of support and personalized troubleshooting can reopen the path to recovery.
What Is CIRS?
Chronic Inflammatory Response Syndrome (CIRS) is a highly complex illness that disrupts multiple body systems and manifests through an array of symptoms. At its core, CIRS stems from an immune system that has become dysregulated, driving persistent inflammation that can feel overwhelming and debilitating.
Diagnosing CIRS is rarely straightforward. It requires more than standard lab work or routine check-ups. Instead, practitioners must rely on in-depth testing combined with a careful review of health history to identify environmental exposures, infectious triggers, and patterns of symptoms that fit the CIRS picture.
Because the condition often presents with broad or non-specific symptoms, it is commonly overlooked or mistaken for something else. Conventional autoimmune panels usually fail to detect it, leaving many individuals searching for answers for years. Accurate diagnosis depends on specialized assessments and clinical expertise that reveal the true underlying drivers. With this clarity, treatment can go beyond symptom management and instead work to rebalance the immune system and promote lasting recovery.
In people with certain genetic susceptibilities, CIRS is often triggered by biotoxins—harmful substances that provoke abnormal immune responses. These toxins can originate from a variety of environmental or biological sources, including:
- Mold and Microbes in Water-Damaged Buildings: An estimated 80% of CIRS cases involve exposure to damp or water-damaged environments. These spaces can harbor mold spores, bacteria, and microbial fragments that remain airborne. Even dead mold particles are capable of setting off intense immune reactions, disrupting both neurological and physical function.
- Vector-Borne Illnesses and Insect Bites: Pathogens transmitted by ticks, such as Borrelia burgdorferi (the cause of Lyme disease), or parasites like Babesia microti, can initiate chronic symptoms. In rare cases, even recluse spider bites have been identified as possible triggers.
- Contaminated Seafood: Certain reef fish carry ciguatoxins, produced by algal blooms. These toxins concentrate higher up the food chain, making large predatory fish the greatest risk for human exposure.
- Toxin-Contaminated Water: Lakes, rivers, and coastal waters affected by harmful algal blooms (such as cyanobacteria or Pfiesteria) release toxins that can trigger immune activation. Exposure may occur not only through ingestion but also by inhalation or direct skin contact.
- Other Potential Sources: Viral infections, specific vaccines, volatile organic compounds (VOCs), endotoxins, and actinomycetes may also contribute to immune dysfunction, amplifying inflammation in those already prone to CIRS.
Biotoxins are tiny, highly reactive compounds capable of slipping through cell membranes, which makes them difficult to detect with standard bloodwork. Although breathing in contaminated indoor air is the most frequent source of exposure, these toxins can also enter the body through polluted food, insect-borne pathogens, or direct contact with contaminated water sources.
It’s also important to understand that exposure alone does not guarantee Chronic Inflammatory Response Syndrome (CIRS). An individual’s genetic makeup and overall health history play a major role in whether the immune system becomes compromised. Stressful life events—such as serious infections, surgery, chemical exposures, pregnancy, or even significant emotional trauma—can overwhelm immune defenses and unleash a surge of inflammatory molecules called cytokines. In people who carry certain HLA-DR genetic variations, this immune overactivation can become the tipping point that triggers CIRS, even if similar exposures were previously tolerated.
In many cases, the body can identify and eliminate biotoxins without long-term consequences. However, for genetically susceptible individuals, the immune system fails to properly tag these toxins for removal. This allows them to persist in circulation, fueling chronic inflammation and ongoing symptoms. Biotoxin illness can therefore appear sudden in onset, develop quietly over time, and linger for years without an obvious cause.
For those with a family history or heightened risk, genetic testing offers valuable insight. Even in the absence of symptoms, testing can reveal predispositions that inform proactive prevention strategies or more precise treatment if CIRS begins to manifest.
For a more detailed understanding of CIRS, click here.
Pro-Tip: If you think you’re suffering from CIRS, you can learn more about CIRS diagnostic testing here.
What Is the Shoemaker Protocol?
The Shoemaker Protocol, created by Dr. Ritchie Shoemaker, is a structured, peer-reviewed treatment plan specifically designed for Chronic Inflammatory Response Syndrome (CIRS) and other biotoxin-related illnesses. It remains the only clinically validated roadmap for addressing the widespread immune dysfunction and systemic inflammation that define these conditions. Unlike symptom-focused approaches, the protocol provides a stepwise method for correcting the underlying imbalances that keep CIRS active.
The sequence begins with the crucial step of identifying and eliminating exposure to biotoxins. Removing these environmental triggers allows the immune system to calm its heightened response. Next, binding agents such as Cholestyramine (CSM) or Welchol are introduced to capture and remove toxins, reducing the cycle of re-exposure and recirculating inflammation.
Later stages of the protocol target deeper layers of dysfunction, including abnormal immune markers, inflammatory signaling, hormonal dysregulation, and impaired communication between body systems. Once stability has been established across these domains, Vasoactive Intestinal Peptide (VIP) therapy can be introduced. VIP is only used when key laboratory values confirm readiness, ensuring the body is prepared for advanced regulatory support.
While the protocol provides a clear, detailed framework, we’ve found that many patients encounter common roadblocks along the way. This is where adjunct supports become invaluable. Both essential and complementary therapies can help optimize each step of the protocol, making treatments more effective and easing patient tolerance. Whether it’s addressing detoxification bottlenecks, supporting the nervous system, or correcting downstream imbalances, these adjunct strategies often make the difference between stalled progress and lasting recovery.
Each stage builds upon the last, and with the right combination of Shoemaker’s methodical steps and carefully chosen adjunct supports, patients are better equipped to achieve true remission.
Why Adjunct Supports Matter in CIRS
Since CIRS affects so many interconnected systems at once, recovery rarely depends on a single intervention, even when that intervention is as essential and evidence-based as the Shoemaker Protocol. Adjunct supports matter not because the protocol is insufficient, but because real-world healing is rarely linear, predictable, or uniform across individuals.
CIRS unfolds in layers.
Immune dysregulation sits at the center, but surrounding it are downstream effects involving the nervous system, endocrine signaling, detoxification capacity, mitochondrial function, gut integrity, and infection burden. These layers are shaped by a person’s genetics, exposure history, prior illnesses, trauma, stress load, and overall physiological reserve. As a result, two individuals following the same protocol steps can experience very different responses, tolerances, and timelines.
Adjunct supports serve two critical roles in this context. In the short term, they can help stabilize symptoms, reducing inflammation, reactivity, pain, insomnia, anxiety, or cognitive strain so that the body is not constantly operating in crisis mode. In the longer term, they can support root-cause healing by addressing factors that fall outside the scope of a standardized protocol, such as nervous system hypervigilance, stagnant drainage pathways, unresolved infections or co-infections, hormonal instability, or foundational gaps in sleep, nourishment, and stress resilience.
This is especially important when patients encounter roadblocks during treatment. Some struggle to tolerate binders, stall despite exposure removal, or experience flares that make consistency difficult. Others discover that mast cell activation, vector-borne illness, viral reactivation, or autonomic dysregulation is quietly perpetuating inflammation. In these cases, adjunct supports can act as a bridge, helping the body regain enough capacity and safety to continue progressing through care.
While the Shoemaker Protocol remains the most validated and indispensable framework for treating CIRS, it was never intended to function as a fully holistic system. It doesn’t comprehensively address nervous system regulation, trauma physiology, all infectious contributors, or every aspect of metabolic and foundational health. These elements, however, often determine whether a patient merely survives treatment or truly recovers.
Adjunct supports are not replacements or shortcuts. When used thoughtfully and personalized to the individual, they enhance the protocol’s effectiveness, improve tolerance, and help integrate the many physiological layers involved in complex chronic illness. In CIRS care, this nuance can be the difference between stalled healing and sustained remission.
Core vs. Adjunct Therapies
In CIRS care, it is helpful to distinguish between core therapies and adjunct therapies, as they serve different but complementary roles in recovery.
Core therapies are the essential, non-negotiable steps required to directly address biotoxin illness and immune dysregulation. The Shoemaker Protocol falls into this category. Its structured sequence forms the backbone of effective CIRS treatment. While Vasoactive Intestinal Peptide (VIP) nasal therapy is an important tool within this framework, not every patient is able to use VIP or requires it to achieve remission. Some individuals reach stability and recovery through alternative downstream supports when VIP is not tolerated, accessible, or clinically appropriate.
Adjunct therapies, by contrast, are not universally foundational requirements. They are optional, supportive tools that can be layered in based on individual needs, symptoms, and treatment response. Adjuncts do not replace the core protocol and are not designed to fix CIRS on their own. Instead, they can help optimize tolerance, support specific systems under strain, help with additional root-cause healing, or address parallel issues that influence recovery.
Foundational Adjunct Supports for CIRS
General adjunct supports address foundational aspects of health that are not directly covered by the Shoemaker Protocol but strongly influence healing capacity and treatment tolerance. While the protocol targets biotoxin-driven immune dysfunction, it doesn’t fully account for factors like nervous system regulation, sleep quality, nutritional adequacy, stress physiology, or histamine and mast cell issues. When these basics are compromised, the body is more likely to react intensely, struggle with binders, or experience repeated setbacks despite following protocol steps correctly.
These foundational adjunct supports help reduce background physiological stress and improve overall adaptability, making the healing process more sustainable. By strengthening the body’s capacity to regulate, recover, and feel safe, they often improve tolerance to treatment and support steadier progress through care. Although not disease-specific or curative on their own, these supports create the internal conditions that allow CIRS therapies to work more effectively in real life.
Nervous System Regulation and Mind-Body Work
Nervous system regulation is a frequently overlooked but critical component of CIRS healing. In biotoxin illness, chronic immune activation places the body in a prolonged threat state, keeping the nervous system locked in fight-or-flight or collapse. This dysregulation amplifies inflammation, heightens pain and sensitivity, disrupts sleep and digestion, and lowers tolerance to supplements, medications, and even well-designed treatment protocols. When the nervous system perceives ongoing danger, the body prioritizes survival over repair, making sustained healing far more difficult.
Mind-body work directly addresses this survival physiology. Practices that support nervous system regulation help calm neuroinflammation, improve vagal tone, and restore the body’s capacity to adapt and respond rather than react. For individuals who struggle to tolerate binders, supplements, medications, or protocol steps, mind-body work is typically foundational. These tools can be introduced before starting the Shoemaker Protocol, layered in during treatment to improve tolerance and stability, or used after remission to maintain resilience and prevent relapse.
Nervous system dysregulation is especially common in CIRS due to the long diagnostic journeys many patients endure. Medical gaslighting, dismissal, and years of unexplained symptoms can leave lasting imprints on the stress response, reinforcing hypervigilance and mistrust in the body. Finding practitioners who understand the interconnectedness of immune dysfunction, neurological signaling, and lived experience can be profoundly regulating in itself.
Recognizing this gap, our private practice, Empower Functional Health, developed a dedicated mind-body program called the Wholeness Method, designed specifically for individuals with CIRS and complex chronic illness. This program supports nervous system regulation, emotional safety, and physiological resilience as core pillars of root-cause healing.
If you’re seeking community support and a deeper, more integrated healing approach, we invite you to explore the Wholeness Method.
Gut Healing and Restoration
Gut health is foundational to overall wellness and becomes especially critical in complex chronic illnesses such as CIRS. The gastrointestinal system plays a central role in immune regulation, inflammation control, detoxification, nutrient absorption, and neurological signaling. In CIRS, this system is commonly compromised due to chronically low levels of melanocyte-stimulating hormone (MSH), which contributes to increased intestinal permeability, commonly known as leaky gut. This breakdown in gut barrier function allows inflammatory compounds, microbial fragments, and toxins to enter circulation, amplifying immune activation and symptom burden.
Low MSH also increases vulnerability to gut-based co-infections, including small intestinal bacterial overgrowth (SIBO) and small intestinal fungal overgrowth (SIFO), both of which are highly prevalent in individuals with CIRS. While these conditions typically require targeted interventions and careful timing within a comprehensive treatment plan, supporting gut function through proper nutrition, hydration, and temporary digestive supports is essential at every stage of healing. In our clinical practice, individuals who have completed gut healing protocols prior to initiating the Shoemaker Protocol consistently tolerate binders and other treatment steps more effectively, with fewer setbacks and inflammatory flares.
Nutrition plays a central role in gut restoration. The carnivore diet offers a powerful therapeutic framework for CIRS by providing highly bioavailable, nutrient-dense nourishment while eliminating inflammatory plant compounds, fiber-driven fermentation, and dietary triggers that worsen gut permeability. This approach also naturally aligns with the low-amylose dietary requirements recommended in CIRS treatment.
As the most anti-inflammatory dietary strategy available, a meat-based diet supports immune regulation, blood sugar stability, and tissue repair. While some individuals may temporarily require small amounts of carbohydrates during healing, a heavily animal-based nutritional foundation remains essential for most patients.
Temporary gut supports can further optimize digestion and absorption while the intestinal lining heals. These may include betaine HCl to support stomach acid production, ox bile to improve fat digestion, digestive enzymes to enhance nutrient breakdown, probiotics to rebalance microbial ecosystems, and additional targeted supports based on individual needs.
Together, these strategies help strengthen digestive resilience, improve protocol tolerance, and create the internal environment necessary for sustained CIRS recovery.[/vc_column_text]
Opening Detox and Drainage Pathways
Detoxification and drainage are closely related but not interchangeable, and overlooking this distinction can lead to unnecessary symptom flares during CIRS treatment. Detox refers to the body’s biochemical ability, largely driven by the liver, to process and neutralize toxins. Drainage is the physical removal of those toxins through bile flow, bowel movements, lymphatic circulation, urine, sweat, and skin. When detox is activated without adequate drainage, toxins are mobilized but not effectively eliminated.
In CIRS, impaired detox and drainage are extremely common.
Chronic inflammation, low MSH, poor bile flow, constipation, lymphatic stagnation, dehydration, and nervous system dysregulation can all slow these pathways. When prescription binders are introduced without first supporting drainage, individuals are more likely to experience intense Herxheimer reactions—worsening fatigue, headaches, body pain, brain fog, nausea, skin flares, mood changes, or inflammatory crashes. These reactions are not a sign that binders are working better, but rather that toxins are being stirred up faster than the body can clear them.
Supporting detox and drainage before and alongside binder use is essential for tolerability and safety. Helpful strategies can include sauna therapy and sweating, dry brushing, vibration plates, lymphatic massage, castor oil packs over the liver or abdomen, maintaining proper hydration, and ensuring adequate electrolyte and mineral balance to support bile flow and elimination. Gentle movement, regular bowel habits, and nervous system regulation also play an important role in keeping these pathways open.
Because drainage involves every major system of the body, a structured and comprehensive approach matters. For those needing deeper guidance, we offer a complete detox and drainage guide that walks through supporting all major detoxification and elimination pathways in a CIRS-informed, tolerable way.
Immune System Modulation
At the core of CIRS is a profoundly dysregulated immune response driven by the biotoxin pathway. In genetically susceptible individuals, exposure to biotoxins triggers an exaggerated and persistent inflammatory cascade that the immune system is unable to shut off. Instead of resolving the threat and returning to balance, cytokines remain elevated, inflammatory markers stay active, and immune signaling becomes chronically distorted. The ultimate goal of the Shoemaker Protocol is to interrupt this cycle and guide immune function back toward a regulated, adaptive state.
However, for many individuals, especially those who have lived with CIRS for years, immune dysregulation extends beyond what a single pathway correction can immediately resolve. Long-standing inflammation, repeated infections, environmental stressors, and nervous system activation can leave the immune system either hyper-reactive or exhausted. In these cases, additional immune modulation may be necessary to help calm excessive signaling, support regulatory pathways, and improve resilience as healing progresses.
Immune modulation in CIRS is highly individualized and must be tailored to symptom patterns, lab markers, and overall tolerance. Support may include low-dose naltrexone (LDN) to gently regulate immune activity, targeted nutrient repletion such as optimizing vitamin D levels, and select herbal or amino acid supports like L-theanine to reduce inflammatory stress responses. Specific supplements may also be chosen to address elevated CIRS markers; for example, omega-3 fatty acids to help lower MMP-9 or resveratrol to support the regulation of TGF-Beta-1.
Sleep Optimization
Sleep is one of the most powerful drivers of healing in the body and becomes even more critical in complex chronic illnesses like CIRS. Deep, restorative sleep is when the brain clears metabolic waste, the liver and glymphatic systems support detoxification, tissues repair, hormones rebalance, and immune signaling resets. Without adequate sleep, inflammation remains elevated, detox pathways slow, and recovery becomes significantly more difficult, even when other aspects of treatment are in place.
Sleep disruption is extremely common in CIRS and is closely tied to low melanocyte-stimulating hormone (MSH), which impairs normal melatonin production and circadian rhythm regulation. On top of this, symptoms such as pain, anxiety, temperature dysregulation, histamine release, and nighttime cortisol spikes can further fragment sleep. Over time, poor sleep reinforces immune dysfunction and nervous system hyperarousal, creating a cycle that keeps the body stuck in survival mode.
Optimizing sleep usually requires a personalized, multi-layered approach. Support can include individualized supplements or sleep aids chosen based on tolerance and symptom patterns, wearing blue light–blocking glasses in the evening, reducing EMF exposure, and prioritizing a fat-rich dinner while avoiding common nighttime triggers such as bacon and cheese. Nervous system calming practices, such as breathwork, gentle stretching, or sleep-focused meditations, can help signal safety and readiness for rest.
Equally important are sleep hygiene and bedroom supports, including consistent sleep-wake times, darkness, temperature control, and minimizing environmental stressors. When sleep is properly supported, the body is far better equipped to detoxify, repair, and move forward in CIRS healing.
Movement and Exercise
Within CIRS care, perspectives on the timing and intensity of movement and exercise can vary, particularly within Shoemaker-focused practitioner circles. While caution around overexertion is valid, we believe that some form of supportive movement at any tolerated level is essential for recovery. Movement doesn’t need to look like traditional exercise to be therapeutic. Even gentle, intentional activity plays a meaningful role in healing.
Many individuals with CIRS experience a pronounced push–pull effect with exercise. Activity may feel beneficial in the moment, followed by delayed symptom flares such as fatigue, pain, brain fog, or inflammatory crashes. This exercise intolerance is driven by immune activation, mitochondrial dysfunction, autonomic nervous system dysregulation, impaired oxygen utilization, and ongoing neuroinflammation. When these systems are under strain, the body interprets exertion as a threat rather than a stimulus for adaptation.
Despite these challenges, movement remains deeply beneficial.
Physical activity supports lymphatic drainage, circulation, glucose regulation, detoxification, mood, and immune signaling. Movement also promotes neurogenesis, helping restore brain health and cognitive function that are commonly impaired by chronic inflammation seen in CIRS. It additionally reinforces nervous system regulation by teaching the body that safe, controlled stress can be tolerated.
For some, movement may begin with breathwork, light stretching, positional changes, or brief walks. Even individuals who are largely bedbound benefit from gentle range-of-motion work, diaphragmatic breathing, or short periods of upright posture if tolerated. The goal is consistency and safety. When movement is individualized and paced appropriately, it becomes a powerful adjunct support, helping recondition the body, reduce fear around exertion, and support long-term recovery in CIRS.
MCAS (Mast Cell Activation Syndrome) and Histamine Intolerance Management
Mast Cell Activation Syndrome (MCAS) and histamine intolerance are both conditions involving abnormal histamine activity, but they are not the same. MCAS is an immune disorder in which mast cells release excessive or inappropriate amounts of mediators, such as histamine, cytokines, and prostaglandins, leading to widespread, multi-system symptoms. Histamine intolerance, by contrast, typically reflects an impaired ability to break down histamine, often due to reduced diamine oxidase (DAO) activity or gut dysfunction. While distinct, these conditions frequently overlap, and both are extremely common in individuals with CIRS.
In many cases, CIRS itself acts as a root cause or a major contributor to MCAS and histamine intolerance. Chronic immune activation, low MSH, gut permeability, nervous system dysregulation, and ongoing inflammatory signaling all prime mast cells to become hyperreactive. As a result, symptoms such as flushing, headaches, rashes, gastrointestinal distress, anxiety, insomnia, heart palpitations, and food or supplement sensitivities can become pronounced and unpredictable.
Although long-term remission depends on addressing root-cause drivers, temporary symptom support is essential during treatment. Actively managing MCAS and histamine intolerance helps reduce immune noise, allowing the body to stabilize, tolerate binders and medications, and focus energy on deeper healing rather than constant reactivity.
Management is highly individualized and generally includes a low-histamine diet, low-histamine lifestyle strategies, and a tailored combination of herbal, over-the-counter, and prescription supports designed to stabilize mast cells or reduce histamine burden. Because MCAS and histamine intolerance symptoms overlap significantly with CIRS itself, as well as with common co-infections and comorbidities, working with a knowledgeable practitioner experienced in MCAS is critical for accurate assessment, safe intervention, and effective long-term care.
Advanced Adjunct Supports and Therapies
As CIRS treatment progresses, some individuals reach a point where foundational supports and core protocol steps are no longer enough to create forward momentum. This is especially true for those with long-standing illnesses, complex comorbidities, or repeated treatment plateaus. In these cases, advanced adjunct supports and therapies can be thoughtfully introduced to help address deeper layers of dysfunction that continue to limit recovery.
These therapies are not required for every patient and are not meant to replace core CIRS treatment. When used at the right time and in the right context, however, they can provide meaningful additional support, helping resolve stubborn symptoms, improve regulation, or restore capacity where progress has stalled. The key is personalization and timing, as advanced adjuncts are most effective when layered into care strategically rather than used prematurely or indiscriminately.
Fungal Colonization and Antifungals
Fungal colonization, including small intestinal fungal overgrowth (SIFO), is commonly observed in individuals with CIRS. Ongoing or prior mold exposure, chronic immune dysregulation, impaired gut defenses, and long periods of physiological stress create an environment where opportunistic fungi are more likely to colonize. In immune-compromised or chronically inflamed systems, fungal organisms can persist quietly and contribute to ongoing symptoms such as bloating, fatigue, brain fog, food reactivity, and inflammatory flares.
Within the Shoemaker practitioner community, the prevailing view is that CIRS is driven by immune dysregulation rather than fungal colonization itself, and that fungal issues should resolve as immune balance is restored through the protocol. While this can be true, we see a subset of patients in clinical practice who continue to experience symptoms despite proper remediation, strict adherence to the Shoemaker Protocol, and normalized inflammatory markers. In these cases, fungal colonization may represent a parallel burden that requires targeted intervention rather than passive resolution.
Addressing fungal colonization is not appropriate for every individual and must be carefully timed and personalized. However, for certain patients with persistent symptoms, treating fungal overgrowth can be an important adjunct that helps remove an ongoing inflammatory and immune stressor. We won’t explore this topic in depth here, but we have a comprehensive research article dedicated to understanding and addressing fungal colonization in the context of CIRS for those who need a deeper clinical framework.
IV PC (Phosphatidylcholine)
High-dose IV phosphatidylcholine (PC) is considered an advanced adjunct support in CIRS care and is typically explored later in treatment, especially for individuals who continue to experience roadblocks or slow progress despite addressing core drivers. Phosphatidylcholine is a phospholipid and a critical structural component of all cell membranes, including those in the brain, liver, mitochondria, and gastrointestinal tract. It plays a central role in membrane repair, cellular signaling, bile production, detoxification, and neurological resilience—systems that are commonly impaired in CIRS.
In the context of biotoxin illness, chronic inflammation and oxidative stress damage cell membranes, disrupt mitochondrial function, and impair detox pathways. High-dose IV phosphatidylcholine delivers PC directly into circulation, bypassing the gut and allowing for a therapeutic-level dose that can support membrane repair, improve cellular communication, and enhance detoxification capacity. For some individuals, this can translate into improved cognition, energy, detox tolerance, and overall resilience when other interventions have stalled.
IV PC can be particularly valuable for individuals with MCAS or histamine intolerance who struggle to tolerate oral supplements. Because IV administration avoids the digestive tract and first-pass metabolism, it is often better tolerated in highly reactive patients who flare with oral phospholipids. That said, oral phosphatidylcholine supplementation can still offer meaningful benefit at lower doses and may be an appropriate option for those who tolerate it well—especially given its greater accessibility and lower cost compared to IV therapy.
Nasal phosphatidylcholine is available as a prescription option, offering more targeted support for cognitive symptoms by delivering PC directly through the nasal–brain pathway. This can be especially helpful for individuals dealing with persistent brain fog, memory issues, or neuroinflammation who may not need or tolerate high-dose IV therapy.
Ozone Therapy and EBOO (Extracorporeal Blood Oxygenation and Ozonation)
Ozone therapy is an advanced adjunct modality that uses medical-grade ozone, a highly reactive form of oxygen, to support immune modulation, circulation, antimicrobial activity, and cellular signaling. In CIRS and other complex chronic illnesses, ozone creates a controlled oxidative stimulus that encourages the body’s own antioxidant defenses, improves oxygen utilization, and helps regulate chronic inflammation and immune dysregulation.
There are several forms of ozone therapy, and most IV ozone therapies also incorporate UVBI (Ultraviolet Blood Irradiation) as part of the treatment. UVBI involves exposing a portion of the blood to ultraviolet light before it is returned to circulation. This process has been shown to support immune regulation, reduce microbial burden, improve blood rheology, and enhance mitochondrial and redox signaling. The combination of ozone and UVBI is intended to amplify immune-modulating and antimicrobial effects while supporting overall circulation and cellular resilience.
High-dose IV ozone and ten-pass ozone involve multiple cycles of ozonated blood being infused back into the body during a single session, often alongside UVBI, creating a more intensive systemic therapy. Nasal ozone is a localized option commonly used for sinus, neurological, or upper airway support, while rectal ozone provides a gentler, non-invasive approach that can still offer systemic immune and gut-related benefits.
EBOO (Extracorporeal Blood Oxygenation and Ozonation) is a more advanced therapy in which a large volume of blood is circulated outside the body, filtered, exposed to ozone, oxygen, and typically UVBI, then returned to circulation. This allows for direct blood filtration, immune modulation, improved oxygen delivery, and reduction of inflammatory and infectious burden. For individuals with CIRS or long-standing, treatment-resistant illness, EBOO can provide an additional layer of support when progress has plateaued.
HBOT (Hyperbaric Oxygen Therapy)
Hyperbaric Oxygen Therapy (HBOT) is a therapy that involves breathing 100% oxygen inside a pressurized chamber. By increasing atmospheric pressure, HBOT allows significantly more oxygen to dissolve into the bloodstream and tissues than is possible under normal conditions. This heightened oxygen delivery supports cellular repair, reduces inflammation, enhances mitochondrial function, improves circulation, and promotes tissue regeneration—processes that are commonly impaired in CIRS.
For individuals with CIRS, HBOT can be particularly supportive due to its effects on neuroinflammation, immune regulation, detoxification capacity, and overall cellular resilience. Chronic hypoxia, impaired oxygen utilization, and ongoing inflammatory signaling are common features of biotoxin illness. HBOT helps counter these patterns by improving oxygen delivery to the brain and peripheral tissues, supporting neuroplasticity, calming inflammatory cascades, and assisting the body’s natural healing mechanisms. Some patients report improvements in cognition, energy, sleep quality, and recovery tolerance when HBOT is appropriately timed within care.
Pro-Tip: Elevation matters when choosing HBOT. In high-altitude locations, hard-shell chambers are required to reach therapeutic pressure levels. In areas closer to sea level, soft-shell chambers may provide some supportive benefit, but true medical-grade HBOT that’s capable of delivering higher pressures and clinical oxygen concentrations is only available in hard-shell chambers.
CIRS Adjunct Therapies FAQ
Here are some of the most frequently asked questions our private practice receives regarding CIRS adjunct therapies and supports:
What adjunct supports are most helpful when the Shoemaker Protocol alone isn’t enough?
Adjunct supports are selected based on where a patient is stalling. The foundation supports listed above are the most commonly needed. We recommend exploring the foundational supports first before considering the advanced therapies.
How do I know if my symptoms are from CIRS itself or from a comorbidity like MCAS, SIBO, or mold-related fungal colonization?
Symptom overlap is common, which is why clinical pattern recognition, timing, and response to interventions are essential for accurate differentiation. Making lists of symptoms with context in mind can help further delineate symptoms that don’t overlap and help you troubleshoot what these signs mean.
Can adjunct therapies slow down or interfere with the Shoemaker Protocol?
When poorly timed, adjunct therapies may not provide any additional benefits but shouldn’t interfere or slow down progress from the Shoemaker Protocol. We recommend working with a knowledgeable holistic functional practitioner to find appropriate timing when considering adjunct supports and therapies in order to make the most of your time and resources.
Why do some people struggle to tolerate binders even when they’re following the protocol correctly?
Poor detox and drainage, herx/die-off reactions, inadequate lipid replacement therapy, nervous system dysregulation, gut dysfunction, MCAS, comorbidities and coinfections like vector-borne illnesses, mineral and hydration imbalances, and being in ongoing exposure can all worsen binder reactions despite correct dosing.
Should gut healing be addressed before starting the Shoemaker Protocol?
In many cases, yes—patients with better gut integrity and digestion often tolerate binders and later protocol stages with fewer setbacks.
Is nervous system regulation really necessary if CIRS is an immune illness?
Yes, immune signaling, inflammation, detox capacity, and treatment tolerance are all heavily regulated by the nervous system, making mind-body work foundational rather than optional for many patients.
Is the carnivore diet required for CIRS, or are there cases where carbohydrates are still needed?
A heavily meat-based, low-amylose diet is strongly supportive for CIRS, but some individuals temporarily require limited carbohydrates based on metabolic, hormonal, or nervous system needs. When choosing to include carbohydrates in your diet, we recommend opting for organic, in-season, and low-amylose options to reduce overall toxin burden.
When should advanced therapies like IV phosphatidylcholine, ozone, EBOO, or HBOT be considered?
These are typically explored later in care when foundational work is solid but progress has plateaued, and only when timing, tolerance, and clinical context are appropriate. However, some individuals find symptom management benefits with these therapies before or during the Shoemaker Protocol. Work with your trusted CIRS practitioner for personalized support.
How do you determine which adjunct supports a specific CIRS patient actually needs?
We use a personalized, root-cause approach that integrates labs, symptom patterns, history, tolerances, and response to care rather than blanket recommendations. Each case is different and requires a nuanced perspective.
Is full recovery from CIRS still possible after years of illness?
Absolutely. Longer illness timelines often require more layers of support, but with the right strategy, healing and remission are always possible.
Closing Thoughts On CIRS Adjunct Supports and Therapies
At the heart of our work is a deep commitment to continually learning, refining, and exploring additional adjunct therapies that can support healing. In a perfect world, strict environmental remediation, a Carnivore-based diet, and following the Shoemaker Protocol would be enough for every individual with CIRS. While these foundations are powerful and can move the needle, clinical practice has shown us that complex chronic illness rarely follows a single, predictable path. Many people require additional layers of support to address roadblocks, restore tolerance, and reach true root-cause healing.
What we’ve learned over time is that plateaus are information. When progress stalls, it typically signals that another layer is asking to be addressed and not that healing is out of reach. There are always more answers, more tools, and more opportunities for troubleshooting when care is personalized, patient, and thoughtfully guided. Healing with CIRS may take creativity, persistence, and support, but it is never a lost cause.
For those who want to hear real-world, anecdotal experiences from others walking this path, we invite you to join our CIRS and Chronic Illness support group, where patients and clients openly share their personal journeys with adjunct therapies, setbacks, breakthroughs, and hard-won progress. Most importantly, we want you to know this: never give up hope. Even when the path feels long or uncertain, healing is always possible, and you do not have to walk it alone.
Work With Our Trusted CIRS Functional Medicine Practitioners
Our Empower Functional Health practice is honored to be trusted CIRS functional practitioners, supporting patients and clients from around the globe. We’re passionate about helping individuals achieve root-cause healing in order to live the life they are meant to, nearly symptom-free. We provide environmental illness thought leadership and evidence-based insights, paired with clinical pearls, to help you achieve your wellness goals. We welcome you to explore our free resources, and if you find that self-troubleshooting falls short, we’re here to guide you with personalized support and protocols. If you’re interested in working one-on-one with our CIRS functional team for your environmental illness healing journey, our CIRS Discovery Call is the best place to begin.
DISCLAIMER: This content is for educational purposes only. While we are board-certified in holistic nutrition and are functional practitioners, we are not providing medical advice. Whenever you start a new diet or protocol, always consult with your trusted practitioner first.
