Anti-Inflammatory Diet

All health care starts with diet. My recommendations for a healthy diet are here:
Anti-Inflammatory Diet and Lifestyle.
There are over 190 articles on diet, inflammation and disease on this blog
(find topics using search [upper left] or index [lower right]), and
more articles by Prof. Ayers on Suite101 .

Wednesday, September 2, 2009

Cure for Inflammatory Diseases

Destabilizing Gut Biofilms by Simple Remedies

The intercommunication between the gut flora biofilms, the cells of the immune system juxtaposed with the intestinal endothelium and cryptic bacteria/tissue biofilms produces stable chronic inflammatory disease. Disrupting the gut biofilms may permit a resumption of effective immunity and remission.

Disrupting Biofilms to Treat ASDs

Cristian Stremiz brought to my attention the work of Dr. Anju Usman on the treatment of autism spectrum diseases by attacking inflammatory gut biofilms.

A Panacea

This approach, based on the use of common food components, to attack the gut biofilm matrix of acid polysaccharides, cations and proteins, should be generalizable to most inflammatory diseases. The interventions also provide facile explanations for the utility of numerous traditional cures such as vinegar, fiber, glucosamine, pectin, whey, proteases and probiotics.

Cures Act via Gut Flora Biofilms

There are numerous anecdotal reports of traditional, simple remedies working for essentially all diseases. Tantalizingly, many of these diseases are also occasionally successfully treated with antibiotics. The common thread seems to be the involvement of inflammatory gut flora and perhaps cryptic bacteria residing in the tissues displaying symptoms. Glucosamine works sometimes for arthritis, but little of the glucosamine that is eaten reaches the blood stream and the aching joints that seem to become less inflamed. Vinegar, pectin, and fiber have also been attributed with curative powers, yet none is likely to impact inflamed joints directly. Impacting gut biofilms is much easier to explain.

Biofilms of Bacteria Attached to Acidic Polysaccharides and Divalent Cations

Acidic polysaccharides are produced by bacteria and divalent cations cross-link the polysaccharides into a matrix. The bacteria have agglutinins to attach to the matrix. Gut pathogens produce agglutinins that they use to attach to the heparan sulfate (HS), the predominant acid polysaccharide of the intestinal epithelium. Mast cells of the intestines normally release heparin, which is a mixture of HS fragments, to stick to the agglutinins and block attachment to the HS of the epithelium. Numerous bacterial species form complex communities on the polysaccharide matrix and prevent access by antibiotics. Biofilms require 100X the antibiotic concentrations and a cocktail of different antibiotics to eradicate the bacteria.

Biofilms Disrupted by Competing Acid Polysaccharide Fragments and Cation Chelators

The Achille’s heal of biofilms is the ionic interaction between the acidic polysaccharide and divalent cations. This interaction can be attacked by both small fragments of similar acid oligosaccharides, by organic acids that can solubilize the cations, e.g. acidic acid in vinegar, or by chelators, such as EDTA. All of these treatments can remove the calcium, magnesium and iron that is essential to the matrix. Small molecules, such as glucosamine, chondroitin sulfate fragments, heparin, and pectin, can disrupt biofilms. Molecules that bind to heparin or nucleic acids, e.g. berberine, quinine (tonic), methylene blue, should also be effective in disrupting biofilms. [Note that the similarity between amyloid production and biofilms, means that treatments should overlap.] Lactoferrin is effective, since it both binds iron and binds to acidic polysaccharides via its heparin-binding domains.

Proteases Cleave Agglutinins

Stomach proteases, e.g. pepsin, specifically cleave proteins to release heparin-binding, acidic polysaccharide-binding domains that inhibit biofilm production in the stomach. Subsequently, the basic, antimicrobial peptides and agglutinins are cleaved by proteases, e.g. trypsin, that hydrolyze the binding domains. Eating proteases, such as nattokinase present in fermented soybeans, dissolves intestinal biofilms by attacking the agglutinins. The pathogenic E. coli and avian H5N1 also have these agglutinins. It is, therefore, wise to avoid establishing gut biofilms that can immobilize pathogens.

Probiotics Protect Against Biofilms

Resident gut bacteria that produce organic acids, e.g. lactic acid or acetic acid, provide protection against biofilm formation. Examples are the bacteria present in common forms of fermentation and food preservation, e.g. Lactobacillus sp., and the bacterium present in exclusively breastfed babies, Bifidobacter sp. Formula fed babies rapidly develop inflammatory biofilms, which explains their high rates of intestinal and respiratory diseases, as well as increased rates of inflammatory diseases.

Biofilm Inflammation Results in Inflammatory Bowel Disease, etc.

Gut biofilms support system-wide chronic inflammation that leads to allergies, autoimmune diseases, degenerative diseases and probably cancers. This attach on the gut also produces a leaky gut that supplies the bacteria that a moved by macrophages of the gut to all parts of the body. This may be how Chlamydia pneumoniae colonizes sites of inflammation throughout the body.

Attacking Gut Biofilms Is the First Step in the Treatment of All Inflammatory Diseases

Many inflammtory diseases, e.g. chronic lyme disease, rosacea, may be refractory to treatment with antibiotics, because of the reservoir of bacteria in gut biofilms. Attacks on gut biofilms with relatively non-intrusive treatments, such as vinegar, EDTA, lactoferrin and proteases, may lower the total resident pathogen load and make subsequent antibiotic treatment more effective.


Terry H said...


Should first word in last sentence be "Attacks"?

Dr. Art Ayers said...

Oops. Thanks.

Anonymous said...

What about using xylitol sweetner in coffee to breakdowwn biofilms in the gut?

Dr. Art Ayers said...

I would expect the biofilms to quickly recover from any single treatment, so they should become accustomed to xylitol and some bacteria in the colonies will probably be able to use it as a carbon source.

Cristian Stremiz said...

Would you mind to edit my surname in the main post? Stremiz instead of Stremitz. You know ... I'm proud of this citation in your post :-)

Anonymous said...

I started reading your blog about a month ago and enjoy it immensely. I suffer from Rosacea. What would be a way to incorporate these protocols listed above? Thank you.

William Trumbower said...

Art What a brilliant post. Think of the complex interactions that must be occuring when a person also has gluten intolerance. The leaky gut must be huge and the chronic inflamatory cascade must be overwhelming to the individual. This must explain some of the health benefits of traditional diets that use lots of lactofermintation and things like kombucha which are high in acetic acid and bone broths that contain glucosamine/chondroitin. Keep up the good work!

Thackray said...

Dr Ayers,

Since gut bacteria cannot consume protein or fats (see: it would seem that a low carb diet should also be effective against the bacteria in gut biofilms. While low carb should limit the bacteria would it ultimately limit the biofilm? Would limiting the biofilm matter if the bad bacteria were limited?

Gluten has been implicated in autism. Is it possible that gluten enhances the bad biofilms in some way?


Philip Thackray

Dr. Art Ayers said...

Sorry about the spelling. I was typing a little fast.
Thanks again.

Dr. Art Ayers said...

I hesitate to make suggestions of possible protocols, because I am not an MD and some of the conditions, such as rosacea are probably a group of different diseases with related symptoms. Explicit suggests could upset a delicate inflammatory balance and release endotoxin (bacterial wall fragments) into a leaky gut. So I just provide the basic idea and hope that wise medical people can administer sound treatment in individual cases.

I know that treatment for rosacea is usually poor, but the patient histories are very complex. What I suggest is to use a gentle method to remove most of the biofilm, probably accompanied by fiber with lots of phytic acid to help remove cations. Hopefully this could be accomplished without a huge flare up. I hope you belong to a rosacea support group and can get good guidance from others knowledgeable about the specifics of your case.

Good luck.

Anna said...

Great information, and I paid special attention to the section on probiotics and gut health, and also the comment on xylitol. I've been an advocate of both for some best to trick these biofilms so they do not become accustomed to these natural treatments?
- Anna M

Dr. Art Ayers said...

William T.,
Thanks for your input. I agree with your observations. The simplicity and explanation to so many other traditional cures gives it a ring of truth.

I woke this morning with another bowel-stirring thought. I complain about X-ray crystallographers using polyethylene glycol to get their protein crystals. The problem is that PEG disrupts the binding of heparin to proteins. As a consequence, the gold standard for structural analysis gives the wrong answer for most protein-carbohydrate interactions, because it ignores the hydrophobic component that is based on water structuring.

What is PEG used for in medicine. If one is over fifty and familiar with colonoscopy, then the idea of clearing out the bowels for office pictures might come to mind. PEG should disrupt biofilms as it gently evacuates the bowel! Colonoscopy pretreatment is light X-ray crystallography, in that both disrupt what they are trying to see.

This also suggests that all of the colon cleaning scams might actually do some good. Detox has nothing to do with removing environmental toxins, but rather it removes the toxic biofilms.

PEG may end up being a general treatment for many diseases. It could be followed by a fecal transplant from a healthy individual. That may be the future of medicine, handling ......

Anonymous said...

"probably accompanied by fiber with lots of phytic acid to help remove cations"

But what would you recommend for this part, whole wheat (yikes), unsoaked brown rice, or are there supplements available? Much appreciation.

Dr. Art Ayers said...

I just mentioned the fiber, because of its multiple advantages of increasing transit times, the efficacy in phytic acid in inhibiting cancers and the chelating ability of phytic acid. Phytic acid gets demonized for the binding of cations, such as zinc. I wanted to show that it might be very useful in treatment of biofilms.

The use of wheat fiber might really increase transit time for some people and perhaps the eating of grains was initially used by humans for annual cleansing of biofilms by causing diarrhea.

Perhaps a more gluten-knowledgeable reader could provide a non-grain source of fiber.

Thanks for the comment.

Anonymous said...

I see, thank you. Do you suppose the Mg trapped in the biofilm is the reason for the Mg deficiency reported in asthma patients, if so would Mg supplementation be the wrong track without dealing with the biofilm first? I apologize for the simplification, I am a layperson trying to get the puzzle pieces lined up and haven't had any luck with my doctors and can guarantee if I start quizzing them about biofilms they'll ask if I've been on the internet again! I found your blog yesterday. Thank you so much

Dr. Art Ayers said...

All I do all day is try to simplify the biomedical literature and make sense of some of the original observations that are camouflaged by industry imperatives.

Magnesium and calcium are critical components needed to stabilize the biofilms. They are also abundant in all foods. Absorption problems are more likely. The asthma is probably the result of gut problems. Adjusting food intake to avoid providing cations for the biofilms is impossible, since they also feed off of the leakage from the intestinal epithelium.

The approach that seems reasonable to me is to remove the food using PEG for whole bowel irrigation, e.g. GoLYTELY; strip the biofilms with chelators, lactoferrin, proteases, vinegar, spices and acidic oligosaccharides along with phytate-rich fiber to keep the whole thing moving; then develop a new gut flora with pre- and pro-biotics. Severe cases may benefit from colostrum and growth factors to close the gut.

This approach will have to be customized for the particular vulnerabilities of each disease being treated. Having a normal, functional gut prior to subsequent treatments for the damage from a leaky gut may make the treatments much less severe.

Thanks for the comments/questions.

Anonymous said...

Thank you very much, Dr. Ayers.

Kennedy said...

Wow, fascinating idea that Hunter-gatherers may have used wheat or grains in a cleansing capacity. Then became addicted to the opioid effects. Gotta remember to keep an open mind with all this stuff!

What about Chocolate? Does it not have fiber and other nutrient binding elements?

Great blog.

Dr. Art Ayers said...

Chocolate is just great stuff. I don't know about the fiber. I just eat it for the satisfying taste, alkaloids and fats. Make sure that it is dark and has as little sugar as possible. Milk is rumored to reduce its health benefits. I don't know why, but I don't miss the milk.

If you enjoyed that paleo-parallel, you probably also enjoyed the application of the inflammatory benefits of agriculture to disease control. Promethian fire brought inflammatory AGE and more protection from diseases spread around progressively more crowded campfires. Cave dwelling during winter decreases vitamin D and increases inflammation to protect against contagious diseases. Selective advantages to dietary/behavioral inflammation.

I enjoy your blog. Thanks for the comments.

Aaron said...

Art, whats your feeling on taking a calicium/mag supplement then?

Dr. Art Ayers said...

I guess from your question that you can see the problems with cation supplements (calcium, magnesium). Clearly your body needs these ions for all aspects of tissue function. Your bones have massive amounts of calcium that are constantly being recycled. Magnesium is needed for the structure of all negatively charged polymers, e.g. nucleic acids, heparan sulfate of basement membrane (integrity of gut, kidneys, blood/brain barrier. At the same time these are very common constituents of all foods and you should have ample amounts unless you have an extreme diet or your gut absorption is disturbed.

If you actually need these supplements, then you probably have some other problem that makes them necessary, e.g. celiac or gut biofilms. It is more important to address these problems and diet-based chronic inflammation. With adequate vitamin D, these shouldn't be a problem.

That's the way it seems to me.

Thanks for the questions.

Aaron said...

Interesting-- at some point soon I am thinking of starting a blog that is going to tackle theoretical nutritional issues. The question of how to maintain mineral sufficiency is one of these questions. I think you are right that if you don't eat sugar-- and keep your gut it order, you probably barely need any minerals.

As a side note, high phytic acid foods scare me alot-- not only do they have low bio-availability of minerals, they may bind to minerals already in the body-- not a good situation!

Dr. Art Ayers said...

You force me to be an apologist for phytate.

After all, phytate is responsible for all of the benefits that are associated with dietary fiber. Phytate also reduces cancer and probably attacks intestinal biofilms. Also remember that phytate is inositol hexaphospate and a major intracellular signal molecule is inositol triphosphate (IP3). IP4 and IP5 are also important to cellular physiology. It is also interesting that proteins that bind to heparin also bind to IP3 and perhaps phytate.

It is fairly easily to remove the phosphates and tame the phytate in grains. All you have to do is let them germinate and activate their phytase.

So please be gentle in your condemnation of phytate.

Thanks for your comments.

Aaron said...

Interesting!-- of course, I have seen your back and forth with Stephan on phytic acid.

Could you point me to any culture that has consumed a diet rich in phytic acid and has shown good longevity and bone structure? So far, I'm not really sure if any exists-- and I'm too lazy to research this!

Of course, I tend to be conservative when it comes to consuming compounds that are contained in grains.

Is it my understanding that you would consider sugar to be more dangerous then say a compound like phytic acid in terms of stealing minerals from our body? Maybe its just low vitamin D that causes this (I'm with you on that!)

As for soaking-- too lazy for that too! What if I want to consume kasha-- it's already toasted so no phytase activity left-- and I don't feel like leaving it in a container with something that has high phytase activity!

I like living the lazy life-- don't feel like i'm missing out either!

BTW-- this article also can be used as a "STRONG" argument for intermittent feeding.

Anonymous said...

Dr Ayers,

I just found your very interesting blog. I have been living with UC (Ulcerative Colitis/Indeterminate Colitis) (IBD) for the past 8 years. The meds are useless and dangerous (e.g. prednisone).

I don't share your enthusiasm for PEG. My UC flares up somewhat after colonoscopies. If your theory of pathogenic biofilms being the causative agents in these sort of diseases are attached by divalent cations, wouldn't another cation with a greater dissociation constant work at destabilizing the biofilm complex? You are not suggesting they are being held together by ionic bonds in crystalline form? I am assuming an aqueous situation in these biofilms.

I don't know if I buy the autoimmune theory of IBD, either. Recent results with the opiod antagonist naltrexone in low-doses at bed time have had very promising results in treating IBD & other 'autoimmune' diseases. The partial opioid receptor blockade seems to promote endorphine, deltanorphine, other endogenous opioid peptide synthesis which stimulate the immune system. And since the gut has many opioid receptors, "they" theorize that's how it helps IBD.

Any opinions? Any suggestions for my IBD? It seems to worsen in late Spring and late Fall. I am controlling my IBD more or less with opioid agonists (which is why I haven't tried low-dose naltrexone yet) that I get prescribed for chronic pain. I've read that opioid agonists suppress the immune system - natural killer cells, T, B, Th1, Th2 cells. For example, this article at NIH:

I am a white male, 42, European extraction.

Thank you for a very informative blog.

Anonymous said...

sorry, your blog software ate my NIH link.


Experimental Evidence for Immunomodulatory Effects of Opioids

Link* (on multiple lines):

*assemble the link in your browser's URL field by copy/pasting the 3 fragments one after another. No spaces or new lines.

Dr. Art Ayers said...

I still think that PEG should be good for biofilms and I think that it also worked in your case. Unfortunately IBD is a pseudo-autoimmune disease, i.e. an inflammatory response to gut bacteria that should produce tolerance. That is why helminth therapy is effective. Heparin also works, both because it is anti-inflammatory by blocking inflammatory signaling mediated by heparan sulfate proteoglycans, and because it is the natural disrupter of gut biofilms by competing with the matrix acid polysaccharides.

In your case, the PEG dislodged the biofilm bacteria and they promptly moved through the lining of your inflamed, leaky gut. This caused a minor flare up, perhaps followed by remission in the temporary absence of the biofilms.

The biofilm matrix is like jelly, a gel formed by acid polysaccharide, pectin, cross-linked with calcium. EDTA can break up the gel by binding the calcium or vinegar/acetic acid can solubilize the calcium and also liquify the gel. It isn't crystalline.

Low dose naltexone seems to be effective in many inflammatory diseases. Opiod receptor seem to mediate many inflammatory events. I think that they mediate the acupuncture-like, pain relieving/anti-inflammatory actions of capsaicin, menthol and castor oil.

Have you tried a castor oil pack applied to your abdomen for your IBD? I think that it may stimulate vagus nerve-based release of opiods in the abdominal organs. It is not as fast as with hand and feet pain, but it is worth a try.

The first thing that I would do for IBD is check my vitamin D and worry a little about malabsorption of other nutrients, e.g. B12. Consider taurine and N-acetylcysteine. Before any manipulation or attack on your biofilms, I would recommend a dose of glutamine to heal your gut.

All of the typical anti-inflammatory diet adjustments are useful in IBD, so shift to the low carb, low grain, anti-inflammatory diet recommended on the blog.

If I were you, I would get as anti-inflammatory as I could by diet and exercise, try to heal the gut as much as possible, and then work on the biofilms. Follow that up with probiotics. Subsequently, you may still be bothered by the cryptic bacteria that have moved into inflamed tissues during flareups or treatments that made your gut leaky.

I hope that this is helpful, even though I can't give medical advice.

Thanks for the comments.

jean said...

Dr. Ayers,
I am curious about the nature of the biofilms.
I have a diagnosis of candidiasis. Before I was diagnosed and treated, I would have, oh about a quarter cup of intestinal creamy white mucus every time I ate any refined wheat bread. Now that I am on an anti-inflammatory diet (definitely wheat free), the mucus is much less, but not gone. I have been treated for about 8 months now with Chinese herbs, probiotics, diet and L-glutamine (recommended for leaky gut). I do mostly follow the diet you recommend.
Does this description (white intestinal mucus) fit the biofilm picture? And, does it seem that one should rotate biofilm treatments, until some stable level of health is reached?
I ask regarding the mucus, because I have not been able to get an answer from any gastroenterolgist, internist, etc., I have consulted. And yes, I have had a colonoscopy.

Dr. Art Ayers said...

From your simple description, I would say that the "creamy white mucus" is lots of yeast. I would guess that the yeast is an overgrowth of your intestines with the foundation being persistent biofilms.

I think that an anti-inflammatory diet can keep biofilms under control, but perhaps what we see as aging and increasing chronic inflammation, is just the gradual accumulation of biofilms and the reduction in healthy, absorptive intestines.

I would say that your yeast treatment just reduced, but did not eliminate the biofilms and yeast. They have just been reduced to a chronic level and the other treatments keep the inflammation in check.

I can't provide medical advice, but if I was in your position, I would probably try to eliminate as much of the yeast as possible by fasting overnight, then a PEG whole bowel irrigation, followed by freshly ground flax seed, lactoferrin, vinegar and pectin, with a chaser of natto (fermented soybeans as a source of nattokinase, an enzyme that degrades biofilms). This assumes that I have already tested all of the components to make sure I tolerated all well and included glutamine to enhance intestine integrity. Then I would focus again on pre- and probiotics and a return to an anti-inflammatory diet and plenty of exercise. I would probably also use a sauna or hot tube to increase my skin and joint temperature to inhibit any cryptic bacterial development.

If it felt like I was improving with this treatment, I would repeat it perhaps once a week for a month, just to be done with it. I would also avoid all grains/gluten for the whole time. This should eliminate all allergies and inflammatory symptoms. Inflammatory symptoms include things like depression, acne, back aches, tendonitis, etc.

Those are my thoughts.

Thanks for your comments/questions.

Joanne at Open Mind Required said...

I've never heard of biofilms before. Thank you for writing about this.

Do you think long-term fasting would have an effect on these biofilms?

Dr. Art Ayers said...


I enjoy your blog.

I think that fasting calms down the biofilms and may make them less inflammatory, but I don't think that it eliminates them. These microbiological communities shield themselves from external chemicals and feed on the nutrients from the leaky gut that they cause. Bacteria in the biofilm can tolerate 100X the level of antibiotics normally effective on them and genetic exchange within the community facilitates the spread of antibiotic resistance genes.

Fasting may be a good prelude to stripping the biofilms using a combination of common or traditional treatments for intestinal problems.

The new aspect of gut biofilms, is that they are the basis for so many common diseases, e.g. asthma, allergies, arthritis, autism, atherosclerosis, Alzheimer's?, etc.

Good luck with your paleo studies.

Thanks for your comments.

Anonymous said...

Dr. Ayers,

Aside from merely positing biofilm as an explanation of a myriad number of inflammatory diseases, are there any biological markers in blood, stool, or urine that would be proof of biofilm being present in a person's body. Or is the only proof a positive response to one of the many interventions mentioned herein?

I'm asking because before someone goes through intermittent fasting or some of the other somewhat extreme interventions, there should be some reason to believe that biofilms are there aside from just being chronically ill.

Stephan Guyenet said...

Hi Art,

Thanks for the thought-provoking post. I have a couple of questions and a couple of references that you might find interesting.

Where in the gut are these biofilms? And does the acetic acid in vinegar make it to them?

I've read a few papers recently that are potentially relevant to this theory. The first one is fascinating:

Changes in Gut Microbiota Control Metabolic Endotoxemia-Induced Inflammation in High-Fat Diet–Induced Obesity and Diabetes in Mice

Antibiotics protect against fructose-induced hepatic lipid accumulation in mice: role of endotoxin

Antibiotics prevent liver injury in rats following long-term exposure to ethanol.

Dietary fructose and intestinal barrier: potential risk factor in the pathogenesis of nonalcoholic fatty liver disease

Dennis said...

There seems to be some evidence that bismuth is active against biofilms. Bismuth subsalycilate is Pepto-Bismol.

Aaron said...

Stephan-- Interesting studies

You could almost use the 1st study as a prelude to reducing fat in the diet. Maybe another reason to up carbs in the form of low anti-nutrient tubers?

The second study is also interesting because while the glucose feeding mice didn't gain as much weight as the fructose feeding mice-- the fructose feeding mice were wreaking their livers-- probably why frutarians can stay thin on fruit (but then also start destroying their bodies!) I also don't want to count out the the possibility that the glucose fed mice weighed more because they had higher amounts of glycogen stored in their muscle tissue from consuming glucose.

thanks for the studies

Dr. Art Ayers said...

How can anyone be skeptical of my grand scheme? It explains so much.

Unfortunately, it is early days in the study of biofilms and inflammatory diseases. I am persuaded because I have been looking for a missing source of inflammation and a source for cryptic bacteria. The biofilms are obvious and candidates

There is a huge push to identify all of the bacteria in or on humans. It should provide a lot of information. It appears that biofilms shed community bacteria and fungi, so feces should tell the story. It might also be possible to use blood samples. I am not sufficiently familiar with the biofilm literature to give a good status report.

The approach that I have outlined is for a rather brief and mild treatment. If I had a major inflammatory disease, i.e. arthritis, I think that I would try something like this for a couple of weeks and change my diet, because it is relatively low impact and has such a high potential benefit -- a cure. Maintenance would just be attention to probiotics and avoiding further inflammation. This seems like a no brainer.

Dr. Art Ayers said...

Thanks as always for your input.

I think that biofilms are difficult to establish in the acidic environment of the stomach, because it should destabilize the polysaccharide matrix. (That may be a problem for babies on formula.) The small intestines and colon would be the common places. Leaky gut would be a problem in the small intestines. I don't know if anyone has examined cadaver intestines of different ages and disease backgrounds for biofilms. There are some very obvious studies to be done.

I need to think about the articles you presented. They are very exciting.

Dr. Art Ayers said...

Bismuth seems obvious ... in retrospect.

Thanks for the reference and comments.

Stephan Guyenet said...


I wouldn't extrapolate that from the rat study, personally. Rats don't react well to a high-fat diet. Maybe precisely because it disturbs their gut flora and causes an increase in intestinal permeability.

When you feed rats a high-fat diet, they eat more, gain weight, become insulin-resistant and inflamed. When you feed overweight humans a high-fat diet, the eat less, lose weight, regain some of their insulin sensitivity and sometimes have reduced inflammation markers.

So I believe that you can't extrapolate the effects of a high-fat diet from a rodent to a human. But high-fat diets in rodents are still a useful model for diet-induced metabolic dysfunction, even if the dietary stimulus isn't the same as in humans. For example, it has given us this nice hypothesis about intestinal dysbiosis/permeability playing a role in chronic disease. Now we should find out what causes the same condition in humans. I'm sure there's some data out there. I doubt the cause is a high-fat diet, but I'm willing to be surprised.


Those would be some interesting studies. I'll look forward to hearing what you think of those papers. The first two blew my mind.

Joanne at Open Mind Required said...

Thanks, Art. I enjoy your blog, too.

The inflammatory diseases you mention all respond exceptionally well to long-term fasting often with complete healing that is sustained when lifestyle and diet are addressed afterwards.

Forgive my ignorance and perhaps naivete, but I've read that the intestinal lining can be replaced in about 72 hours when fasting. I've also read that bacteria do not feed off living tissue but decaying matter.

Is it possible at all that a long fast could restore gut integrity and starve out these biofilms? Or am I just the victim of bad science?

I'm having a hard time reconciling the great success fasting has reducing and eliminating inflammatory diseases.

Dr. Art Ayers said...

So, the beef industry uses antibiotics in feed to manipulate gut flora to produce obesity in cattle fed a high carb, corn diet? Tell this to Michael Pollan.

Dr. Art Ayers said...

My first overview of the provocative articles that you brought to my attention, is that biofilms produce both chronic inflammation and leaky gut. Fat and fructose can aggravate the biofilms and produce disease symptoms.

The high fat diet used to produce obesity and diabetes was mostly corn oil, i.e. omega-6 oil. Once again, the high fat would be read by most to mean saturated fat, but in actuality, I think the article should read, "Corn oil causes obesity and diabetes via gut biofilms."

The use of antibiotics in the papers is to eliminate biofilm bacteria and demonstrate their involvement in symptom development. In humans antibiotics select for biofilms that are inflammatory and cause leaky bowel.

Thanks again for your contributions.

Dr. Art Ayers said...

You make an excellent point about intestinal development. The villi of the small intestines are constantly being regenerated by stem cells in the crypts. It is in the relatively stable crypts that antimicrobial peptides are produced. It seems that the expensive constant production and shedding of the tips of the villi is highly advantageous to avoid biofilms. It would mean that celiacs with flattened villi would be highly susceptible to biofilms.

Fasting should minimize food contribution to feed biofilms and force the biofilms to gain nutrients from the leaky gut. Blood sugar should also be at a low level. Perhaps the biofilms become dormant and perhaps even slough off during fasting. If this is the case, and it is supported by your anecdotal evidence, then fasting might be a good first step prior to the stripping procedure that I have suggested. Fasting may also be all that is necessary and may be the natural solution to most of our health problems.

Thanks for your perspective.

Kennedy said...

That is cool yeah, although while I think I understand the concept, I am not quite so clear on what exactly is Promethian fire? Excuse my naivete.

The Inuit like rotten fish, and Vilhjalmur Stefansson eventually took to it during his stay. Perhaps this has a specific benefit involving biofilms.

I imagine everybody has a buildup of biofilms to some degree, does this mean we can all benefit from regular probiotics or other measures periodically? I am all for fermented cabbage and whey protein! Dr. Stephan's Sauerkraut recipe of course, the stuff I currently have in the fridge is pretty foul.

Do you have any aversion to the use of fermented soy, nattokinase in treating biofilms? Hearing regular soy eaters have smaller brains by and large is very scary.

Dr. Art Ayers said...

I think that nattokinase is a great idea. I expect that this protease clips proteins at a novel amino acid context that is exposed, but involved in adherence of bacteria to the biofilm matrix polysaccharide. It might be related in specificity to some of the proteases (MMPs) that modulate cell signaling by altering binding to cellular heparan sulfate.

Prometheus brought fire to humans.
Mary Shelley wrote "Frankenstein: or The Modern Prometheus."

gunther gatherer said...


That is a great point about the possible effects of fasting on biofilms. It stands to reason that the entire biofilm-stripping protocol can be easily reproduced with a simple two week fast.

This also agrees with many anecdotal accounts of a "flushing", or massive diarrhea, occurring at about day 10 or 14 of fasting. This diarrhea is most likely a combination of dead biofilms, pathogenic bacteria, parasites and endotoxins which have accumulated over the course of a lifetime.

Aside from the understandable lightheadedness that must come from such a fast, the anecdotal evidence also gives numerous accounts of feeling full of energy, boosted mood and renewed zest and strength. I can imagine that one feels pretty young again after getting rid of all that junk.

Dr. Ayers, do you think that is what's going on in these fasts? Perhaps your protocol should include fasting too. Thanks for your great blog.

Dr. Art Ayers said...

Gunther Gatherer,
I think that it is quite possible that fasting has a major impact on gut biofilms. I don't think that it has been studied, because it would not be a mainstream subject of research and would be difficult to get funding. There would be no pharmaceutical support.

It would be interesting to see the results of people who are pursuing fasting for their own purposes.

Fasting would be an natural adjunct to some of the other approaches outline here for biofilm removal.

Bill said...

Dr. Ayers,
Coincidentally, 2 weeks ago, I had to fast for almost 48 hours, prior to having a colonoscopy, with 2 doses of picolax to help clear out the system. Drinking only clear liquids, which comprised of frequent cups of green tea and some black coffee and lots of water.
The ordeal went well and an interesting visual journey, 1.2 metres up my bowel all the way to the caecum, which was deemed normal.
On returning home, I took the dog on a brisk 4 mile walk. What amazed me, was how I was full of energy after 48 hours of no food.
The only "food" was the sugar in the sachets of picolax.
I literally felt to have more energy than I can remember.

I intend to continue carrying out 48 hour fasts, on a regular basis, to see if I enjoy energy boosts and I am assuming that it will be good for the body.

My question is, should I also use the PEG or picolax to help cleanse the system each time?
How often is prudent? I was planning on every 2 weeks.
Would it be useful to use turmeric added to the drinking? Can you suggest any other additives?
I have also considered using turmeric powder when brushing my teeth, to help reduce the plaque biofilms and prevent gum recession.

Dr. Art Ayers said...

Your observations are very interesting. As long as you have no symptoms of inflammation, i wouldn't think that it is necessary to do the whole PEG cleanse more than maybe once a year. After the biofilms have been stripped, it would make sense to keep them from building up again by using an anti-inflammatory diet and supporting the growth of probiotic gut flora. Plenty of tumeric, pepper and other spices should be helpful.

I would think that using tumeric to avoid dental plaque would be a bit unsightly. Some other readers may be able to recommend less dramatic alternatives. Chewing xylitol gum, for example, may address some of your needs and the saliva growth factors would stimulate gut repair. Hot tea is probably another good idea, except for the staining. Those may also be helpful during fasting.

I don't know enough about fasting to recommend length and frequency. I would probably seek the wisdom of traditional practices. It probably also makes sense, as others have pointed out, to move away from the standard three meals a day, to fewer meals. The idea of more frequent, smaller meals is designed for high carb diets. With low carb diets, there is less blood sugar swing and consequently, less hunger.

Thanks for your observations.

Dr. Art Ayers said...

Vinegar, acetic acid:
I think that the link between acetic acid and biofilms is interesting and has nothing to do with acid. I think that sodium acetate would also work. The seems to me to be that acetic acid makes soluble compounds with the divalent cations, e.g. magnesium, calcium and iron, that are holding the anionic polysaccharides of the biofilm matrix together.

This may also be a good use for phytic acid. A healthy gut may be the best way to ensure absorption of adequate minerals and vitamins.

Kriss said...

Hi Dr. Art,
Thank you for all the information on this blog.
There is a website from a man in Australia who is a kefir (probiotic drink) guru.
He describes his cure for ulcerative cholitis and IBD in general on this page:

It is a 7 day diet of brown rice (phytic acid?)and kefir grain enemas.
There is also a diet called the 'biofilm carbohydrate diet' that is modified SCD diet:
both are difficult to read and not as 'scientific' as your blog...but the ideas are there.

StephenB said...

I posted about EDTA in your August 3 blog comments section.

I further suggested that vitamin K2-MK4 might be a potential biofilm breaker.


dr j said...


just musing...

1. I wonder about the electronic charge role of Lithium in your biofilm big picture. My friend had it just last week and made an immediate big difference that now I wonder about the cation replacement effect on the biofilm.

2. Like Bill, I too have huge improvements after bi annual colonscopy ( we have a 2 generation terminal colon cancer issue and I dont want it to be a third).

3. As a semi-retired scientist, I dont have nice toys to work up my insights any more, just simple toys, internet and observation ( probably more perceptive now!) My biofilm study is limited to (my) tooth biofilms. I was recently struck by how white our uSA friends teeth were, and to my suprise, no peroxide, they used mouth squishing with sesame oil ( a technique called oil pulling). Weird. After 2 weeks on my experiment, I had a peer review this morning( ie my wife) and no more yellow near the base of the teeth. Peer reviewer now expecting same results on herself. Most of the film has been almost negligible since no grains, vitd etc, but the base has persisted slightly. I notice from my nose test on the floss at night, in some teeth gaps I can smell anaerobic bugs, so maybe there is a gradient of different species involved

4. Any thoughts on whether the amount of glucose carried in saliva and gut extrudate ( as an blood glucose leveling secondary mechanism ) is similar or greater than blood levels or is it volume driven.


Dr. Art Ayers said...

I think that most traditional remedies have a molecular basis. My explanation of how they work probably differs from the traditional view.

Probiotics and controlling the composition and function of the gut flora is a major components of health. Biofilm formation is an illustration and keeping destructive biofilms off the gut surface is very important in overall health. Kefir helps to develop a benefical gut flora.

Brown rice or rice in any form is going to be hyperglycemic at some level. It doesn't seem to be as inflammatory as wheat and doesn't have the gluten problem. I don't know if ingesting or otherwise using lots of brown rice affects biofilms. I would be skeptical.

Dr. Art Ayers said...

In retrospect, I was wrong about my initial perspectives on EDTA. I had thought that people were trying to remove heavy metals from their systems with EDTA and I thought that was neither the problem nor a reasonable solution.

Use of EDTA to treat the gut surface is a different matter and combining that with the removal of cations from a bacterial polysaccharide matrix now seems reasonable. Of course EDTA would be just a one shot treatment in which the amounts must be carefully controlled, otherwise mineral deficiencies are certain.

All of the vitamin K treatments are interesting and I don't know enough yet to comment. I have know idea what to expect of vit K on biofilms.

Thanks for your input and persistence.

Dr. Art Ayers said...

Dr J,
I have no idea how Li would affect biofilms. I would think that the impact would be minimal because it is competition of a monovalent for a divalent, e.g. it takes a lot of Na+ to supplant Ca++. Li is a lot smaller with a more prominent + charge, so maybe it would destabilize the biofilms anyway. Since I don't have a rationale for how lithium impacts mental disorders neurologically and most mental conditions have their foundations in nutrition or gut problems, maybe lithium should be examined for its impact on biofilms.

Oil pulling seems to be an attempt to impact biofilms by altering water structure using emulsions. A large amount of oil relative to mouth water is vigorously forced through the teeth to convert a water-oil mixture into an emulsion of structured water next to oil droplets. The result is that little randomly oriented water remains surrounding the polysaccharide matrix that hold the bacteria in the biofilm on the tooth surface. Since the polysaccharide/bacterial agglutinin interaction is primarily hydrophobic and dependent on random water, the bacteria are released from the polysaccharide.

This is a process akin to hydrophobic interaction chromatography. In which hydrophobic binding is first enhanced to get proteins to stick to a hydrophobic matrix and then the hydrophobicity of the solvent is gradually increased to elute proteins based on their hydrophobicity. Ethanol could also be used. Blue Listerine is claimed to impact plaque and it uses ethanol with menthol and thymol. It is also blue, and several blue dyes, e.g. Coomasie Brilliant Blue and methylene blue, bind to negatively charged polysaccharides.

It would be interesting to see a colonoscopy after a quick rinse with a dye that binds selectively to biofilms.

I don't know the relationship between saliva composition and serum, but it would be very interesting to know the relationship between diet, saliva and biofilms (tooth and gut).

Thanks for the provocative observations.

dr j said...

thank you for the great effort you have gone to over my qns!

Re Methylene blue, i read some time ago that this was given to soldiers in WW1 for infections and they hated it as their urine was blue and it could be seen while visiting the latrines!

re teeth , following your thoughts, the first step to me at the macrolevel is to disrupt the boundary layer. I could get a paint brush and paint the tooth/gum interface with vodka , then paint methyl blue over that and then do a forced oil squish to allow some infacial interactions to proceed. and then observe.

Much of the biofilm control must come from the saliva chemistry and pH as it is a constant batheing.

You've sure got my brain ticking..

Dr. Art Ayers said...

Dr J
Thanks for reminding me about the medicinal uses of methylene blue. I used to use it to cure my aquarium fish if ick, a scale fungal infection.
Methylene blue and fluorescein have related structures. It is interesting that fluorescein is used as a revealer to show plaque on teeth.

That also reminds me that my wife used gentian violet to treat our kids for thrush when they were nursing. The dye transfer was very amusing -- I suffered in silence. I also read that gentian violet (also called methylene violet) was used to treat WWI soldiers for STDs when they returned from leave. It sounds like a variant of the voting procedure used in Afghanistan.

Kennedy said...

Dr. Art and others,

I think the beneficial effect from Lithium in Mental Disorders comes from it causing Hypercephaly, somewhere in the region of 15% in certain brain areas in those who take it.

It apparently suppresses the efflux more than the influx of choline into the brain. Could involve a healthier BBB I suppose.


Oh Penelope said...

So, Dr. Ayers, you would recommend using treatments like vinegar, pectin fiber, etc. instead of antibiotic treatment for H. Pylori? Or would it be best to use antibiotics, but first try one of your recommended treatments? I was just diagnosed but would like to avoid the mega doses of antibiotics that are necessary for treatment, which I believe will just lead to greater problems down the line.

Do you think there is some credence to the theory that H. Pylori is part of normal flora (in small amounts) and one shouldn't attempt to eradicate it completely with antibiotics?

For dissolving biofilms, would vinegar or kombucha be contraindicated in the case of H. Pylori because of the acid content? I also have a yeast allergy.

What are heparin and bismuth, mentioned for treating biofilms?

I take MK7 (nattokinase) pills about 3 times a week. Is this effective, or do you recommend securing it in food/liquid form, or breaking open the tablets?

Finally, I currently supplement with large amounts of iron, magnesium, calcium, and other vitamins. Is this a bad idea, taking biofilms into account, and if I cleanse my bowels, should I stop this for the duration of my cleanse?

Nick said...

Art, I hope all is well with you and you are enjoying a great vacation somewhere!

Dr. Art Ayers said...

Sorry that I didn't get back to your comments sooner.
Nick seems to have noticed my dereliction.

H. pylori reveals how little we know about gut bacteria. I think that the species designations are bogus, to begin. That means that H. pylori is actually a diverse group of bacteria defined by their habitation in the stomach, i.e. they have all of the genes needed for their existence in that environment, but sequencing of genomes of Hp from different sources would produce very different results.

So there are races or strains of Hp, dependent on prevailing diets. Some of these strains, particularly in Asia, tend to cause stomach cancer. Interestingly, genetic predisposition to stomach cancer is dependent on genes involved in inflammation, e.g. Il-1, TNF.

So retaining Hp is problematic. I also think that H. p in the stomach probably does not involve biofilms, because of the acid environment. So, attacking the biofilm matrix with simple approaches is not an option. It is probably impossible to eliminate Hp with simple dietary approaches.

I would personally probably opt for the antibiotic treatment and use it as an opportunity for a whole body purge of biofilms and cryptic bacteria. At the same time, I would be very concerned with keeping my gut closed and start to shift to probiotics as soon as possible. I would not start if I had any other sources of inflammation. It might also be a good idea to prepare by fasting and then adhering to anti-inflammatory guidelines for diet.

Bismuth is something of a traditional (Pepto-Bismol) treatment for diarrhea. It is a metal, related to arsenic. I haven't looked into it, but would treat it carefully.

Heparin is a mixture of fragments of the sulfated acidic polysaccharide that is attached to the surface of most cells. Heparin is released from mast cells and these fragments interfere with interactions/signaling at the cell surface. Heparin is released onto the surface of the intestines to protect against binding of bacteria and viruses. Heparin also interacts with dozens of steps in blood clotting and complement action. Heparin is widely used to block blood clotting, i.e. a blood "thinner". There is a major effort to find a formulation for heparin that can be given orally, since heparin is rapidly recycled by the lining of the intestines.

I think that heparin should be developed for oral treatment of the gut. It should close the gut (kidneys and brain) and also block adhesion of pathogens. It could be a modern treatment for the modern inflammatory diet. Doctors are afraid to pursue heparin use outside of IV use, because of bleeding fears.

I would stick to natto, because I don't know the impact of concentrated application of nattokinase in pill form. The fermented soy beans have a protease related to the enzyme used in detergents. I would go with the traditional use.

I don't understand the large use of mineral supplements. We should have tremendous amounts in whole foods. If I were trying to attack biofilms, which I would only do periodically, then I would avoid mineral supplements, since calcium and magnesium cross-link biofilm matrices.

I don't think that most bowel cleanses actually remove what I think is the target, biofilms. Most just empty the colon contents and leave the biofilms clinging to spots on the small intestines and the colon.

I don't think that most multivitamins do much. I think that lots of different vegetables and larger amounts of selected vitamins, e.g. D3 and C, may be a cheaper and more effective approach. Of course, this is in an anti-inflammatory context of low carbs, higher protein/fat. I think that most of the focus on anti-oxidants comes from a response to the inflammatory quality of most modern, i.e. high carb, low fat, diets.

Thanks for your comments and questions.

Nick said...

Hey Art, brain slip on my part, I thought it was the 20th yesterday! I am very appreciative of all the effort you put into your blog!

Anonymous said...

Doug Kauffman ( recommends psyllium husk as fiber supplement in aiding removal of fungus from body/gut etc. Very interesting stuff that I made a lot of connections to as I read your blog.

As a grass fed beef producer, thanks for your support! Although we don't sell to the supermarket so they aren't grass fed after they leave her unfortunately. We do feed a few of our own for about 6 mos with oats and hay before we butcher for our yearly meat supply. We have been talking about trying to do it just grass for ourselves.


Dr. Art Ayers said...

You grass feeders are among the few bright spots on the food scene.

I think that feeding grain/corn to cattle is a way of producing metabolic syndrome and obesity that ultimately would kill the cattle. The industry has to hurry to butcher them before they die.

Keep pushing for healthy, grass-finished beef. I think you guys are food heros.

Cristian Stremiz said...

I think you'll find interesting:

Dissolve Biofilms With Fibrinolytic Enzymes

Dr. Art Ayers said...

That is another great article that points out another piece to the biofilm puzzle. It seems that one of the characteristics of the biofilm matrices is binding to fibrin. The biofilm becomes like a decorator crab adorned with host proteins.

This also partially explains why some proteases are effective against biofilms.

Thanks for you ongoing input.

Pastor LN said...

I wonder if vinegar would be appropriate in my situation...I eat an anti-inflammatory diet, take fish oils,probiotics, and glucosamine daily.
I broke a tooth, got a bacterial infection, was prescribed a "cocktail' of clindamycin/prednisone by the dentist.
Within 2 days diarrhea began, in 10 days I had severe flu symptons. 7 days later the diarrhea returned w/blood &pus in the stool.
Diagnosis: c.diff.
Began flagyl and the same day intense swelling in the wrist and knee. Can't walk or use my hand.
Doc says it is an inflammatory attack. I upped probiotics, ibuprofen, anti-inflammatory foods.
Should I add vinegar?

Dr. Art Ayers said...

Pastor LN,
This is rather complex. I assume that you are under continuing medical care and will only make supplemental suggestions.

I suspect that the antibiotic/steroid combination killed some bacteria and suppressed inflammation. Since the response was increasing inflammation, I assume that there was a reservoir of cryptic bacteria and biofilms that were disrupted, releasing endotoxin into your system. Following that with NSAIDs will produce local leaky gut and contribute more bacterial exposure.

For immediate relief, I would start using the vagal stimulation procedures suggested by Nigel in comments on my current post from last week. I would apply castor oil in a wide area around the inflamed joints. (Menthol/Vicks VapoRub or capsaicin may also provide relief and reduce inflammation. A hot tub may also provide some relief.

I would then get plenty of sunshine (never burn) and make sure that I had optimal vit.D. I would try to close my gut with glutamine and make sure that I had no wheat or other grains in my diet. I would do a whole bowel irrigation with PEG, e.g. GoLytely, and then follow with vinegar, pectin and nattokinase. Then I would build my gut flora up with probiotics, increase the fish oil and add freshly ground flax seed (fiber, pytic acid, ALA).

This is a one day cure. It should be relatively gentle. Let me know how it works out.

Pastor LN said...

Thanks so much for responding quickly. I AM under medical care. Doc just called back w/blood test results. Red/white blood cells are great. CRP very high along with ASO, indicating systemic strep. Where did that come from???
He is sending over Amoxicillin (considered clindamycin but knew I'd balk since it started the whole process!).
I am already doing most of the things you suggested but haven't tried the GoLytLy....had fresh flax seed this morning! I'm in Colorado...thank goodness it's a sunny day. Am supplementing D. Also taking Sunday off!
I definitely appreciate your response and am grateful for the research you are doing. Blessings!

Cristian Stremiz said...

Dr Ayers,
something about EDTA inactivating Clostridium difficile toxins:

Augustin said...

For more info on Dysbiotic Biofilm check out this post from Dr. Kara Fitzgerald:

Quorum Sensing/Quorum Quenching: Treating Dysbiotic Biofilm

Dr. Art Ayers said...

A quick read of that article indicates that the toxins bind divalent cations and EDTA should be a good chelator of the same cations. Hence, EDTA should inhibit the function of the toxins.

Thanks for all of your interesting inputs!

Dr. Art Ayers said...

That article and others on this commercial site for stool analysis, basically reinforces all of the molecular relationships that I have put together on this blog. Their recommendations seem to point to biofilms, but don't overcome the inherent refractory quality of the biofilms to analysis, i.e. biofilm community members will be underrepresented in feces, and elimination.

I think that the stripping approaches make sense. I have also written an article about the ability of spices to block quorum sensing.

It is interesting to read a compilation of all of the same ideas that I have developed from basic principles reading the biomedical literature.

Thanks for the input.

Dr. Kara Fitzgerald said...

Dr. Ayers-
I am glad you found the blogs at to be in keeping with your own findings. I hope you enjoyed reading them as well.

Yes, it is difficult to assess biofilm using a stool sample. I know some clinicians consider stripping just prior to collection, however I am not sure of the efficacy (or evidence) of this approach. I think at this point the only way to assess for dysbiotic biofilm is clinical history combined with a stool sample that included microbiota and chemistries such as IgA and fatty acids.

I hypothesize on what a functional assessment of healthy biofilm might be in my blog post IgA: The "I" Stands for Interesting. I think that making sure the "ingredients" are present for a healthy bowel environment will aid in the inhibition of pathogenic or dysbiotic biofilm proliferation.

Your blog is fantastic. Also- I’d be interested in reading the article on spices and biofilms. Is it available?

Sue said...

How much vinegar, pectin, natto? What is source of pectin - green apple?

Justin said...

Dr. Ayers,

Your blog is awesome. I have a question for you that may be related to your biofilm/inflamitory disease theory. A friend of mine has been diagnosed with Idiopathic Pericarditits accompanied with pericardial effusion. I assume that idiopathic means they have not found a root cause. He is currently in the hospital for a possible stroke (not sure if related to his condirion). I was wondering if you have any experience with this kind of condition? They are currently treating him with prednisone but he was not real happy about the side effects. Not sure if he uses NSAID's on a regular basis either. He originally developed the condition in high school (12 to 15 years ago). Any insight/information that you could give me would be greatly appreciated. Thanks for the awesome blog and I look for to your next post.


Dr. Art Ayers said...

I haven't pondered this inflammation of the membranes surround and lubricating the heart so that it can moves under the ribs and next to the lungs.

Typically, pericarditis is considered to result from viral infections or as a consequence of some autoimmune disease, e.g. lupus. In either case, the inflammation means that the vascular system of the membrane is signaling for the offloading of macrophages, neutrophils, etc.

My response to inflammation is to treat with my recommended Anti-Inflammatory Diet. Check for optimal vitD, lots of omega-3 fish oil and supplemental probiotics. In this case, I would also recommend vagal stimulation exercises. The NSAIDs are a possible problem with subsequent leaky gut.

Those are my thoughts. Of course they do not replace normal medical attention.

Justin said...

Dr. Ayers,

Thanks a lot for your feedback. I gave my friend the URL to your site and also let them know about the inflammatory diet and vagal nerve stimulation.

While doing some searching on the web I saw where someone applied for a patent on a treatment protocal using guaifenesin to treat lymphedema. They also imply that the root cause is related to leaky gut syndrome caused by the usual offenders (gluten, casein, NSAIDs). The undigested proteins are able to permeate the intestines and then make it into the different cavities of the body. This then triggers the immune response and then inflammation follows. Kind of interesting.

Thanks again for your help.


Heather Twist said...

A note on phytic acid: I've been taking IP6 to help with iron overload. It has worked nicely. It is NOT bran ... wheat bran would about kill me and I find rice bran irritating. I take it between meals so it does not interfere with absorption of magnesium. UNLESS the meal is high in iron. Then I take the phytate to prevent iron uptake.

I also take konjac. It *is* a biofilm of sorts, but it is one that does it's own fighting against other bacterial films.

I don't think the whole iron issue is talked about enough though. Iron feeds many of the less desirable bacteria, and many of the foods associated with health (tea comes to mind) interfere with iron absorption. Iron is taken up by the gut cells and stays there unless needed, but in the meantime, the gut bacteria can access it.

Dr. Art Ayers said...

Heather Twist,
I enjoy your perspective on iron and phytate. There is a lot of competition for iron in the gut. A very nasty example comes from a comparison of breast milk vs. formula. Interestingly the breast milk has only a small amount of iron bound to carriers like lactoferritin. The formula contains about 500 times as much, because it contains free iron and formula quickly causes a shift in the newborn gut flora to become adult gut flora. It takes 500 times as much to avoid iron deficiency, because the gut flora grab it all. The formula companies then brag that they have much more iron and without that level the babies would be deficient, which would be quite possible with partially breastfed babies. Isn't industry wonderful?

Iron control is a big deal for organisms. Human lactoferrin is produced as part of the innate immune system. Eggs also control iron to maintain sterility. Bacteria secrete siderophores to chelate iron and permit proprietary capture of iron.

Phytate is very special. It was found bound in the center of a plant hormone receptor, when crystals of the receptor were analyzed by x-ray crystallography. And of course phytate and its sisters interfere with proteins binding to heparin, i.e. phytate mimics nucleic acids and GAGs by binding to groups of basic amino acids.

Gut bacteria may keep us healthy by removing excess iron from our diets.

Eating red meat without a properly adapted gut flora to remove the excess iron may lead to health problems.

Thanks for your comments.

doug said...

Dr Ayers,
Do you have any opinions on the use of DMSO as a carrier to treat biofilms? I have used DMSO/colloidal silver (50/50) and it seems to do a good job.


Dr. Art Ayers said...

DMSO is an extraordinarily powerful solvent and I use it very carefully in the lab. It has lots of bizarre effects and can readily transport other chemicals into the blood stream. I would not use it as a carrier for anything to be taken internally.

DMSO is too cheap to be considered for drug development, so it is essentially unexplored. I think that it may have many beneficial uses in medicine, but I wouldn't touch it until it was examined for safety issues.

Thanks for your comments.

Anonymous said...

Thank you for this very interesting blog. As someone who has had chronic inflammatory issues, set off by Lyme disease and subsequent damage to the gut by antibiotics, I wonder if you can explain why many of the things you recommend leave me with agonizing abdominal pain. For example taking glutamine causes severe pain in the gut and I cannot continue takinig it. Also, certain probiotics, proteolytic enzymes, curcumin. The pain is unbearable, so it is not just a simple die-off reaction to be endured.

Dr. Art Ayers said...

I have been puzzling over the paradoxical reaction of antibiotic-compromised GI to typical anti-inflammatory treatments for the last year. You can find an article that I wrote on the subject by searching "paradoxical".

Many of the chronic diseases, CFS, Lyme, rosacea, have a powerful gut component. Most of the anti-inflammatory suggestions that I make, including fish oil, vitamin D, probiotics, vagal stimulation and even low starch, can lead to profound GI responses and trigger inflammation in other areas of the body.

Likely candidates are antibiotic resistant gut biofilms, gut lining, immune system components. Compromise of these components by antibiotic treatment will also lead to dysfunction of the immune system, because development of T cells takes places predominantly in the lining of the gut. Tampering with the gut flora or with chronic inflammation of the gut may lead to histamine release.

I would be curious to know if there is anecdotal evidence that oral anti-histamines or oral heparin mollify the effects of the paradoxical treatments.

Thanks for your comments.

Dave Mc said...

Hi Art,

Great thread, love the comments...

Questions: would another laxative work (eg. Senokot), or would PEG be best?

What source of pectin would be good?

Looking forward to trying this...

Dave Mc

Dr. Art Ayers said...

Dave Mc,
I think that there are big differences in the way that laxatives work and their impact on biofilms.

Continuous use of laxatives is destructive to the gut and gut flora. Constipation is the typical reason for laxatives and constipation is a deficiency in bacteria in stools (not insufficient fiber or dehydration.)

Senna and other irritant laxatives cause inflammation of the bowels and should be avoided.

PEG is an osmotic laxative that absorbs water as it hydrates and swells. PEG also disrupts biofilms by attacking the hydrogen bonds that hold the acidic polysaccharides together and to the bacteria. That is why I recommend PEG for biofilm stripping.

Thanks for your questions/comments.

Dr. Art Ayers said...

Dave Mc,
I don't think it matters what the source of pectin is. Some people use the liquid pectin packaged in envelopes for jam and jelly making. I think that apples may also be a good source to try.

Dave Mc said...

Thanks. I have an unopened package of the Senokot lying around, thought I might save a few bucks, but I'll go with the PEG.

Thanks for all the posts; the biofilm angle is very interesting.


NICHOLAS said...

Hi Art,

Thanks for the link to this thread.

I was hoping you could clarify the benefits of pectin in treating biofilms.

In one of your responses you stated "The biofilm matrix is like jelly, a gel formed by acid polysaccharide, pectin, cross-linked with calcium."

I took this to mean that pectin is part of the structure of the biofilm matrix. However you also mentioned that taking pectin can disrupt the biofilm structure.

Also, would orally administered vinegar in water reach the large intestine, and is apple cider vinegar a suitable type.

Thanks again,


Dr. Art Ayers said...

Some people find that pectin gives them relief from inflammatory diseases, such as arthritis. Since it is unlikely that pectin leaves the gut, there is a suggestion that it influences inflammation via the gut flora. Since pectin is an acidic polysaccharide, related in structure to the acidic polysaccharides produced by biofilm-forming bacteria, it follows that pectin acts like those biofilm polysaccharides, but alters the biofilms to lead to a healthier effect. Bacteria live in biofilms throughout the GI tract, with most of the bacteria in the colon, but most of the surface area is in the small intestines.

I would guess that most of the immune system impact is in the small intestine and part of the rapid turn over of the villi cells may be to shed biofilms. Most of the defensive anti-microbial peptides are produced at the base of the villi.

Pectin is supposed to help probiotic bacteria develop in biofilms and vinegar is supposed to remove minerals that stabilize biofilms. I don't know how far ingested vinegar/acetic acid moves into the intestines before being absorbed. I think that all forms are equivalent with respect to the acetic acid.

NICHOLAS said...


Thanks for clearing that up. I really appreciate this blog.

Also, are you referring to the regular apple pectin.



Dr. Art Ayers said...

I think that some pectins are methylated, but I don't think that it much matters after you eat it. Apple pectin is fine and is probably the most common.

Pectin is a common constituent of all primary plant cell walls. I was a graduate student in the lab that determined the structures of many of the plant cell wall components.

Thanks for the comments.

generic viagra said...

In my opinion, many of the cures for diseases are on the same substances that the body produces. As mentioned in my blog, many diseases are treated successfully with common atibiĆ³ticos, but others must be treated with antibiotics made from various substances in the body.

Anonymous said...

Dr, Thanks for all this great information. I would like to know if N-acetylglucosamine help to strip the candida albicans biofilm matrix.

Dr. Art Ayers said...

I would expect any effect of N-acetylglucosamine to be minor on biofilms. I can't think of any mechanism except perhaps interacting with transglutaminase, but that shouldn't have much impact on biofilms.

Berberine might be useful, since it interacts with some negatively charged polysaccharides and has broad anti-microbial activity.

I still think that antifungals would be more powerful in the presence of biofilm destabilization.

Let me know what happens.

Anonymous said...

I forgot one important thing that I need to tell you to get your best advice. I was diagnosed with Gluten intolerance by So, it is my belief it can be the root cause of my candida and leaky gut. I am not an expert but reading I have discovered that the intestinal villi play an important role in the immune system and allow the proper secretory IGA function inside of the gut. I have been gluten free but not as serious as I should. My point of view now is I won't get done with my intestinal candidiasis until the villi be healed and the gut immune function be recovered. Dr, I would like to get your opinion about it because I know you are an expert in this matter. Thanks for your time... we need hundreds like you!
Many Thanks,

Dr. Art Ayers said...

Gluten intolerance/celiac is under diagnosed and contributes to a substantial portion of autoimmune diseases. The compromise in autoimmunity may be made to have more severe consequences by secondary infections, such as candidiasis. Loss of microvilli may also contribute to pathogenic biofilm formation.

One of the other things that you might do to help recovery is fasting. Spices and herbs may also be helpful.

Bifidobacteri probiotics also help to eliminate gliadin protein fragments that contribute to celiac symptoms. Glutamine should also help.

I would continue to work to eliminate both the celiac as well as the candidiasis, as you work on a health gut and gut flora.

lalla said...

there has been mention of vagal stimulation. i can't find information on this blog about this therapy. wikipedia gives and explanation and says there is a device one may buy. is that what is being referred to?

Dr. Art Ayers said...

I put links to vagal stimulation exercises into the article that mentions them and entered as a tag in the index. The search function for the blog is at the left in the blue bar at the top of the page.

Anonymous said...

Do probiotics form a beneficial biofilm?

Dr. Art Ayers said...

Probiotics and biofilms:

The bacteria commonly found in probiotics and fermented foods produce biofilms, interfere with the biofilms of pathogens and temporarily alter the dynamics of gut flora. The impact of probiotics is dependent on the existing gut flora.

Dozens of different bacteria and fungi inhabit any given biofilm. The inhabitants of the biofilm continually change. Biofilm formation also stimulates exchange of genes between bacteria of different species in the biofilms. The biofilms are continuously shed along with the surface cell layer of the gut as new epithelial cells are produced and differentiate.

The food eaten, existing gut flora and communication with the cells of the gut all continually change biofilms and gut flora. Probiotic bacteria are gradually diluted and are only temporary members of the gut flora, but they do alter the gut flora that remains.

Thanks for the question.

Anonymous said...

Hi Dr Ayers,

I've been doing apple cider vinegar enemas to strip what I think is a candida biofilm from my large intestine. I do the enemas after doing a PEG flush and have on numerous occasions produced a mostly white slimy film which also has a clear component. I was convinced this must be a candida biofilm, however lab tests that I arranged thru my Dr. came back as inconclusive or as "bowel mucus", which is very frustrating. Do you think it matters what type of microscope the lab is using to view the specimens? Do you think a confocal scanning laser microscope or electron microscope is what's needed or would a regular optical microscope suffice? Whatever it is I feel much better after eliminating it from my body. BTW Virgin Coconut Oil which is high in medium chain fatty acids also seems to help strip this film from the intestine. Does that seem to fit in with what you already know about biofilms. Thanks for your help.

Bob said...

RE: apple pectin, "an apple a day" and other thoughts.

NOW Foods (a supplement company) provides a product called: Apple Fiber - with Apple Pectin (12 ounces - 340 grams per bag) I bought my bag for $3.20 on 09-05-10. Ingredients: 100% pure apple fiber.UPC code: 3373905908
I created a solution of this pectin product using spring water from Ozarka Natural Spring Water (which in my area comes from two springs in Texas - pH: 6.25), and then put one (1) Now brand Calcium Citrate tablet into the solution for 30 minutes (UPC code: 3373901230).
I also created a "control" using the same water and dropped another tablet into that solution.
The way the tablet in the apple fiber/apple pectin solution broke down was very interesting - especially compared to the control. The control dissolved in a manner similar to what you might expect.
I suspect within the chem lab world the unexpected method of breakdown in the apple fiber/pectin solution might be easily explained - but as a layperson it was most curious to me. Instead of simply dissolving it appeared to "grow very slowly" and turn into a fluffy powder form and come apart. When left overnight on a flooded bed of wet apple fiber the original ("horse pill size" - i.e. 9mm x 21 mm x 5 mm) calcium tablet made some interesting additional changes (creating a glue-like substance - which I suspect is pectin probably isolated from the apple fiber).
My thought is: if there is calcium citrate in a biofilm, it sure looks like dietary pectin may be able to wreak havoc on it - and yet I believe in this blog there is a note that suggests pectin may be incorporated into such a biofilm. Based on what I saw the apple fiber/pectin do the calcium tablet - that seems very likely. What it created was a glue-like substance that contains calcium granules. My thought is: maybe the fiber in the apple fiber or even in an apple is what "moves" that stuff along in a normal transit time situation - but in an impacted situation it might have time to "attach," etc.
Whether or not the pectin would work on other forms of calcium is also open to discussion. But this may help explain why "an apple a day...." works so well. The other interesting part is that pectin's ability to work on the calcium may be able to "survive" oral/stomach/small intestine ingestion, whereas any other obvious (i.e. acidic) substances may well be altered to a more alkaline state in the duodenum.
Two more interesting side notes: the calcium tablets used were coated with (vegetable) magnesium stearate, silica and vegetable "coatings." This only proved to be a problem when testing various other options when the tablet was immersed into a solution of Epsom salts - which appeared to have a difficult time "peeling" the coating. Willard Water also wreaked havoc on the tablet in an hour's time. WW and WW-mixtures are generally highly alkaline. Aside from its normal surfactant capabilities, the level of alkalinity may be able to at least in part survive transit through a normally acidic stomach - that may help to explain why people who drink properly diluted (mixed) Willard Water and spring water (e.g. on occasion - not all of the time) appear to have better bowel conditions – although it could just be due to the unusual capabilities of the Willard Water (see: Aqua Vita, ©1987-1992, by Roy M. Jacobsen). Similarly, vinegar may be beneficial in such situations due to the enzymes in it, rather than any acidic action (which might not exist after having transiting the stomach/duodenum).

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Heather Twist said...

Re: Phytic acid and calcium: there seems to be a sea change going on in the attitudes toward this. Phytic acid might actually HELP in bone production, and it doesn't seem to impair zinc absorption either. Given that societies that eat whole grain are typically healthy (unless they get very, very little meat or other food), this makes sense. See:

Also, on red meat: Thanks, Dr. Ayers, for the info on bacteria handling the iron, and formula. I think infant formula might well be one of the BIG reasons kids are having so many health problems these days. But I'm also curious about the whole neu5gc issue: human beings don't produce it, and many find it inflammatory. Which might be another big problem with beef in the diet. But also: isn't neu5gc produced by some microbes?

I've been experimenting with a "Japanese diet" of mostly fish, eggs, and chicken, with white rice. And my IP6 and konjac, and some vinegar daily (I make a great dipping sauce!). My gut is absolutely working great these days. No inflammation at all. My joint swelling also disappeared.

[M] said...

Thank you for the informative article. Do you think that things like goldenseal and tonic water are useful in disrupting biofilms? If so, is tonic water safe for children? Are things like liquid bentonite/zeolite useful in "mopping up" after the the biofilms have been disolved (when mixed with pectin/fiber)?

rmagliozzi said...

This is a great post. I have a 7 yr. old with autism and PANDAS. however, I would not give him whey. Anything with casein in it makes him and many autistic kids act totally crazy and regress. Is there a few formulas you know of that have some of these biofilm destroying agents in them? I always change it up to keep ahead of the bacteria and yeast and inflammation, both antifungals and probiotics, but would love to have another option on our radar we can rotate in every few months or so.

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Anonymous said...

Someone had asked in an earlier comment of how much vinegar, pectin and lactoferrin followed by a shot of natto (fermented soybean), Can you give a dosage?

Alex said...

I'm currently struggling with C. freundii dominated biofilms. I used nattokinase for 2 days; on the second day I got a nosebleed that lasted for 15-20 minutes, and was using 1/3 of the bottle-prescribed "therapeutic dose". I'd just like to warn people that nattokinase is essentially a blood thinner, and a powerful one. Be careful with it.

After that debacle, I switched to garlic, an enzyme mix, doxycycline, and heavy probiotics (all on an empty stomach, first three at night and probiotics in morning and midday). Results are quite visible after only a few days - the white coating on my tongue is receding somewhat and my acne is almost completely gone (which is good considering I had about a hundred spots at the height of the infection).

Anyways, biofilms seem to be a good thing unless bad bacteria establish themselves. Then it's a huge pain to get rid of them.

David Sullivan said...

Hi Art

Great blog. I suffer from "canida related complex" or yeast overgrowth. Candida Albicans is the likely suspect, and biofilms gives good reason as to why people initially respond to anti-fungals like diflucan, but when they go off the medication, the symptons return. This reminds me of the initial AZT experience in the treatment of HIV in the 90's actually. Very parallel reasoning with, once again, pathogens hiding out. Anyway, I just read a 1982 paper on the temperature profile of Candida Albicans in the Journal of Basic Microbiology, and well growth stops at 42 degrees celcius, and the deathrate climbs from there. Do you think biofilms would have a similar heat profile, or even if they could withstand greater temperatures, could the translation of heat cause damage to the microbes housed within biofilms?


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Monica Perdomo said...

Hi, I have been reading all of the comments for while. Very interesting information and hypothesis. I have autoimmune problems, had had psoriasis since I was 10 and it then developed to fybromialgia and food allergies/intoleances. I have been using nystatin, candida diet and disenzitizing therapy with some success but I have relapsed. I Kept wonderinf if I had yeast, and it went away, why would it come back. The biofilm theory makes a lot of sense to me. I reckon it has to be a combination of yeast and other microbiota in my gut. I do not want to keep taking medicine to keep the symptoms at bay, I am sure there are ways to cleanse my gut and repopulate... but for what I have read, lactobacillus are not in a grown up gut for long, unless you are an infant that consumes milk. And also the microbiota is so diverse that after you kill lots of good and bad bacteria, how do you repopulate other than probiotics? I have read that the appendix has a starter culture... how do I get rid of mercury, rid of the suspected biofilm then repopulate with a good variaty of bacteria? What would be the best protocol you reckong? Thanks.

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Leila said...

Dear Dr. Ayers,

I have tried many of the remedies recommended on your blog. But after substantial improvement during the first weeks, I am currently geting side effects from whatever I try. Currently, if I take nattokinase, coconut oil, lactoferrin or culturelle, it is ok for a few days and then bumm! I get extremely strong pounding heartbeat at night. It feels absolutely prohibited to continue. I stop for a day or two and continue with the same or something else and then again the same procedure. what the holy cow can this be? I am totally stuck and desperate... don't know any further...any hint would be more than appreciated! Thank you!!!!!!