Since there's been some discussion of an alternate version to the Autoimmune Bug Killin' protocol, something that relies more on supplements than pharmaceuticals, I thought I'd share some of the things I've been thinking about that would be helpful. I'm hoping this thread will lead to some networking about it and maybe we can all come up with a feasible protocol for killing off stealth microbes.
This protocol will, hopefully, be a viable alternative for those who don't have access to the pharmaceuticals or find it's too expensive. It could also act as a "phase 1" protocol to both determine whether or not a person needs the "nuclear option" using the pharmaceuticals or as a way to mitigate the negative effects of the main protocol.
It should be stated, though, that we don't really know if a supplement protocol would be effective in the same way the pharmaceutical protocol is. It may be that it's simply not strong enough. I would caution anyone, therefore, not to dabble in this. If you threaten the microbes, but don't kill them, you could end up making the problem worse. If someone was to try something, but not seriously, they may end up simply driving the bugs further into stealth mode, hiding in biofilms or cysts. This is a long-term plan; possibly requiring one to be on it for years. For this reason, I think it's important to take this seriously before embarking on anything - make sure the diet is on track, do work that needs to be done first, like heavy metal protocols, getting the liver up to speed and making sure your channels of elimination are working as best they can (including lymphatic system, kidneys, colon and that you sweat properly through the skin).
What follows is what I've deduced and gathered from the main Autoimmune protocol thread, in my own research and knowledge base. It's by no means exhaustive, so it would be good if others could add what they know or what they find out. I'm sure there's stuff I've missed in the main thread also, so anyone who finds something there that isn't included here could migrate it over. The goal will be to find a viable alternative to the pharmaceutical protocol with alternatives that can account for availability of supplements. These are listed in no particular order.
Biofilm Dissolvers
Bromelain - A proteolytic (protein digesting) enzyme that breaks up mucous and protein component of biofilm. Also modulates thromboxanes (clotting agents released by lysed parasites) and acts as an anti-inflammatory to deal with Herx reactions. See the following posts in the main thread:
http://cassiopaea.org/forum/index.php/topic,38053.msg591436.html#msg591436
http://cassiopaea.org/forum/index.php/topic,38053.msg591441.html#msg591441
http://cassiopaea.org/forum/index.php/topic,38053.msg591513/topicseen.html#msg591513
Other proteolytic enzymes - serrapeptase, nattokinase, lumbrokinase (more effective than nattokinase in studies), protease, papain
Monolaurin/Lauric Acid - solubilizes the lipids and phospholipids in their protective envelope. Inhibits replication of viruses by interrupting the communication and binding of virus to host cells. See here. Also kills Lymes and many coinfections.
Boron - Destroys biofilms and increases cellular integrity, preventing invasion. See this post from the main thread.
Lactoferrin - Chelates iron, blocking the ability of biofilms to form. Also bolsters the immune system the immune system, increasing phagocytic activity of leukocytes as well as stimulating the production of natural killer cells and cytokines.
Capryllic acid - helpful in breaking up biofilms. See here.
NAC - Considered a must have - breaks up mucous, dissolving biofilms. Precursor to glutathione, which is antiviral and the body's most important anti-oxidant (which will help with Herx reactions and in detoxifying all the toxic die-off "stuff). Also a liver protectant.
Nitric Oxide - "Nitric oxide has also been shown to trigger the dispersal of biofilms of several bacteria species at sub-toxic concentrations. Nitric oxide has the potential for the treatment of patients that suffer from chronic infections caused by biofilms." From Wikipedia.
There are several supplemental forms of nitric oxide, most are L-arginine and precursors (this for example, or this). I haven't figured out if these supplements simply increase N02 for body processes like increasing oxygenation, vasodilation and reducing inflammation or if they will also affect biofilms. I'm in the process of contacting the naturopath from AOR (I've met him a couple of times) to see if he can give me any insight.
Cellulase - a digestive enzyme, (not produced by humans but produced by the bacteria in our guts) used to break down beta bonds in carbohydrate molecules (ie. the fiber called cellulose). Some bacteria, including candida, incorporate cellulose into their cell wall as protection and this enzyme has been shown to destroy such bacteria. You can find cellulase in some candida formulas (see here - note this formula also includes protease for digesting proteins which would likely also be helpful for dissolving biofilms. See Proteolytic Enzymes, below). Cellulase has also been found to inhibit biofilm formation, at least on external surfaces.
Iron chelating agents - EDTA is probably the best one as it actually causes "detachment and killing of biofilm cells" (see here), but there's also IP6 and DMSA to consider. Also see Lactoferrin, above. By chelating free iron in the system, these substances starve biofilms of one of their much needed resources.
Oxidizing agents like hydrogen peroxide sound like they might not be the best option while the microbes are hidden in biofilms. See here and here (note that these studies are based on surface biofilms encountered in industry settings, but it doesn't seem reasonable to assume things would be different for biofilms inside the body). It may be that these would be useful in conjunction with known biofilm dissolvers however, as a kind of clean-up crew to kill pathogens once they're no longer protected.
Antimicrobials
Not much explanation for most of these as they've mostly been well documented.
Boron
Olive leaf extract
Astragalus
Andrographis
Grapefruit Seed Extract
Oregano oil - this is a good product; it's emulsified.
Garlic
Clove
Neem
Saccharomyces boulardii
berberine (goldenseal, barberry, oregon grape)
glutathione - antioxidant, antiviral. Since glutathione is broken down by the digestive system, taking it in liposomal form is probably best. You can also take precursors (NAC, ALA)
1,3/1,6 Beta glucan
Medicinal mushrooms - agarikon, chaga, reishi, shiitake, cordyceps, maitake... Note that these mushrooms have antibacterial, antifungal and antiviral compounds over and above just the Beta glucans. Two really great products here and here.
Caprylic acid
Undecylenic acid - 6x more effective than caprylic acid.
Cutting edge stuff
This is all stuff I've found in my research that is rather obscure and maybe difficult to obtain.
Phage Therapy - There's an experimental therapy known as "Phage Therapy" (see here), otherwise known as "biocontrol", which is apparently successful in treating pathogenic bacterial infections. It basically involves introducing an virus that replicates inside the bacterial cells. From wikipedia: "Bacteriophages are much more specific than antibiotics, so they can hypothetically be chosen to be indirectly harmless not only to the host organism (human, animal, or plant), but also to other beneficial bacteria, such as gut flora, reducing the chances of opportunistic infections.[3] They would have a high therapeutic index, that is, phage therapy would be expected to give rise to few side effects. Because phages replicate in vivo, a smaller effective dose can be used. On the other hand, this specificity is also a disadvantage: a phage will only kill a bacterium if it is a match to the specific strain. Consequently phage mixtures are often applied to improve the chances of success, or samples can be taken and an appropriate phage identified and grown." It all sounds a bit risky, but apparently it's currently being used successfully to treat antibiotic resistant ear infections caused by P. aeruginosa, as was reported in the journal Clinical Otolaryngology in August 2009 (see here)
Dispersin B - an enzyme that dissolves N-acetyl-glucosamine that composes the matrix of the biofilm. See here. Note that "Currently there is interest in Dispersin B as a commercial anti-biofilm agent that could be combined with antibiotics for the treatment of bacterial infections." It may pay for us to keep an eye on the market in case this shows up at some point.
Deoxyribonuclease - "(DNase, for short) is any enzyme that catalyzes the hydrolytic cleavage of phosphodiester linkages in the DNA backbone, thus degrading DNA." (see here). It looks like this is primarily being used for biofilms in the lungs at this point.
Probiotics
As with the pharmaceutical protocol, probiotics are an absolute must when you're killing things off. You need to "fill in the spaces" left by killing off the bad guys with good guys to prevent opportunistic bad guys filling in those spaces again. This is particularly true of fungus (which is why Nystatin is so important on the other protocol).
Probiotics should be high dose - 50 billion or above (I've seen as high as 450 billion). Ideally they should be taken daily, away from antimicrobials, definitely away from pharmaceutical antibiotics.
Adjuncts
MCT Oil/Coconut Oil
Essential oils
Xylitol/Erythritol
Colloidal Silver
Vitamin D3
Vitamin C
Magnesium
Turmeric extract (curcumin) - to control inflammation and help the liver
Fermented foods - unpasturized sauerkraut, kimchee, pickles, etc.; provide friendly probiotic bacteria
This protocol will, hopefully, be a viable alternative for those who don't have access to the pharmaceuticals or find it's too expensive. It could also act as a "phase 1" protocol to both determine whether or not a person needs the "nuclear option" using the pharmaceuticals or as a way to mitigate the negative effects of the main protocol.
It should be stated, though, that we don't really know if a supplement protocol would be effective in the same way the pharmaceutical protocol is. It may be that it's simply not strong enough. I would caution anyone, therefore, not to dabble in this. If you threaten the microbes, but don't kill them, you could end up making the problem worse. If someone was to try something, but not seriously, they may end up simply driving the bugs further into stealth mode, hiding in biofilms or cysts. This is a long-term plan; possibly requiring one to be on it for years. For this reason, I think it's important to take this seriously before embarking on anything - make sure the diet is on track, do work that needs to be done first, like heavy metal protocols, getting the liver up to speed and making sure your channels of elimination are working as best they can (including lymphatic system, kidneys, colon and that you sweat properly through the skin).
What follows is what I've deduced and gathered from the main Autoimmune protocol thread, in my own research and knowledge base. It's by no means exhaustive, so it would be good if others could add what they know or what they find out. I'm sure there's stuff I've missed in the main thread also, so anyone who finds something there that isn't included here could migrate it over. The goal will be to find a viable alternative to the pharmaceutical protocol with alternatives that can account for availability of supplements. These are listed in no particular order.
Biofilm Dissolvers
Bromelain - A proteolytic (protein digesting) enzyme that breaks up mucous and protein component of biofilm. Also modulates thromboxanes (clotting agents released by lysed parasites) and acts as an anti-inflammatory to deal with Herx reactions. See the following posts in the main thread:
http://cassiopaea.org/forum/index.php/topic,38053.msg591436.html#msg591436
http://cassiopaea.org/forum/index.php/topic,38053.msg591441.html#msg591441
http://cassiopaea.org/forum/index.php/topic,38053.msg591513/topicseen.html#msg591513
Other proteolytic enzymes - serrapeptase, nattokinase, lumbrokinase (more effective than nattokinase in studies), protease, papain
Monolaurin/Lauric Acid - solubilizes the lipids and phospholipids in their protective envelope. Inhibits replication of viruses by interrupting the communication and binding of virus to host cells. See here. Also kills Lymes and many coinfections.
Boron - Destroys biofilms and increases cellular integrity, preventing invasion. See this post from the main thread.
Lactoferrin - Chelates iron, blocking the ability of biofilms to form. Also bolsters the immune system the immune system, increasing phagocytic activity of leukocytes as well as stimulating the production of natural killer cells and cytokines.
Capryllic acid - helpful in breaking up biofilms. See here.
NAC - Considered a must have - breaks up mucous, dissolving biofilms. Precursor to glutathione, which is antiviral and the body's most important anti-oxidant (which will help with Herx reactions and in detoxifying all the toxic die-off "stuff). Also a liver protectant.
Nitric Oxide - "Nitric oxide has also been shown to trigger the dispersal of biofilms of several bacteria species at sub-toxic concentrations. Nitric oxide has the potential for the treatment of patients that suffer from chronic infections caused by biofilms." From Wikipedia.
There are several supplemental forms of nitric oxide, most are L-arginine and precursors (this for example, or this). I haven't figured out if these supplements simply increase N02 for body processes like increasing oxygenation, vasodilation and reducing inflammation or if they will also affect biofilms. I'm in the process of contacting the naturopath from AOR (I've met him a couple of times) to see if he can give me any insight.
Cellulase - a digestive enzyme, (not produced by humans but produced by the bacteria in our guts) used to break down beta bonds in carbohydrate molecules (ie. the fiber called cellulose). Some bacteria, including candida, incorporate cellulose into their cell wall as protection and this enzyme has been shown to destroy such bacteria. You can find cellulase in some candida formulas (see here - note this formula also includes protease for digesting proteins which would likely also be helpful for dissolving biofilms. See Proteolytic Enzymes, below). Cellulase has also been found to inhibit biofilm formation, at least on external surfaces.
Iron chelating agents - EDTA is probably the best one as it actually causes "detachment and killing of biofilm cells" (see here), but there's also IP6 and DMSA to consider. Also see Lactoferrin, above. By chelating free iron in the system, these substances starve biofilms of one of their much needed resources.
Oxidizing agents like hydrogen peroxide sound like they might not be the best option while the microbes are hidden in biofilms. See here and here (note that these studies are based on surface biofilms encountered in industry settings, but it doesn't seem reasonable to assume things would be different for biofilms inside the body). It may be that these would be useful in conjunction with known biofilm dissolvers however, as a kind of clean-up crew to kill pathogens once they're no longer protected.
Antimicrobials
Not much explanation for most of these as they've mostly been well documented.
Boron
Olive leaf extract
Astragalus
Andrographis
Grapefruit Seed Extract
Oregano oil - this is a good product; it's emulsified.
Garlic
Clove
Neem
Saccharomyces boulardii
berberine (goldenseal, barberry, oregon grape)
glutathione - antioxidant, antiviral. Since glutathione is broken down by the digestive system, taking it in liposomal form is probably best. You can also take precursors (NAC, ALA)
1,3/1,6 Beta glucan
Medicinal mushrooms - agarikon, chaga, reishi, shiitake, cordyceps, maitake... Note that these mushrooms have antibacterial, antifungal and antiviral compounds over and above just the Beta glucans. Two really great products here and here.
Caprylic acid
Undecylenic acid - 6x more effective than caprylic acid.
Cutting edge stuff
This is all stuff I've found in my research that is rather obscure and maybe difficult to obtain.
Phage Therapy - There's an experimental therapy known as "Phage Therapy" (see here), otherwise known as "biocontrol", which is apparently successful in treating pathogenic bacterial infections. It basically involves introducing an virus that replicates inside the bacterial cells. From wikipedia: "Bacteriophages are much more specific than antibiotics, so they can hypothetically be chosen to be indirectly harmless not only to the host organism (human, animal, or plant), but also to other beneficial bacteria, such as gut flora, reducing the chances of opportunistic infections.[3] They would have a high therapeutic index, that is, phage therapy would be expected to give rise to few side effects. Because phages replicate in vivo, a smaller effective dose can be used. On the other hand, this specificity is also a disadvantage: a phage will only kill a bacterium if it is a match to the specific strain. Consequently phage mixtures are often applied to improve the chances of success, or samples can be taken and an appropriate phage identified and grown." It all sounds a bit risky, but apparently it's currently being used successfully to treat antibiotic resistant ear infections caused by P. aeruginosa, as was reported in the journal Clinical Otolaryngology in August 2009 (see here)
Dispersin B - an enzyme that dissolves N-acetyl-glucosamine that composes the matrix of the biofilm. See here. Note that "Currently there is interest in Dispersin B as a commercial anti-biofilm agent that could be combined with antibiotics for the treatment of bacterial infections." It may pay for us to keep an eye on the market in case this shows up at some point.
Deoxyribonuclease - "(DNase, for short) is any enzyme that catalyzes the hydrolytic cleavage of phosphodiester linkages in the DNA backbone, thus degrading DNA." (see here). It looks like this is primarily being used for biofilms in the lungs at this point.
Probiotics
As with the pharmaceutical protocol, probiotics are an absolute must when you're killing things off. You need to "fill in the spaces" left by killing off the bad guys with good guys to prevent opportunistic bad guys filling in those spaces again. This is particularly true of fungus (which is why Nystatin is so important on the other protocol).
Probiotics should be high dose - 50 billion or above (I've seen as high as 450 billion). Ideally they should be taken daily, away from antimicrobials, definitely away from pharmaceutical antibiotics.
Adjuncts
MCT Oil/Coconut Oil
Essential oils
Xylitol/Erythritol
Colloidal Silver
Vitamin D3
Vitamin C
Magnesium
Turmeric extract (curcumin) - to control inflammation and help the liver
Fermented foods - unpasturized sauerkraut, kimchee, pickles, etc.; provide friendly probiotic bacteria
