Rebuilding your Gut Microbiome to Heal Lyme, Autoimmune Disease, and other Chronic Illnesses.

Rebuilding your Gut Microbiome to Heal Lyme, Autoimmune Disease, and other Chronic Illnesses. 1

After years of suffering with chronic fatigue, depression, anxiety, joint pain, skin problems, constant colds, malabsorption of nutrients, and a complete lack of resilience in life, I finally found my way out. It was long, lonely, and difficult path to healing, but it has been worth every step. Eventually I got some official diagnosis of Lyme disease, PTSD, small intestinal bacterial overgrowth and some other gut and central nervous system infections including klebsiella pneumoniae and enterobacter cloaca. Western doctors were completely useless in my quest to understand what was going on with me. Luckily, I had a background in neurobiology and started researching the existing literature on autoimmune conditions. I then ended up under the care of an amazing naturopathic doctor, Dr. Heath Mcallister at his facility Pure Vitality Rejuvenation Center.

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I did a lot of research, and a lot of trial and error. I had to employ multiple modalities, all hitting a different angle. They were all crucially important together, and eventually after persistence and determination, I got better. Now, taking this valuable knowledge I became able to provide nutritional consultation for other people suffering with autoimmune conditions, lyme disease, depression, anxiety, gut issues etc. I realized that so many of these people were being negatively affected by the illness and struggled financially, something I definitely experienced myself.

I decided to make this guide available for free so that those with the motivation can take their healings into their own hands.

This protocol is appropriate for a variety of chronic, inflammatory conditions such as lyme, chronic fatigue, fibromyalgia, depression, anxiety, addiction, joint pain, mild inflammatory bowel conditions, epstein barr virus, brain fog, mold exposure, food sensitivities, allergies, indigestion, constipation, eczema, acne, recurrent colds etc. All supplements have links provided to purchase brands that I recommend, based on the cleanliness, bioavailability and quality of their supplements. Note: The link are affiliate links, so I do get 5% of any purchases you make, at no additional expense to you. 

What is an Autoimmune condition?

If you’re reading this, unfortunately you or someone you love is likely affected by an autoimmune condition. According to the American Autoimmune Related Disease Association (AARDA), approximately 30% of American’s have some type of autoimmune condition. There are over 100 autoimmune conditions defined in the medical literature. They express as different symptoms but many experts agree that the etiology is the same. Meaning, THEY ALL HAVE THE SAME ROOT CAUSES. The same mechanisms are seen in all of these autoimmune conditions despite the differences of symptoms. The incidence of autoimmune problems are rising globally, particularly in the US where the Standard American Diet (SAD) is prolific. An autoimmune disease develops when your body’s immune system treats healthy cells in your body as foreign cells and attacks these healthy cells. Autoimmune disease refers to illness or disorder that occurs when healthy tissue (cells) get destroyed by the body’s own immune system.

What causes an autoimmune condition?

In a nutshell, a chronic stressor. or two. Usually the cause of an autoimmune condition is multifactoral, but the consistent pattern is that there is some chronic stressor to the body that compromises the individual overtime until there is some big hit that is finally the straw that breaks the camels back. The person’s body goes all caddy-whompus and thus the obvious symptoms of an autoimmune condition emerge after a long gradual cultivation period. Sure, some people have genes that make them more or less susceptible to an autoimmune condition developing, but many of the genes that they have linked to autoimmune conditions are largely dispersed amongst the majority of the population, so obviously genes aren’t the whole story. There are a variety of things that can act as a chronic stressor including:

  • Chronic infections such as lyme or herpes

  • Mold exposure

  • Bacterial and fungal overgrowths in the gut microbiome

  • Exposure to toxins in food, air, water, pillows, plastics, cleaning products etc.

  • Emotional trauma or stress

  • Advanced glycated end products (result of sugary, unhealthy processed foods)

Chronic Infections

Often times there are chronic infections as part of the equation such as the bacteria that causes lyme disease borrelia burgdorferi, the epstein barr virus, herpes, or other bacterial/viral infections that put stress on the systems. Organisms that live in your gut can become overgrown and crowd out “healthy” bacteria and can become pathogenic and qualify as a mild infection once they overgrow to a certain point. This is something you see a lot with Candida albicans (yeast), H. pylori, streptococcus strains and many other bacteria that normally reside in our gut. When there is an imbalance or overgrowth occurring in the gut, this is often one of the first problems that contributes to an autoimmune condition arising. This can lead to something called “Leaky Gut” which we will discuss in more detail later.

Recent research has been highlighting the importance of the Microbiome, or microbial population balance in the gut environment, on our health and well being. Antibiotics and pesticides on fruits and vegetables can wipe out existing “good” bacteria in the gut, and allow “bad” bugs to overgrow and over colonize. The microbiome is especially important for dictating brain health, the immune system, metabolism and inflammation. When your immune system is constantly trying to keep a current infection at bay, whether it be an imbalanced microbiome or Borellia burgdorferi, it will compromise your immune systems ability to prevent other organisms from coming in and settling down inside your body.

Mold exposure is also a big trigger of autoimmune conditions. Very often living in a moldy house or working in a moldy building will bombard your body with mycotoxins, compromise the immune system, and then allow opportunity for some other infectious organisms to take hold and thrive. Often times people affected by Lyme disease have also had mold exposure. Many mycotoxins are potent neurotoxins and damage the nervous system. Mold exposure can lead to immune reactivity to small amounts of mold in food such as peanuts, chocolate, coffee, nuts or powdered herbs like ginger, or turmeric.


With our modern day diets, pollution, and manufactured products, it’s nearly impossible to avoid exposure to toxins. It is estimated that each child is born with approximately 229 synthetic man-made known toxins already circulating the blood stream. A toxin can be loosely defined as a substance that causes some sort of cellular or  tissue damage. In many cases, people with autoimmune conditions have developed something called leaky gut, which contributes to developing food sensitivities.

Foods can have toxic proteins or compounds in them that can actually inflame and damage our gut. Often times, people with an autoimmune condition are reacting to the toxic gluten protein in wheat, as well as the casein protein in dairy. Then there are other things such as lectins, oxalates, and alkaloids that are harming the sensitive gut of the already inflamed individual. Heavy metal buildup also appears to be common in people with autoimmune conditions, with many of them having an innate metal metabolism defect.

Emotional Trauma

Emotional trauma is one of the primary root causes of the development of an autoimmune condition. Now, at first glance, that can sound a bit like quackery right? Actually, there is some solid scientific exploration into this, and some physiological theories that make sense. Scientific research has illustrated that people with increased Aversive Childhood Experiences (ACE’s) are statistically more likely to be hospitalized as an adult for the autoimmune disease. Studies looking at fibromyalgia patients, a type of autoimmune condition, who are primarily women, show that 65% of women with fibromyalgia experienced sexual abuse as a child.

Now, anecdotally, I have found the presence of unresolved trauma to be curiously present in almost everyone I’ve ever met with an autoimmune condition. Sometimes you see someone who likely had some underlying food sensitivities or chronic infection brewing under the surface and then something traumatic or upsettling happens and triggers the onset of their symptoms.

One convincing explanation is the physiological effects of chronic emotional stress. Elevated stress hormone has numerous documented detrimental effects on all sorts of body systems, especially the immune system. When something traumatic happens or a person is in a long-term chronically stressful environment such as an abusive household, the body becomes stuck in this chronic sympathetic nervous system stress response. This causes an array of issues such as depleting nutrients, burning through neurotransmitters, causing inflammation, suppressing the immune system, and inhibiting digestion and nutrient absorption.

When the body thinks it is in danger, it shuts down all processes that arent necessary for survival in that split moment. It prepares you to run from the lion, allocating all your extra resources to your muscles and your heart to flee. This process shuts down the parasympathetic nervous system response as a result, suppressing digestion and the immune system. When someone’s nervous system is stuck in this flight-or-flight mode, it downstream affects immune modulation, inflammation, and digestion. Being in this state compromises the body and makes it a sitting duck for some opportunistic organisms to take up residence while you’re immune system is down.

What is a Leaky Gut?

Rebuilding your Gut Microbiome to Heal Lyme, Autoimmune Disease, and other Chronic Illnesses. 2In the intestine, there is a thin layer of cells that line the gut called the epithelial layer. It is only one cell thick. The cells in this lining are linked together by something called tight junctions. They act as little gates, keeping cells connecting and not allowing any particles through that havnt gotten the green light to pass through into the blood stream. Normally the body breaks down proteins, fats and carbohydrates into smaller pieces such as amino acids, fatty acids and glucose. Once broken down, the cells in the epithilial layer have specialized transporters that grab nutrients and bring them across the epethelial layer and deposit them into the blood stream to be carried to other parts of the body and nourish those cells. The body has very careful selective mechanisms for deciding what nutrients get through at what point in the digestive process. This functions to keep out undigested food fragments or potentially dangerous bacteria.

Bacterial overgrowths, pesticides on food, and inflammatory proteins such as gluten, can loosen tight junctions that seal cells of the gut lining together. When this happens, you get these gaping holes in the gut, making it permeabile like a cheesecloth. Now, large undigested food fragments and bacteria can slip past these epithelial cells and go straight into the blood stream. The body recognizes that these particles do not belong there, and quickly launches an immune response. This is the beginning of food sensitivities.

Say you develop a leaky gut that is allowing food particles to prematurely enter the bloodstream due to damaged tight junctions. Now you are eating a banana every day. Little pieces of the protein chains from that banana continue to slip through the cheesecloth gut you have, and into the blood stream. Your body starts to recognize that this is happening consistently when you eat bananas. It responds by now launching an immune attack every time you eat an banana,. You now have a banana food sensitivity and everytime you eat a banana, you feel tired, depressed and inflamed.

Learn more about Leaky Gut Here.

What is the difference between a food sensitivity vs a food allergy?

A true allergy is defined by the type of immunoglobulin molecule that responds to the allergen. If someone has a peanut allergy, when they consume peanuts they have what is called an IgE mediated immune response. These type of responses can be very dangerous and cause something called anaphylactic shock. This can be deadly. True allergies can commonly occur in response to nuts, pollen, mold, and various other foods. This is defined by the presence of the IgE mediated response (immunoglobulin E).

A food sensitivity is also an immune response, but it takes a different molecular pathway and often involves IgA and IgG antibodies. Generally the effects are more like a cascade of events in the body than an immediate reaction. Sometimes people who are having an IgA or IgG mediated immune response to a food will not even know because the peak effects occur 1-2 days after the consumption. These food sensitivities do not cause anaphylactic shock like an IgE allergy but they have more long-term damaging effects.

Learn More  The Top 4 Best Probiotics for Mood and Anxiety

Mast Cell Activation and Dysfunction

Mast cells are a type of immune cell that mediates many immune responses. They are notoriously involved in releasing histamine and initiating an allergic response in the body. They are also important for determining if a bacteria is friend of fo, immune tolerance of food-based proteins, and blood-brain-barrier function. Recently, the implication of rogue mast cells has become more and more apparent in their connection to autoimmune conditions, food intolerances and inflammatory diseases. When mast cells are chronically exposed to some sort of allergic trigger, such as an allergenic protein in dairy, mold toxins, or even pathogenic bacteria, they can get overwhelemd, disoriented and hypervigilant. This is called Mast cell activation. The mast cells can become so dysregulated that they blindly launch histamine-mediated reactions to virtually anything. This usually results in multiple food sensitivities and inflammation and fatigue after eating virtually any type of food, even “safe” foods”. You can eat a pristine diet, build the perfect microbiome and still have major reactivity. The reason is because even though your gut bacteria are balanced and you’ve removed most inflammatory foods, your mast cells have still gone bizurko and are over-reacting to every little thing. Even though western medicine claims that Mast Cell Activation syndromes have no cure other than lifetime management with steroids, this is simply not true. Unruly Mast cells can be tamed and returned to a normal state of response. I’m living proof of this. Interestingly enough, different prebiotic dietary fibers seem to help reduce mast cell activation by feeding good bacteria that produce butyric acid as a short-chain fartty acid biproduct. The butyric acid appears to reduce mast cell release of histamine and other pro-inflammatory cytokines. Addressing this is included in the step by step guide below.


When an individual has a bunch of biotoxins, heavy metals, or infectious organisms in their body, often their body can get sorta of “clogged up” and unable to effectively shuttle out toxins from the body. Many people with autoimmune conditions have innate or acquired compromised detox pathways. People with the HDL DR gene polymorphism, tend to have problems with their immune systems identifying the biotoxins secreted by organisms like lyme, candida, and mold. Therefor they never get properly disposed of. When this happens, someone can have whats called “biotoxin illness” where it’s actually just the biotoxin load not getting removed that keeps them sick, even if their levels of lyme or mold exposure are quite low.

This makes it especially uncomfortable when you are doing the microbiome antimicrobial cleanse, which is usually accompanied by “die off” effects and increased biotoxin released as organisms burst open and die. In some cases, you should start the biotoxin binding agents before doing any antimicrobial cleanse. There are some things that can act as binders, attaching to these molecules and helping to remove them from the body. Below are some suggested binding aids  if you feel like your body is having a hard time detoxing the bad stuff out. The modified citrus pectin and charcoal are best to take 2 hours before or after any meal, so that they do not simply bind to nutrients in your food.

Glutathione: Glutathione is the most abundance antioxidant that your body produces. Not only does it prevent and repair damage from free-radical compounds, but it also acts as a binder, shuttling heavy metals such as mercury, and lead out of the body. This is a supplement that is overall very beneficial to all aspects of health. a liposomal form is best, or you can take N-Acetyl Cysteine, which is a precursor to glutathione. Learn more about glutathione.

Modified Citrus Pectin: Modified citrus pectin is derived from the naturally occurring citrus pectin, and altered to be a shorter chain of molecules, and therefor absorbable by the body. It has significant clinical research in regards to it’s use in cancer, heart disease, inflammation and immune health. studies show that it binds to heavy metals and biotoxins and excretes them through the urine. It also blocks an inflammatory signalling molecule called galectin 3, which prompts cell to build fibrous tissue, which is great for biofilms and biotoxins to hide. Learn more about modified citrus pectin.

Activated Charcoal: Activated charcoal is a godsend for when you eat a food that wasn’t kind to you. If you’re like me, and have reactions to everything, eating out creates a lot of anxiety. Luckily if you do get hit with something, taking activated charcoal can relieve the damage quite a bit. It’s also great for removing biotoxins directly from the gut, as organisms in the gut start to die during a cleanse. Take activated charcoal within 3 hours after eating a triggering meal, or take it in between meals to remove toxins from microbiome bacterial  overgrowths. Learn more about activated charcoal.

These are the binders I have had good experiences with, but there are others you may want to look into.

How do I apply all of this information to my own healing?

Here is a summarized outline of the actions required to heal from an autoimmune condition, lyme disease or chronic fatigue syndrome.

  • Clear out existing overgrowths and infections
  • Remove inflammatory and problematic foods from the diet.
  • Heal the lining of the gut and reduce “leakiness”
  • Reinoculate the microbiome
  • Reduce  exposure and eliminate toxins
  • Restore proper Mast cell function
  • Retrain the nervous system

Below is a step-by-step guide on what tools you can use to do this.

A: Clearing out infections and rebuilding the microbiome.

As mentioned earlier, chronic infections and intestinal overgrowths are commonly a perpetrator of autoimmune conditions. There are several ways you can target this process from multiple angles via herbs, diet, fasting, probiotics etc. I suggest doing all of them simultaneously to stop the bacteria from having any chance to resisting your efforts.

1. Antimicrobial herb regiment.

Rebuilding your Gut Microbiome to Heal Lyme, Autoimmune Disease, and other Chronic Illnesses. 3Using antimicrobial herbs is one of the most important pieces of your healing process. This regimen will require you to invest some cash on products, and have to swallow a large amount of capsules every day, but it is absolutely crucial and I guarantee, you will not achieve optimal health without this step. Taking multiple herbs at once, and then cycling off to a different combination is a great way to make sure that no organism can sneak past. Each herb contains it’s own unique combination of antibiotic compounds that target different types of bacteria, fungi and viruses. Not only do they contain natural antibiotic properties, they also contain prebiotic fibers and polysaccharides that can feed beneficial bacteria as well, making them more effective and less detrimental to commensal flora than a pharmaceutical antibiotic.

Why not use pharmacuetical antibiotics to do this? There are a few problems with conventional antibiotics for this purpose. One, antibiotics typically only contain one type of compound. This usually means it has a limited number of species that it will effectively target.  This tends to wipe out lots of commensal or beneficial bacteria, and not wipe out all the bad, giving them opportunity to over colonize now that the competition has been wiped out. Many times antibiotics were a main contributor to the gut microbiome dysbioisis in the first place.

Also, infectious organisms, especially lyme, are particularly good at evading the immune system and hiding where antibiotics can’t reach them. Herbs have been shown to more effectively reach even dormant forms of bacteria by dissolving their protective biolfilms. Also, with this type of treatment, you generally need a long-term antimicrobial treatment. Being on pharmacuetical antibiotics long term often has detrimental effects, given the toxicity of the antibiotics to our mitochondria, nervous system and microbiome. Herbs offer a more sustainable and safe way of killing organisms over a long period of time. Plus, as I mentioned earlier, they aren’t simply killing bacteria. They are often selectively killing pathogenic and overgrown bacteria, while providing prebiotic food that boosts beneficial bacteria and promoting bacteria diversity.

They not only act as an antibiotic, but also boost good bacteria and help heal and support your body’s own immune system, allowing it to participate in eliminating these chronic infections. They provide anti-inflammatory, immune modulating, and nourishing effects as well. Human beings evolved consuming medicinal plants for thousands of years, and it is my belief that healthy bacteria in the gut have co-evolved with us consuming these plants and are therefor less likely to be negatively effected by the herbs than a pathogenic strain that did not co-evolve to occupy the human gut in the way we see due to modern lifestyle (ei. candida overgrowths due to increased sugar consumption).


Step 0 : Biotoxin Removal Protocol with Modified Citrus Pectin

Before we blast out a bunch of infectious organisms or overgrown yeast, we need to make sure the body can actually effectively removed biotoxins, otherwise you could potentially feel more sick after doing the cleanse.

Start with 1 capsule of Modified Citrus Pectin to see how your body responds. If you take a full dose immediately, it may cause you to detox too quickly. Adjust dose according to how your body is responding. Go slow.

Take on an empty stomach first thing in the morning. Allow atleast 30 mins-1 hour before eating or taking any other supplements. You can repeat this in the afternoon between meals if you like, depending on how fast you’d like to detox and how your body is handling the process. You may want to continue this protocol for several months, increasing your dose over time. Do the modified citrus pectin alone for 1 week daily before starting the antimicrobial cleanse.

Antimicrobial Herb Cleanse

*Note: When doing any antimicrobial protocol, “die-off” effects may leave you feeling lethargic, achy, depressed, diarrhea or cause some intestinal cramping. These are all normal symptoms and are an indication that the herbs are killing off bacteria. This usually only lasts a couple of days. If you can, try to push through it and continue the regimen. If after 6 days, you are still experiencing fatigue or discomfort with no improvement, back off or discontinue the herbs.

STEP 1: First Round of Antimicrobial Herbs

For first 2 weeks, I recommend this regimen of herbs

Take this full combination 2 times a day for 2 weeks on an empty stomach if possible. I suggest morning before breakfast and afternoon or evening before dinner. Sometimes the herbs can energize you at night, so best to take 2nd dose in afternoon.  

*If you find that you are more sensitive, or experiencing heavy dieoff, just go with the herbs with the *asterisk next to them and skip the others for now. You can also reduce dosage at any time. Listen to your body.

*Goldenthread– 2 capsules

Morinda (noni)– 3 capsules

*Artemesia (Chinese wormwood)– 3 capsules

*Zenbiotic spore probiotic– 2 capsules-at night before dinner.

After 14 days, discontinue the herbs. Then you start another 2 weeks on a different set of herbs.

STEP 2: Second Round of Antimicrobial Herbs

Take 2 times per day for 2 weeks on empty stomach.

*Melia (neem)-2 capsules

AC formula II– 2 capsules

*Woad– 3 capsules

*Zenbiotic spore probiotic– 2 capsules-at night before dinner.

After 2 weeks, discontinue.

STEP 3: Reinnoculate and Normalize Mast Cell Activity (a 2 fer 1!)

Immediately after finishing your 2nd round of herbs, you will start the reinoculation process where you use probiotics and prebiotic to feed beneficial bacteria and regrow a new population dynamic in your gut! You may remember the mast cell activation that we mentioned earlier. Luckily, the secret in reducing mast cell activation is in prebiotic fibers, which also happen to feed the good bugs.

Follow this regimen for as long as you like. You can use this as a daily maintenance regime for continued health. You can always revisit the antimicrobial herbs if you feel that you have slipped back in progress or become out of balance again.

Prebiotics should be eaten on an empty stomach for best effects.

2 TBSP of Organic Psyllium Husk Powder– Add water, stir and consume promptly. Wait 30 minutes before taking any other supplements.

*Zenbiotic spore probiotic– 2-3 capsules a day before a meal

Add some Arabinogalactan Larch Extract, a powerful immune boosting pre-biotic to a drink and take 2-3 times daily

Take one scoop of Hyperbiotic Prebiotic, a combination of green banana flour, acacia fiber, and jerusalem artichoke fiber.

Take 1/4 TBSP or 400 mg of PEA (Palmitylethanolamide). . This is a natural  fatty acid amide that reduces inflammation in the nervous system as well as reduces mast cell activation.

*If you are highly sensitive to probiotics, open up the capsules to adjust dosage. Start small and gradually increase until your body is no longer reacting.

Optional: Take 2 capsules or make a tea out of some Slippery Elm extract 2 times per day.Use 1/4 tea spoon for tea.

STEP 4 (optional): Third Round of Antimicrobial Herbs (gentle)

Only take if you feel there is still clearing out that needs to happen. If the other rounds of herbs produce extreme effects, you can substitute these herbs instead. Take 2 times per day for 2 weeks.

Chrysanthemum- 3 capsules

Dan Shen– 3 capsules

Schizandra– 2 capsules

Eluethero– 1 capsule

After 2 weeks, discontinue.

(Only necessary if you did STEP 4) STEP 5: Reinnoculate Repeat

Repeat STEP 3 with:

2 TBSP of Organic Psyllium Husk Powder

*Zenbiotic spore probiotic– 1 capsule-at night before dinner.

Arabinogalactan Larch Extract, a powerful immune boosting pre-biotic to a drink and take 2-3 times daily

One scoop of Hyperbiotic Prebiotic

 1/4 TBSP or 400 mg of PEA (Palmitylethanolamide). 

Optional: Take 2 capsules or make a tea out of some Slippery Elm extract 2 times per day.Use 1/4 tea spoon for tea.

Darkness before the Dawn

At this point, you should feel tremendously better. After doing the initial cleanse, you can repeat any of the steps at any time if you feel like you need a reset or that there is still stuff left to clear out. You are likely to experience something called “Die-off” for a few days after starting your new herb regiment. Also called the herxeimer effect, Die-off occurs when many organisms are being killed by an antibiotic or herb and are dying and consequently bursting their cells open and releasing endotoxins such as lipopolysaccharide (LPS) . This can create a variety of symptoms as the body works to shuttle out all the dead bacterial debri. It’s common to feel lethargic, achy, have diarrhea, intestinal cramping,  or feel a little grumpy. This generally only lasts a few days and gets better over time. If feelings of sickness persist past a week, discontinue the herbs, take a break and later try switching to a different combination.  Each round of herbs you’ll likely experience some die-off. Generally when someone is having these symptoms, it’s a good sign that the herbs are working and that they are clearing out a lot of infectious organisms.

Learn More  How brain chemistry can influence our perception, reaction, and interpretation of life.

***If someone is particularly sensitive to die-off symptoms or highly reactive to herbs, you can start with the 3rd (gentle) set of herbs prescribed above in STEP 4 (the chrysanthemum, dan shen etc.) because they are very mild and generally don’t drop a huge bomb like some of these herbs. You can also reduce your dosage by half if needed. I encourage you to just push through it if you can though. The sooner you clear things out, the sooner you’ll feel great.

2. Kambo

Rebuilding your Gut Microbiome to Heal Lyme, Autoimmune Disease, and other Chronic Illnesses. 4Kambo is a traditional amazonian medicine in which the skin secretion of the Giant green Waxy treefrog (phyllomedusa bicolour) is collected and then applied to burn marks made the the person skin. The skin secretion contained hundreds of bioactive peptide molecules that have been studied scientifically for a multitude of medicinal purposes. Many of the individual peptides are pharmacuetical medications or are  on their way to becoming one. These peptides exhibit potent antimicrobial, anti-cancerous, anti-inflammatory and immune modulating effects. Kambo has been effectively applied to a variety of conditions such as depression, anxiety, addiction, chronic pain, autoimmune conditions, chronic fatigue, lyme disease, herpes, arthritis, cancer and more.

The experience involves a purgative effect in which toxins are pulled out of various tissues in the body and vomited out. It is quite a potent detox tool. It also has a strong spiritual element and can help resolve stuck energetic blockages, negative emotions, or trauma stored in the nervous system and body. Kambo is not hallucinogenic.

Kambo in conjunction with the antimicrobial herbs has been very powerful to killing infectious organisms like lyme and candida. It has been one of the most impactful tools on my personal recovery. It is generally a very safe procedure and is 100% legal. The medicine provides a holistic healing experience by addressing the physical, emotional and spiritual imbalances causing dis-ease. As far as a treatment that delivers a lot of power, Kambo can accelerate your healing process and open new doors of your healing path that you werent even aware of.  You can learn more about Kambo here

B. Dietary changes

  1. Eliminating problematic foods

This should ideally be done at the same time as the herb clearing regimen.


Eliminating foods that are hurting you, and replacing them with foods that are healing you is crucial to healing your gut and autoimmune coition. Anyone with an autoimmune  or chronic health condition that is still eating gluten (wheat) and dairy, I would highly recommend that you consider cutting these both out. These are 2 of the most inflammatory foods and have been clinically shown to damage the gut, lead to microbial overgrowths, and contribute to rampant inflammation

If you are reacting to gluten or to dairy, chances are you are also reacting to both, because gluten and casein (a protein in dairy) have a very similar protein arrangement and often times antibodies towards one will attack the other. Gluten and Casein are opioids and act on the opioid receptor sites, causing disruption, inflammation and even addiction to the foods that contain them. You can read more about why Gluten and Dairy are so problematic for compromised individuals

If possible, I suggest you see a naturopathic doctor or nutritionist and get a food immune antibody test. Ideally that looks at both IgA and IgG antibody responses. You’ll likely have some foods on there that you didn’t realize were immune challenges for you. Sometimes it can be something very random like green beans, or pears.


Sugar is another food substance that can be detrimental. The processing of sugar by our body’s results in something called glycated end products. These yield damaging free radicals which can destroy cellular tissue and cause inflammation. Sugar also tends to feed infectious and overgrowth organisms, contributing to yeast overgrowth. Sugar also feeds cancers. You can read more about the detrimental effects of sugar here.


Many times, people will have to eliminate grains for a period of time to fully heal their gut and autoimmune condition. Grains contain a number of inflammatory proteins, antinutrient binding substances, enzyme inhibitors and are typically starch heavy, meaning they also feed bad bacteria and yeast. Read more about why grains may be problematic for you here.


The nightshade family, scientific name the Solanaceae, are a group of edible and non-edible flowering plants. This family contains potatoes, tomatoes, bell peppers, paprika, eggplants, chillis, tomatillo, and gogi berries. It also contains some psychoactive plants such as tobacco and datura. The nightshades have varying levels of toxicity to them, and for about 20% of the population, they are inflammatory. Studies have shown that nightshade spices such as cayenne and paprika actually increase intestinal permeability (aka leaky gut). The nightshades all contain a compound called solanine, which is toxic. For some people, eliminating nightshades is a crucial part of their healing process.  The ayurvedic herb ashwaganhda is a nightshade, but is the only member of the nightshade family that does not contain solanine. Read more about nightshades here.


Histamine intolerance is very common in autoimmune patients. Often times people with a chronic condition have an MTHFR gene variant which inhibits their ability to methylate molecules in the body. This “undermethylater” biotype typically correlates to increased amounts of histamine in the body. When someone has elevated histamine, they may be prone more to seasonal allergies, dust, mold, and react to foods that are high in histamine. Rogue mast cell’s as mentioned above, also tend to increase histamine levels. Foods high in histamine include spinach, avocado, nuts, vinegars, fermented foods, chocolate, tomatoes, citrus fruits. You can learn more about histamine intolerance here.


Many times people are having immune responses to things like chocolate, soy, eggs, nutritional and brewers yeast (I highly suggest you stay away from added yeasts), MSG (monosodium glutamate), coffee, Be sure to investigate these as well. Tune into your body and pay attention to what you ate before you started feeling grumpy, tired or inflamed.

2. A Ketogenic diet

A ketogenic diet is one that is generally high fat, low carb and medium protein. The premise of it is that you deprive your body of access to glucose, and it switches to burning ketone body’s from fat metabolism as an alternative. There has been ltos of research on ketogenic diets as medical interventions for people with epilepsy, cancer, diabetes and chronic inflammatory conditions including autoimmune disease. A ketogenic diet has epigenetic effects on genes that play a crucial role in immune response and inflammation. In addition to being a great tool to combat inflammation and a wonky immune and nervous system, it also starves out organisms that thrive on sugar and cancer cells. Infectious bacteria and yeast LOVE sugar aka glucose. When you swithc into ketosis, these bacteria and such can’t metabolize ketones as an alternate fuel source, so they end up starving. I highly suggest doing a ketogenic diet in conjunction with the antimicrobial herb routine to hit the bad bugs from all angles.

I have found that in the beginning it can be helpful to go on a ketogenic diet and oscillate between ketosis and eating low-glycemic index carbohydrates. I had to strictly eliminate grains for about 1.5 years, and also couldn’t tolerate fruit. I was mostly in ketosis for this entire time, and then slowly was able to tolerate carbohydrates without the intense inflammatory, disruptive effect that had given me in the past. You can learn more about a Ketogenic diet here.

3. What on earth do I eat then?

It may seem like I just told you to give up a million things. and the truth is, I kind of did. But there’s still a lot of amazing things you can still eat. Quality organic meats, eggs, vegetables, nuts and seeds are great. You don’t have to cut out all of the things I described above, they are just potential problematic foods. I recommend eliminating one thing at a time for a month or so,and then reintroducing it to see how it makes you feel. Generally, you don’t know something is making you feel crappy until you remove it from the diet, and then reintroduce it.

Eating organic, clean, nutrient dense whole foods is vitally important. Pesticides have endocrine-disrupting and gut inflaming effects and can exacerbate symptoms. Be sure to buy meats and animal products that have no added hormones or antibiotics. In general, try to use single ingredient food items to create your own dishes, rather than processed items that contain many things, including chemical additives, preservatives and artificial colors and flavors.

Here are a couple of anti-inflammatory eating guides to help you start.

30-day autoimmune Reset diet plan.

C. Eliminating toxins

We’ve already talked quite a bit about eliminating toxic foods and why buying organic meat and produce is important. Lets talk about some other less, obvious ways to reduce the amount of toxic load our body’s are burdened with.

1. Clean water

It seems obvious, but not everyone has jumped on this train yet. Water makes up the vast majority of our cells, so it’s important that we have a clean available supply. Depending on where you live, Tap water can either be fairly decent, or can be full of nasty washed up chemicals and residual pharmaceuticals. Tap water can contain high amounts of chlorine, fluoride, heavy metals from piping, and even birth control hormones that are peed out and recycled back into the water supply! Making sure you have water that is either untreated mountain water, or reverse osmosis water with mineral’s added is important to supplying your body with clean water to help it remove daily toxic loads. If you have mountain spring water with some chlorine added only, you can easily filter that out with a carbon filter. If you have other things added to your tap such as flouride, you’ll likely want purified water that has been remineralized.

2. Air

The quality of the air be breathe is also important. Sometimes living in a big city or near a busy freeway can expose us to more toxic particulates in the air. Also, dust, and mold spores in the air can be problematic. Having indoor plants and an air filter are great ways to clean the air that you breathe. Be sure to get out of the city and breath some fresh natural air once in a while!

3. Household supplies

You might not think of it, but every cleaner, pillow, dish soap, plastic dish, and tupperware container might be putting you at risk. Many items are made with industrial chemicals and solvents and contain endocrine-disrupting chemicals that can throw our whole endocrine system out of whack. Try to buy biodegradeable dish and laundry soaps, use glass containers to avoid plastics, and organic pillows.

4. Personal hygiene products

This is a vastly underemphasized important part of health. Our skin is our largest organ and incredibly absorbable. Consider this when buying shampoos, shower gels, face washes, body lotions, hair products etc. Also if you’re a woman, tampons are crucial to buy organic. The vagina is a highly absorbable mucus membrane. regular tampons can contain bleach, pesticides from the cotton, and all sorts of nasty chemicals that are going straight into your blood stream. Menstrual cups made of silicon are also a good option for women.

5. Kambo Frog Medicine

As mentioned above, Kambo is a powerful detoxifying traditional medicine that comes from an Amazonian tree frog. It helps your body remove heavy metals, biotoxins, parasites and other infectious organisms, and removes bile that may have accumulated toxic substances over the years. Read more about Kambo here.

D. Retraining the nervous system

Rebuilding your Gut Microbiome to Heal Lyme, Autoimmune Disease, and other Chronic Illnesses. 5I cannot emphasize how important this part is to the entire healing process.It should be done while taking the herbs, changing the diet, and frankly should be integrated into your daily life. Often times a person with a chronic autoimmune condition has had their poor body under so much stress for years whether is be due to a chronic infection, emotional trauma, nutrient deficiency, or unknown food sensitivity. This will inevitably deplete the adrenals, and put the nervous system in a long-term flight or fight stress response. Overtime this stress response will have negative downstream affects on the immune system, inflammation, digestion and nutrient absorption.

It is crucial to teach the nervous system to shift out of this stress response as the default state in order to achieve a full recovery. If you do all the gut healing protocols but don’t address the nervous system, your progress will not stick. The nervous system will continue to negatively influence the gut environment until brought back into balance. It will keep pulling your immune system, inflammatory processes, and microbiome into a maladaptive pathological state until it has restored regularity, no matter how many other things you have done to heal.  You are essentially retraining your brain to feel safe. Often times an emotional trauma can be the initial trigger of this, but then the nervous system gets stuck even if the trauma as been resolved. Here are some ways I recommend retraining the nervous system.

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 1. Mindfulness meditation

Meditation has a multitude of scientifically documented physical and emotional benefits. It’s free and anyone can do it anywhere at anytime. This is something that can and should be implemented into a daily practice to help you heal, and maintain wellness for all of life. If you’re looking for a good book to read as a guide, I highly recommend this book.

I also, highly recommend a silent meditation retreat such as a vipassana. If you have a chronic health condition, I suggest signing up for a shorter retreat at a center that is flexible about sitting in posture and can accommodate special dietary needs. Typical 10 day vipassanas can be quite strict as far as sitting in posture, which can be very painful for someone with chronic inflammation, so I decided to do a 6 day at Spirit Rock Meditation Center in Marin county, CA. I was able to use a back jack and chair when the pain from sitting became too unbearable. They also labelled all of the food and provided gluten free, dairy free options. I highly recommend doing a silent vipassana meditation retreat there to really retrain the nervous system. You’ll come back with a new sense of balance and calmness to your mind that is invaluable.

2. Qi gong

Qi gong is an ancient chinese practice that is essential a moving meditation. It involved breath, and the movement of “Qi” or energy to flow through the body. It is great place to start for people who feel they cannot sit down and focus long enough in a sitting meditation, because it employs movement for the antsy individual. It’s a great way to balance the nervous system, bring blood flow to joints and ligaments, and release energetic stagnation of Qi. Learn more about Qi gong.

3. Breathwork

Similar to mindfulness meditation and Qi gong, but also it’s own thing. There are various methods of breathwork techniques. Breath work is a powerful tool to restore balance to the autonomic nervous system, which governs our unconscious and involuntary bodily functions. Some great methods of breathwork to explore are holotropic breathwork developed by famous psychologist Stan Grof and the Wim Hoff method. Breathwork is amazing for recalibrating an imbalanced nervous system and restoring regularity to all of the downstream organ systems and processes controlled by the autonomic nervous system. Breathwork is free, easy to do, and accessible to everyone. There’s no good reason not to do it! Learn more about breathwork exercises here.

4. Sensory Deprivation Floatation Tanks

A pitch dark float tanks filled with epsom salt water sounds scary, but is actually quite a safe-feeling and relaxing experience. The tanks are very spacious, and generally do not make you feel claustrophobic. They are light and sound proof, providing a still and quiet dark environment. Being in a float tank feels very much like being in your mother’s womb. Float tanks have recently exploded in popularity and have ongoing clinical research showing their effectiveness at treating eating disorders, depression, ptsd, chronic pain and a variety of other conditions. Its even safe to do while pregnant, and often times you can hear your baby’s heart beat!

The idea is that when you deprive the brain of sensory stimulation, it funnels the brains energy and attention to normalizing more primitive parts of the brain that control basic functions such as fear, emotions, digestion, breathing, sleeping etc. Float tanks enhance something called proprioception, which is the conscious awareness of internal processes. Research with float tanks shows that this cultivation of proprioception awareness can normalize activity in certain brain regions that are associated with anxiety, depression, addiction and pain making float tanks a safe, non-invasive treatment that just about anyone can do.

60-90 minute floats are generally affordable at rates between $25 and $60 a float. Find a float center near you.

5. Neurofeedback training

Neurofeedback training is a modality where a practitioner uses QEEG (quantitative ElectroEncephaloGram) technology to map a person’s brain activity, and then train the brain to alter it’s wave emissions to create more balance and synchronization between brain regions. Various programs utilize audio and visual input to reward and teach a brain to adopt certain electromagnetic frequencies. The client will have electrodes placed on the scalp, measuring brain wave activity in real time. Typically a movie will be put on the screen, and based on the parameters set by the practitioner. The screen will warp, shake, and/or dim until the brain finds the wave pattern that turns the screen clear and bright. The brain subconsciously learns that it prefers the bright and clear screen, and learns to adopt the set brain wave pattern that the practitioner has set, by rewarding the brain with dopamine dump. Over time, the brain will create new neural pathways and maintain this new brain training, imprinting long term positive changes that lead to a more balanced and healthy brain.

Neurofeedback has been used for a variety of conditions such as depression, anxiety, addiction, sleep issues, PTSD, autism, and less popularly gut problems and inflammatory conditions. I personally found that after neurofeedback training, my sleep improved, my reactions to inflammatory foods were less dramatic, and my brain activity felt way more energetically balanced and stable. It can be an expensive procedure, usually requiring atleast 15 sessions for permanent changes to occur, but I found it to be very useful in getting my nervous system to chill out, which downstream helped tremendously with my autoimmune and lyme symptoms. If you’re in Southern California, I suggest the Alpha Theta Center. Dr Michael Villanueva is one of the best in his field.

6. Psychedelics

Did she just say psychedelics? Like the drugs? Why yes, I did. After being banned in the 60’s, psychedelic research is making a comeback. Classical psychedelic compounds such as LSD, psilocybin “magic” mushrooms, DMT, mescaline, and ayahuasca are all non-toxic, non-addictive drugs that are virtually safer on the human body than almost any other substances. They are very healing to the nervous system for a variety of reasons. Psychedelic molecules are shaped similarly to serotonin. They bind to serotonin receptors and create a unique mood enhancing effect that seems to last for many months according to several studies. Psychedelic compounds have been found to boost the creation of new neurons (brain cells), and neural structures. This process promotes neuroplasticity and the development of new neural networks. It can combat the atrophy of brains cells and degeneration of brain tissue due to inflammation, chronic infections, and free-radical damage. So there you go, psychedelics dont kill brain cells, they actually help you grow new ones!

Psychedelics also show some evidence as being anti-inflammatory and immune modulating. There are a lot of implications about how psychedelics may be a novel approach to helping mitigate the symptoms associated with autoimmune conditions. You can learn more about that specific application in this video HERE where I did a presentation of psychedelics as a novel approach to autoimmune conditions.

You can learn more in general about the benefits and ongoing research assosciated with psychedelic medicines by visiting these sites:
Multi Disciplinary Association for Psychedelic Studies (MAPS)
Aware Project: Rethinking Psychedelics
Psychedelic Times
-The Third Wave

E. Managing Symptoms

So, we’ve gone over what tools you can access to actually correct the issue. Rebuild the microbiome, heal the gut, and retrain the nervous system. Those things are imperitive, and until they are done, everything else you do will likely be just managing symptoms. That being said, this process takes a lot of time, and its not linear. There will be many days where you don’t feel well and need some help managing symptoms while you do the hard work of rebuilding your gut/brain axis. Below are some helpful tools to help comfort you while you’re on the healing path. Remember, not all herbs work the same for everyone, so find out what works best for your body. It will be different for everyone.

1. Mood

Generally people with rampant inflammation usually have some sort of neurological or psychiatric effects too. The brain is very susceptible to inflammation and is usually the first organ to be hurt and show symptoms when there is systemic inflammation from an autoimmune problem going on. Often times people experience depression, anxiety, brain fog, insomnia, and a number of nervous system imbalances.

As far as an all-in-one mood supplement, I recommend TransZen Mood Enhancement and Stress support. It has 17 scientifically studied ingredients and was formulated by a neuroscientist who specializes in mood disorders. It contains high quality forms of vitamins, minerals, amino acids and plant extracts that are the most bioavailable to your body. Many people have reported being able to get off their pharmaceutical medications or avoid medications completely using this formula. I personally use it almost on a daily basis to keep things happy and bright.

All of the below supplements are included in the TransZen above, but you can also try some of the supplements on their own.

5-HTP: an Amino Acid precursor that gets converted into serotonin

Mucuna Pruriens: An herb that contains a high amount of L-Dopa, an amino acid that gets converted into dopamine.

B Vitamins: B vitamins play a crucial role in brain health and neurotransmitter synthesis, among many other functions. Be  sure to get a methylated B complex for better absorption.

Trace Minerals: Minerals such as Zinc, Selenium, Magnesium, Chromium and other essential nutrients play a huge role in brain health and normal cell function. Make sure you have adequate levels of these very important biochemical components.

Many of the supplements below will also improve mood by reducing inflammation.

2. Pain

People with Lyme and autoimmune conditions often have a lot of pain and inflammation. The products I find the most effective are below:

-CBD (cannabidiol): a non-psychoactive compounds from hemp plants.

Fish oil: Full of omega-3 fatty acids important for brain health and managing inflammation, fish oil reduces inflammation and  provides fatty acids to repair cell membranes.

Curamin: A combination of potent anit-inflammatory, pain-killing herbs including a patented form of curcumin and  boswellia extracts.

Scutellaria (Skullcap): A powerful anti-inflammatory herb that also improves mood.

Dan Shen: A traditional chinese herb used to improve blood stagnation. Increases circulation and reduces pain. Great as a sleep aid.

White Willow Bark: This herb contains Salicin, which is a compound similar to the active ingredient in aspirin.

3. Sleep and Anxiety

-Cannabis: A full spectrum cannabis product with THC, CBD and terpenes can be a great sleep aid. An oral application usually ensures that you stay asleep all night long, vs smoking which can sometimes wear off in the middle of the night. There are a variety of medical cannabis products and locations to buy them depending on which state you live in.

Lemon balm: This herb activated GABA receptors and helps many people fall asleep and stay asleep. It also has the added benefit of potent anti-viral effects against herpes simplex virus (HSV) as well as anti-inflammatory effects.

Passionflower: Passion flower is another amazing herb for reducing anxiety and helping some people get to sleep. It contains GABA activating compound, as well as trace amount of harmaline and harmine, which are monoamine oxidase inhibitors (MAOI’s). MAOI’s increase serotonin by blocking it from being broken down by the body.

Dan Shen: Dan shen, mentioned above for pain, is also a great sleep aid. It reduces blood stagnation and inflammation, and can help your body relieve tension that is keeping you up

L-theanine: L-theanine is an amino-acid that occurs naturally in green tea. It has a very balancing calming effect, improving cognition, while also increasing relaxation. It can help take the edge off before sleeping.

4. Fatigue and Energy

L-Tyrosine: This amino acid is a precursor to dopamine and norepinephrine as well as an important nutrient for thyroid hormone production. It provides a nice boost of mental and physical energy. Dose carefully, sometimes this supplement can leave you a little twitchy at night.

Creatine: Traditionally a workout supplement to boost athletic performance and muscle gain. I found this supplement helpful for boosting my mitochondria and helping combat my daytime fatigue. Be sure to drink plenty of water when using this supplement.

Gingsengs: All of the Ginseng types help sustain energy and resilience. Siberian ginseng, American ginseng, or Panax Ginseng are good choices.

Mucuna Pruriens: An herb containing L-Dopa, another precursor to dopamine. Has an activating, yet calming effect. It is also an aphrodisiac and adaptogen.

5. General well being and healing.

These are nutrients that I recommend you supplement with to make sure you are properly resourced. Sometimes something as simple as one nutrient can keep you from getting better.

Multivitamin: Almost everybody is deficient is some nutrients. Vitamins and minerals play vital roles in facilitating biochemical pathways in the body, especially in the immune system and brain health. Make sure you are getting adequate amounts of Zinc, Magnesium, Boron, Selenium, Molybdenum, Manganese, Iron,  Copper and other trace minerals. It is also possible to have too much of a mineral or vitamin, so I only recommend taking it daily until your basic nutrient levels are sufficient, and then maintaining with every other day doses.. Getting a micronutrient panel done is the best way to know what you’re deficient in and what you’re good on. Be sure to get a multivitamin supplement that contains bioavailable forms of the nutrients such as methylated b vitamins and high quality minerals such as chelates or citrates. I recommend Thorne Multivitamin. It has the most absorbable forms of minerals.

B vitamins: B vitamins play many essential roles in neurotransmitter synthesis, cell repair and replication, and normal biochemical functions. B vitamins can improve energy level, mood, levels of pain, resilience to stress, and overall health.  It is very typical for someone with an autoimmune condition to have a gene variant called the MTHFR gene, which means methylating B vitamins is difficult for their body. I suggest getting a methylated B complex. I recommend this product.

Spirulina/Chlorella complex: Natures multivitamin. They contain all essential nutrients and have proper ratios of everything you need to thrive. While multivitamins like this Thorn product are great, I prefer the spirulina and chlorella tablets, though I personally alternate between taking both.

Fish oil: Fish oil contains omega 3’s which are critical fatty acid chains important for a number of processes such as making hormones, controlling inflammation and building fatty tissue such as that found in cell membranes. It is one of the healthiest supplements for your brain, heart and skin. Order some fish oil here.

Vitamin D: People with autoimmune issues tend to be deficient in vitamin D. Vitamin D is crucial for building hormones, modulation of cell growth, neuromuscular and immune function, and reduction of inflammation. It plays an important role in gut health. Anyone with chronic inflammation or an autoimmune conditions should supplement with vitamin D.


I could list about a thousand other supplements that I’ve found helpful, but I’m sure this long article is overwhleming enough. It seems like alot, and it sorta is. Alot of time, dedication, money and supplements. But, if you follow this protocol, you’re almost gauranteed to be feeling like a whole new person. I’d suggest you look at this process as an investment in your health and your future as a healthy, happy person living disease free. Buying the supplements, doing the modalities and sticking to the regimens will yeild dramatic results if you are compliant.

Remember, YOU ARE WORTH IT. Without our health, we have nothing. Once it’s gone, there’s not always a guarantee that it can be reclaimed. Don’t waste anymore time waiting around for something magical to happen. YOU are the magic. Your hard work, dedication and self love is the missing ingredient to your health journey. I strongly encourage you to take this advice here and discover the new, energetic, happy, vibrant version of yourself that was always in you.

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