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 .

Saturday, March 15, 2014

Health Diagrams II — Curing Autoimmunity and Allergies

In this second in a series of posts explaining the concepts that I think are central, but misunderstood, about health, I am focusing on how diet and gut flora impact the immune system and cause autoimmunity and allergies.  This cause also suggests a simple cure.
Gut Flora to Tregs to Suppression of Autoimmunity
It is important to understand at the outset that autoimmunity and allergies are caused by a damaged immune system, and repairing the damage cures the diseases.  Damage to the immune system typically represents a break in the continual development of immune cells in the lining of the intestines.  Immune cell development in the gut is dependent on bacteria, the gut flora.  Damage to the gut flora, e.g. by antibiotics, processed foods that lack flora feeding fiber or extreme diets, disrupts development of immune cells.  Typically, loss of the immune cells that keep the aggressiveness of the immune system in check, regulatory T cells or Tregs, results in autoimmunity.  Fix the gut flora and autoimmunity recedes.  


Health Requires Suppression of the Aggressive Immune System
For simplicity, I am focusing on the T cells of the immune system that develop in the intestines and either kill other human cells that are dangerous, e.g. virus-infected or cancer cells, or provide protection by regulating the aggression, Tregs.  Normal functioning of the immune cells permits elimination of damaged or dangerous human cells, while at the same time avoiding rampages of lethally armed T killers.  Examples of untamed T killers in action are degenerative autoimmune diseases, such as arthritis, asthma, prostatitis, celiac, Hashimoto’s thyroiditis, type I diabetes, inflammatory bowel diseases and atherosclerosis. 

Milk Births Baby Immune System
It should not be surprising that the focus of immune system development is the gut.  We start as babies with explicit links between nourishment and immunological protection.  Milk connects the immune systems of mother to baby.  Immune cells from the mother are transferred in milk and colonize the respiratory and digestive system of the baby — the mother’s immune system coats and buffers the baby’s exposure to the world.  Milk hormones close the baby’s gut and milk bacteria are the first probiotics that exploit the milk prebiotics (bifidus factor, human milk oligosaccharides) to produce a gut flora.  [Also note that most commercial probiotics are adapted to grow on cow’s milk and hence these dairy probiotics do not survive in adults.]  The lymphatic system of the breast terminates at the nipple and samples antigens/pathogens from the baby’s mouth, resulting in baby-specific secretory antibodies that return in the milk.  Milk supports a starter set of gut flora, essentially dairy probiotics, that stimulates development of the baby immune system, but inhibits adult gut flora that would digest the protective components of milk.  Formula, on the other hand, is inflammatory to the baby gut, because it supports adult gut flora before the immune system is ready.  Inflammation and stimulation of innate immunity is sufficient, if supported with high levels of sanitation, to permit survival of babies fed formula.  Milk of any type is incompatible with adult gut flora, so breast milk will attack adult gut flora and adult gut flora will digest and inactivate the otherwise beneficial components of the milk.
Aggressive and Suppressive Cells of Immune System Develop in Intestines
Gut bacteria are required for the development of immune T cells in the lining of the intestines.  Mice grown without gut flora do not have functional immune systems.  In humans, extensive antibiotic treatment produces defective immune systems that are either overly aggressive, i.e. autoimmune, or susceptible to infection and cancer.  They can’t be both.  Aggressive T killers are stimulated to develop by filamentous bacteria and Tregs develop in response to members of the Clostridium family.  In a healthy body, there is a balance between aggression and suppression; there are functional defenses against infection and cancer, while also avoiding autoimmune disease and allergies.

Suppressive Tregs are Deficient in Autoimmunity
Immune cells result from replicative divisions of stem cells.  Antibody producing B cells are produced through a million random rearrangements of antibody genes and those B cells producing antibodies against common self proteins are killed (clonal deletion).  Similarly, T cells are produced by rearrangements of receptors and those that would recognize self are eliminated.  The T cells then migrate to the intestines where they can develop into killer T cells or Tregs, in response to gut flora.  The Tregs act to suppress killer T cells that mistakenly recognize healthy self cells.  Thus, the initial elimination of self-attacking T cells or for B cells that produce antibodies that bind to normal cells, is not perfect and the Tregs are needed to avoid the mistakes.  Tregs are necessary to avoid the immune attack on healthy cells that is the basis of autoimmunity.

Autoimmunity Starts with Inflammation, but Requires Deficient Tregs
Bacterial or viral infections, or physical damage causing inflammation is the first step in autoimmunity.  It is the inflammation that initiates the interactions between proteins, autoantigens, of normal cells and cells of the immune system that bind, internalize, fragment and present the antigen fragments/peptides to activate B or T cells with corresponding receptors.  The activated B cells make antibodies specific for the antigen and the T cells will kill cells displaying the antigen.  It is interesting that most proteins are not autoantigens and are never involved immune reactions.  Only proteins with an unusual triplet of basic amino acids, similar to the quartet of basic amino acids used to transport proteins into the cell nucleus, are candidates to be autoantigens or allergens.  In fact, since nuclear proteins already have a quartet, i.e. the nuclear localization signal, they are common autoantigens.  The last requirement for autoimmunity is a deficiency in Tregs, because if the Tregs are functioning, they will block attack on healthy cells.  Treg deficiency usually results from loss of the type of gut bacteria that stimulate Treg production in the lining of the intestines, i.e. species of Clostridium.

Hospitals are Notorious for Clostridium difficile Infections
Fecal transplants are now recommended as a safe and efficacious treatment for C. diff hospital infections.  That makes sense, because hospitals are where antibiotics are routinely used and C. diff can only infect people missing their healthy species of Clostridium.  Thus, the hospitals wipe out the gut flora with antibiotics and then recolonize them with their own antibiotic resistant C. diff.  More antibiotics can’t fix it, but providing healthy gut flora (transplant) can.

Autoimmune Diseases are Treated/Exacerbated with Antibiotics
Both the aggressive and the suppressive immune cells require gut flora, so after initial antibiotic treatment wipes out bacteria required for suppression and results in autoimmunity, the remaining aggressive half of the immune system can be eliminated by blasting the remaining gut flora with more antibiotics.  Of course this will leave a highly compromised, incompetent immune system that will ultimately yield more extreme symptoms.  This is the typical medical progression for Crohn’s disease, for example.  The alternative is just fixing the gut flora to begin with and curing autoimmunity.

Cure Autoimmunity by Feeding Clostridium Resistant Starch
Autoimmune diseases, by their symptoms, show that sufficient gut flora to stimulate the aggressive half of the immune system is still present.  What is missing are the Clostridium species that convert soluble fiber, such as resistant starch, into short chain fatty acids, e.g. butyrate.  Patients treated with antibiotics usually walk away from the hospital with a suggestion to eat some yogurt to repopulate their missing gut flora.  Unfortunately, dairy probiotics don’t survive in the gut and cannot repair the gut flora and immune system.  The result, after the gut fails to repair and the immune system crashes, is autoimmunity.  There is a more appropriate possibility to avoid or fix autoimmunity.  Some people suffering from autoimmunity (and with remnants of their gut flora intact) have simply fed their gut flora on resistant starch and achieved complete recoveries.  Others fail to respond, because their gut flora is too severely damaged and necessary bacterial species are gone.  Those individuals need to eat the missing species of bacteria and some probiotics (more common in Asia) contain Clostridium species.  Consistent with this use of soluble fiber to feed gut bacteria that produce butyrate and stimulate the suppressive immune system are reports of healing by combining potato starch (RS) and probiotics with Clostridium butyricum (Probiotic-3).  Repair of the suppressive immune system by repair of gut flora (including fecal transplants) and feeding gut flora with appropriate soluble fiber, may be a general approach to the cure of most autoimmune diseases and allergies.

76 comments:

Ross Lamb said...

Hi Art,

Before I ask a quick question, I would just like to thank you for the contributions you make on your blog. I have only been coming here for little under a month, but already I have learnt a lot of very valuable information. You seem to be a humble individual, too, despite your obvious brilliant intellect, so please accept my sincere gratitude for sharing your thoughts.

As for my question, it is related to garlic.

What effect does garlic, or more specifically, allicin, have on gut flora?

I occasionally take Aged-Garlic extracts (supplement) as a general tonic.

Can you inform me if I'm inadvertently harming my microbiome?

Many thanks,
Ross



Tim Steele said...

Art - Really great description of T cells and their functions. This is one of the first readable explanations I've seen. This is such a confusing, yet important aspect of RS but it puts most people to sleep.

The very first study I read on RS was done on pigs and described the healthier Peyer's Patches and turning of naive T Cells into Tregs. At the time, it didn't mean anything to me, but now I go back and see that was maybe the most important discovery at the time.

The BG regulation, satiety, and sleep improvements are great (and noticeable), but the effects of butyrate in an SCFA-starved gut on the immune system are largely unnoticeable but one of its greatest contributions to our health.

Thanks,
Tim

Raj said...
This comment has been removed by the author.
Naxossa said...

So Art, if I read you well mother's milk would do the trick? In other words a market for it? Could be fermented?

Dr. Art Ayers said...

Ross,
Garlic, like all plants, are antibacterial and provide soluble fiber. Your gut flora can adjust to both. Plants are also naturally toxic, so don't eat too much of any type.

Thanks for your kind comments.

Dr. Art Ayers said...

Tim,
I used to teach immunology, so I am a little embarrassed by some of the short cuts in the explanation. I think it is still basically true.

Thanks for watching.

Dr. Art Ayers said...

Hi Raj,
The husk is just another soluble fiber and it can be digested by the appropriate gut flora, but it is based on a sugar other than glucose. You apparently have the right gut flora.

It is interesting to ponder the social ramifications of diet and health.

I think that most of the human body is continually replaced, so unless there is severe structural damage most of the symptoms of disease are reversible.

You should be able to clean out the gut and start from scratch with new bacteria and result in a rejuvenated immune system. That happens with bone marrow transplants and autoimmune diseases, e.g. T1 diabetes, are cured. Impact on the nervous system may be more recalcitrant.

Thanks, as always.

Dr. Art Ayers said...

Naxossa,
All of the mother's milk should be reserved for babies and be supplemented from milk banks in hospitals, if there is a medical reason. Formula should be excluded, because it has permanent negative impact on gut flora and subsequent health. Special care should be taken in all medical settings requiring antibiotics to fully repair gut flora damage. Dairy probiotics are not adequate and are misleading.

Thanks for your questions.

Anonymous said...

Dr. Ayers,

You seem to be saying type 1 diabetes can be cured. I am skeptical, but hopeful, as my son has type 1. (We adopted him as a baby, and had been on soy formula, which we continued until he turned one.)

I've been reading your blog for years, and am grateful to you for sharing your knowledge.

Jan

David said...

This is fascinating Dr. Ayers!

Can I get your opinion on the state of my little gut friends? ME/CFS, elevated antibodies for many bacteria and virus, chronic constipation with Bristol 1, bloated/tight feeling at cecum.

Started VSL3, Prescript-Assist and had awesome Bristol 4 BMs for 2.5 months. Added PS and psyllium shortly after the probiotics. Still good.

But at that 2.5 month mark I started having the Bristol 1 and constipation again. Like somebody flipped a switch. Stool test from shortly after starting the probiotics shows low but in range commensal bacteria, low pH, Campylobacter.

I've tried variations of the probiotics and RS to no avail.

Anything I'm missing?

Thanks!

Raj said...
This comment has been removed by the author.
mfairchild said...

Dr. Ayers,
Thank you for this series. I'm on the autoimmune attack side of the equation and just had my third dose of Probiotic-3. I have everything else in place: diet, ferments and RS. I have my fingers crossed!
If Clostridium butyricum is the keystone gut bug to enhance Treggs and thus balance the immune system from autoimmune attacks, what species is missing on the other half of the equation if a person has frequent illnesses and cancer? Is there a keystone species for that?

Jan said...

Hi Dr Ayers,
I too am on the autoimmune attack side of things with Hashimoto's developing into food sensitivities and a slow MMC with a SIBO diagnosis in November. I do a completely organic diet, gluten free, with RS and PS, as well a fermented foods. I can't digest raw veggies or high fodmap foods even when cooked. They cause more constipation, gas and fullness. I have been taking Prescript Assist for a while and a Custom Probiotics blend with pretty good results. This week I added AOR-P3 and seem to have itching skin areas and back to small amt of stool. I feel plugged up! Am I missing something to be able to benefit from the clostridium ? If I continue to take it with RS will it improve things over time? Are there any other sources of probiotics or SBOs that could help? Thanks for all of your great, informative posts. All of this truly helps so much!

Tamara Jurado said...

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SK said...

With regard to fermented veggies, how much should be eater per day?
I eat some kraut and pickles from Raw Pickles, a co-op in NE of organic fermented; they are naturally fermented.



Anonymous said...

Some sources suggest that Clostridium butyricum can produce botulinum toxin just like Clostridium botulinum and thus cause botulism ... What about that ??

Lola said...

Thank you so much for all of this information. I'm starting everything right away. I'll let you know how it goes.

Anonymous said...

Dr. Ayers, Have you heard of fluoroquinolone antibiotic toxicity? I have been completely disabled for over six years now since the age of 21 after 12 days of Levaquin. Now at 27 I am still deteriorating and feel like I don't have much time left. All I eat are grassfed meats, organic steamed veggies and water. I react to almost everything and especially have major reactions to probiotics. My CNS goes wild whenever I eat and I am suffering from severe malnutrition as a result. I was hoping you could help me or give me some idea as to what you think I can do. I suspect that I have not been able to make adequate stomach acid/enzymes as a result of being ruined by levaquin, but I would love to speak to you via email if you wouldn't mind listening to a quick version of my story/symptoms. I so appreciate your blog, and find it so informative and interesting, I am just at a loss for what to do since I react to everything and anything. My email is kelbel586@hotmail.com.
Thanks,
Kelly

Ashwin said...

Dr Art, Thank you for a most interesting and informative article. I have a question for you. What are your thoughts on the new thinking behind the function of the Human Appendix? There are some who believe that the appendix is a storage vesicle for the Human gut Microbiota and that this store is used to re-populate the GI tract after damage to the microflora as is caused after a course of wide spectrum Antibiotics. This may suggest that all you need is appropriate food source for the microflora, as in prebiotics, Resistant Starch, etc. What are your thoughts?

Ted said...

It's unfortunate that Dr. Ayer's posts always get flooded with commentators seeking medical advice. It'd be nice if we can discuss the science, not personal questions that are better suited for a medical clinic.

George Henderson said...

Excellent post Art!

In humans, Treg differentiation requires retinol derivatives. vitamin A deficiency possibly a factor in development of autoimmunity (retinoids are common pharmacological treatments for autoimmune conditions).
Some pathogens trick Tregs into working to "mask" their presence. This co-opted immune tolerance helps a virus like HCV become chronic, but because it suppresses inflammation, can also make it possible for some people to survive long-term infection with little damage.
Tim, it is probably not the butyrate converting the Treg, so much as direct contact with the bacteria itself. The bacteria is somehow able to identify itself as "friend", and the general message, conveyed from the Peyer's patches, that friends outnumber enemies, puts the immune system into a more relaxed state. The butyrate being anti-inflammatory at a metabolic level no doubt re-inforces this.
You are right about how confusing it is. To study Tregs you need a kaleidoscope, not a microscope.

Fred Hahn said...

Dr. Ayers,

Really enjoying and learning from your posts. Keep 'em coming!

Q: As far as plant matter goes, I want to be clear on your position...

You seem to be saying they are a necessary evil. That the fiber is the part you want and NOT the juice or the meat since these contain the pants antibiotics.

You also seem to be saying fermented veggies are best.

I would LOVE for you to do a post dedicated to the bottom line on plant matter for human health.

Thanks!

Anonymous said...

Ted, the reason Dr. Art gets so many medical questions is that there are many desperate people out there who are getting little or no help from the medical community. In answering the questions, Dr. Art is helping not only the questioner, but also the dozens of us out there who have the same question.

If it were my choice, I would confer sainthood on Dr. Art for the help he is giving to those of us who are functional illiterates when it comes to science and biology but who need help on our journey to restoring health.

gdcreston said...

What is the bst way, short of fecal transplants from a healthy donor, do you replenish a gut flora damaged by several courses of antibiotics?

Raj said...
This comment has been removed by the author.
antonio sabarro jr said...

Just wanted to thank Dr Ayers for another great post, this blog has been a life saver for many of us suffering from autoimmunity. For people gearing up to grow their own vegetables this year for fermenting and soil-based organisms I definitely recommend the book TEAMING WITH MICROBES. Also been having some success with consuming raw maple sap as a natural probiotic if you have access to it.

Anonymous said...

Hi Dr. Ayers,

What are your thoughts on people receiving fecal transplants that haven't been cured autoimmunity? My thoughts are it could be incompatible/not healthy enough gut flora from the donor or not enough transplants, but I'm interested to know your thoughts. I have actually had one done via colonoscope, and I did some supplemental ones on my own, but unfortunately, it didn't seem to help my Crohn's colitis. I've also read conflicting studies on fecal transplants for others with IBD, some it helped and some not, so I wonder what we need to factor in to these cases.

Also, as far as breastfeeding goes, do you know if the mother has an autoimmune disease if it somehow compromises her breastmilk or the benefit of the breastmilk to the baby?

Thank you for your contributions on your blog. It's encouraging to see people use their knowledge and background to help promote health and reverse autoimmunity.

Kor said...

Also to Ted:
What is the point of doing the science if it can't be applied practically? In this case the application is in helping people achieve greater health, ya?

john said...

Kor and others,

Ted is right. This isn't the place to list all your symptoms and ask for a diagnoses and treatment plan from Art. That should be obvious. Also, he has several years of posts. Everyone should be able to read though and generalize for themselves. Then go to a medical professional and discuss.

Ted said...

john, +1, exactly my point :)

Dan Reese said...

Art,

I always enjoy and look forward to your posts.

You mention Clostridium as an important keystone species for proper immune function. Are there any other "honorable mentions" or otherwise important species that play a critical role in immune/digestive health?


Thank you,
Dan

Lori2 said...

Dr. Ayers,

Thanks from a first time poster, long time reader.

You advise us to avoid anti-biotics. Does this include food sources such as garlic which is purported to have antibacterial activities?

Anonymous said...

When you speak to curing allergies are you including airborne allergies: hayfever, pollen, ragweed,etc?
There are immune cells in the skin

Anonymous said...

In reply to Dan Reese,

The following study suggests that the probiotic, bifidobacterium infantis is likely helpful in this area also.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744517/

I believe this is the active component in the probitic called Align. I've seen this in most larger chain drug stores/pharmacies.

Art

Anonymous said...

Dr. Art,

I was watching this video where Dr. Wayne Hancock is discussing how they are exploring the possibility of limiting or reducing tregs in an attempt to fight cancer. By limiting or reducing tregs, they are hoping that the body will better be able to mount a full immune system attack of existing cancer in the body without the tregs mobilizing to limit this immune response. Assuming I understood him correctly, my question is, if a person happened to have cancer, but was not aware of it and started taking RS to increase treg cell production, could this lead to the cancer more freely multiplying?
http://on.aol.com/video/treg-cells--a-new-way-to-fight-cancer--517904297

Thank You.

Art

Dr. Art Ayers said...

Art,
I think that you are correct. Cancers go to a lot of effort to stimulate Tregs.

Most people have antibiotic and processed food damage to their gut flora. My impression is that leads to greater deficiency of Tregs and more autoimmune disease than cancers. Further damage may produce infectious disease susceptibility and cancer as well. This may be the immunocompromised people who get food poisoning.

There are a lot of people who are so dysbiotic that they are intolerant to everything including probiotics and soluble fiber. We need an approach to construct the gut flora from scratch with common sources of bacteria. With the exception of fecal transplants, I don't think it is being researched. It could be very cheap and would cost the medical industry billions in profits.

Thanks for the comments/questions.

Anonymous said...

Dr. Art,

Thank you for the reply.
It would certainly be great to be able to fix many of our common ills with something possibly as simple as a specific bacteria appropriate enema or suppository!
I guess that would be too simple, easy or inexpensive to ever think it could realy become common practice though, or could it.

Art

Anonymous said...

If one important aspect of taking RS is to increase or protect treg cells in the colon to help control chronic inflammation there, then folate / folic acid may be a possible supplement to consider as part of the regimen if the following study is correct.
http://www.jimmunol.org/content/189/6/2869.long

Art

Cooper Mor said...

Re: folic acid that's pretty interesting and corroborates the above comments on cancer and what Chris Kresser says about the supplement - that it increases cancer risk.

"One of the major risks associated with excessive intake of folic acid is the development of cancer..." (Sources cited in his post)

http://chriskresser.com/folate-vs-folic-acid

Like you said, it's about finding immune system balance.

Marybeth said...

Hi Dr. Ayers,
A commenter posted this question to you, "if a person happened to have cancer, but was not aware of it and started taking RS to increase treg cell production, could this lead to the cancer more freely multiplying?"

And you replied that you thought it was correct. I have gone back to read all your posts on Tregs. And am thoroughly confused.

So by adding RS to my diet along with with fermented food, a non inflammatory diet (no processed food, no gluten and sugar) and and a probiotic containing Colistridium B. I am helping my body rid itself of my autoimmune disease but may be feeding cancer to multiply more freely if present?

From a confirmed "fermentista"
Marybeth

Sally Leone said...

Mary Beth, I am right there with you! Dr. Ayers really shifted the ground under my feet last night when I read the comment about RS being good for auto immune but tricky for cancer? I am a early stage (no chemo) BC survivor since 2009 and since then have been reading as much as possible to do all that I can to avoid a relapse. I am not trained in medicine so the going is slow. But about 4 months ago I found 'Cooling Inflammation' and all the pieces began to fall into place. Most of the sites I read were above the microbiota level. As someone said, 'everyone forgets the biome'. I have spent hours and hours researching my various snps including MTHFR. I had finally come to the realization that all the expressions of the SNPs would fade into the background, if I fed my gut right. But now, if I am interpreting Dr. Ayers correctly, what may be good for some bacteria that control auto immune diseases arising, may be bad for the bugs that control the rise of cancer? Please Dr. Ayers, expand on this. Which bugs should I concentrate on with what substrate, if Clostridium and RS are not the ones for cancer protection?

Dr. Art Ayers said...

MaryBeth and Sally,
I don,t worry at all about increasing cancer risk by fixing suppressive immunity and Tregs, any more than I worry about getting infections when I avoid eating inflammatory food, as I see it, our bodies have robust defenses over a broad range and it is only the crazy extremes that get us in trouble. Antibiotics, sugar, vegetable oils and foods lacking soluble fiber are outside that range. That is also why paleo diets and unprocessed food are in the range.

In the crazy periphery, all of your genetic uniqueness will be problematic, but anywhere within the reasonable is carefree. Antibiotics quickly lead to the crazy extremes promoting autoimmunity or cancer, and more antibiotics are frequently used as therapy to remove the remaining half. Little research has been done on how to repair severe gut dysbiosis, although this is the most important part of a cure for most diseases. Chronic disease and therapy is much, much more profitable. My simple website costs the medical industry hundreds of thousands of dollars each year.

The bottom line is that I think fixing any part of the gut flora and immune system is a good thing. Most problems are reversible. The optimal strategy for each person toward a healthy gut flora and immune system is empirical right now. There are some reasonable combinations of probiotics, soluble fiber and fermented veggies that are available at sites such as Animal Pharm and Free the Animal.

Keeping asking questions if you think I can be helpful. Let me know how you are doing.

Anonymous said...

Dr. Art,

To be a more direct regarding RS, clostridium, soil based probiotics and cancer, if a person knows they currently have some form of cancer, would it still be advisable to use the RS, clostridium and soil based probiotics for their potential to repair the broken gut biome or should they be avoided as long as the cancer is present?

Thank you.

Art

Sally Leone said...

Hi Art,

You might want to check out FTA. I cross posted the question I asked Dr. Ayers over there and got responses similar to Dr. Ayers but more specific to your question. If you look in the comments section of 'How Eating Heaps of Safe Starches Cured My Diabetes' you will see my comment and several very good responses.

Sally Leone said...

Dr. Ayers,

I wanted to thank you for your response to my question regarding BC and RS. I'm sure I'm not alone when I say that sites like yours give so much hope to people who have been through western medicine's ringer. Your generous nature is very much appreciated. I am doing much better now and read your blog as well as the others you mentioned in my continuing journey of gut repair and health optimization.

Anonymous said...

@Sally,
Thanks Sally!That was my next stop as I have been following FTA and Animal Pharm since January 2014.

Mary Beth

Mary Beth said...

Dr. Ayers,
I too am grateful for your response to my question and the time you devote to sharing your research on inflammation etc. I am by no means out of the woods right now, but believe I am on the right road.
Thanks again!
Mary Beth

Cooper Mor said...

Hey Dr. Ayers,

What are your thoughts on this research that (if I understood it correctly) claims T-reg cells can be inflammatory

"In patients with psoriasis, Tregs readily turn into IL-17-expressing cells, thus potentially perpetuating the inflammatory process that characterizes the disease."

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3366427/pdf/nihms378706.pdf

I just started implementing this protocol, and am curious about your interpretation of this research!

Thanks for all you do,
Cooper

Hormone Fairy said...

I am very confused. Can you clarify for me? I have infertility most likely due from an autoimmune disorder. My doctor things that I have low grade viruses in me, stemming from working in the health care industry. He thinks that the egg is being attacked by my immune system and not letting it to implant, most likely from my immune system being overactive.
I eat fairly good, and recently started a gluten free, lactose free, egg free and starch free diet. I have been taking probiotics with 14 strains and SBO on and off. I consider my gut fairly healthy. Would you recommend that I DO take probiotics or DO NOT take probiotics to down regulate my immune system, and do you recommend the SBO probiotics?

Debbie said...

I was wondering if you have any suggestions for dealing with menopause related recurrent urinary tract infections? My understanding is that lack of estrogen and vaginal atrophy cause e-coli to overgrow in the urinary tract. I've tried D-Mannose and am on the third course of antibiotic treatment since the fall. Very upsetting. Oral probiotics don't seem to work either; I found a very expensive vaginal probiotic containing several strains of lactobacillus, but I'm not sure that will work either - and at $50 for 6 it isn't feasible to use daily. I eat tons of fermented vegetables and take probiotics. I can't find any information on this important topic. Many post menopausal women suffer from recurrent UTIs. I don't want to take an estrogen supplement. If you have any insights or thoughts on this I'd be so grateful to hear them. Thanks so much.

Sally Leone said...
This comment has been removed by the author.
Sally Leone said...

@Debbie

I use a mix of supplements: grapefruit seed extract, D-mannose, cranberry, UTI Support by Designs for Health, empty bladder before and after, cleanse, drink a lot of water, and take the above supplements. Also, I supplement with resistance starch (see Dr. Ayer's post on potato starch and resistant starch or 'Free the Animal' posts on RS). I'm hoping the supplements taken 3x day of, the RS+probiotics, and the regime is working. I had two UTI's in 4 months and started this protocol about 2 months ago, Not very romantic but cautiously optimistic that I may be able to avoid infections this way. Also, Dr. Art answered a question I had about this not too long ago: http://coolinginflammation.blogspot.com/2014/03/health-diagrams-iii-inflammation-from.html?showComment=1395692587981#c2130982744238588005

Hormone Fairy said...

@Debbie,
I own a compounding pharmacy. We sell probiotic vaginal capsules for $1.50 each so well worth it. It has worked well for many of my patients. Sometimes, replacing the vaginal estrogen with estriol vaginal cream will replenish the cells and prevent recurrent UTI's also. I have also seen some Dr's prescribe Boric Acid 600mg vaginal suppositories too.

Me said...

Hi,

Thank you for this post and all the time and effort you put into providing information for folks.

Was wondering if you recommend RS and/or Probiotic-3 if SIBO is an issue.

Thank you,
Kristina

Debbie said...

Thanks Hormone Fairy and Sally.

Anonymous said...

I have an interesting observation (n=1) regarding the psoriasis - cancer connection mentioned earlier by commenter Cooper Mor.

An older relative became, relatively suddenly, sick in psoriatic arthritis. She had never before had an autoimmune disease. About a year later, she passed away in advanced stage pancreatic cancer.

I have tried to understand if there could be a connection. From the info I found here, this seems to be the connection: The cancer stimulated the Tregs, which later turned into IL-17-expressing cells.

Thus, an autoimmune disease as a symptom of cancer.

Aaron Kaskowitz said...

Art,
My uBiome results showed lower than average Clostridium. I was about 2.34% and healthy omnivores' data had over 3%. Do you think this is likely a contributing factor to my Multiple Sclerosis?

Should I focus on that and try to fix it by taking potato starch and AOR-Probiotic 3?

Any suggestions or more information that I should follow regarding MS would be VERY welcome. Thanks!

Aaron

Professor Lars said...

Random musings -

(partly an unasked-for answer to Aaron):

1.
Microbiome measurements seem to be inherently imprecise.

https://www.sciencenews.org/blog/gory-details/here%E2%80%99s-poop-getting-your-gut-microbiome-analyzed

Perhaps it's a good idea to send in the p**p to several different places.

2.
Speculation: Home-grown, unwashed, vegetables probably contain the bacteria we need to populate our guts with. No need for pills. One example: there exist oxalate-digesting gut bacteria. They will save you from a certain type of kidney stones (calcium oxalate - people who get those tend to get them repeatedly).
Where might one obtain those bacteria? On the leaves of oxalate containing vegetables, of course. Unless those leaves were first soaked in various herbi- and pesticides and then washed.
Conclusion: make sure you have access to a wide variety of unwashed, purely organically grown vegetables.

Professor Lars said...

Aaron:

Dr. Wahl's protocol seems quite popular with MS patients. It's a very nutrient dense paleo eating style.

Aaron Kaskowitz said...

I also had EXTREMELY low prevotella - .34% compared to a uBiome healthy omnivores' sample average of 7%. Perhaps this is related.

van Nieuwstadt said...

Dear Prof. Ayers,

I found your blog not long ago and I am impressed by your knowledge and eagerness to help others. I think that you have the knowledge to help me with fighting inflammatory diseases that I suffer from (I would be extremely grateful for your advices):

a) Skin inflammation – my dermatologist says it’s caused by a bacteria from staphylococcus family. This was the first one and the most problematic to me, I keep it under control but I am simply tired of doing this for around 15 years (I am 27 now). To cure the symptoms, I use a cream with erythromycin, triamcinolone and pasta zinci.

b) Sinuses inflammation – I always breathe through 1 and ½ hole because one hole is partially blocked. I love swimming but I have to stop it because it was causing an inflammation of my sinuses. The problems started in 2010, after deviated nasal septum surgery.

c) Colitis ulcerosa – autoimmune bowel disease. It developed in 2012 after having trauma after my father’s death from bladder cancer. I managed to cure it by changing my diet to Paleo-like – I have no symptoms for the last 2 years.

d) Blepharitis – it developed in 2013/14, I do not use and medicaments to treat it, just have occasional eye inflammation, I noticed it’s very related to sinuses and gets worse after swimming. If I don’t swim for many consecutive weeks it seems to be completely gone (until next swimming trial).

How to treat all of these? My diet is clean from high-carb and junk food, absolutely no added sugar, in other words nothing that can increase inflammatory effect. I found your blog couple of weeks ago and decided to:

1) add fermented foods (pickles, Brussels sprouts, okra) and symbiotics in pills (are pills necessary?)

2) exclude dairy probiotic products (I used to eat high-fat Greek yoghurts and occasionally kefirs)

3) I temporarily excluded eggs because I found that they also may trigger inflammatory reaction (I implemented this one week ago, is it necessary in your opinion and if so, how long should it take to see if it works?)

On top of that I exercise every day to keep inflammation at bay and try to eat 2-3 gloves of garlic almost every day. I am in good overall shape: 183cm/80kg, athletic body.

Where is the key to win this battle? I know how being healthy feels like, because 2 years ago I had a treatment with minocycline and it had tremendously positive effect on all of diseases mentioned above – they were all gone for around 3 weeks. I never felt better in my live before. I wrote that because it may be a good indicator of what I should do to win the battle with all those diseases.

I would be very grateful if you could read my lengthy post and reply to it, I believe it may be helpful for other readers too.

(Apologies for all typos – I live in Europe and English is not my native tongue).

Best regards,
Karol

Dr. Art Ayers said...

Karol,
It seems to me that your problem is inflammation and immune system dysfunction all based on damaged gut bacteria. You have already started to address this with fermented vegetables and I hope you are making your own.

Inflammation, such as in your case, also suggests that your vitamin D production will be poor. Check your vitamin D levels, supplement as needed and check again. High levels of serum vitamin D usually decreases inflammation symptoms.

You should also be aware of omega-3 oils (excluding omega-6 vegetable oils) and prebiotic fiber.

Inflammatory responses to food usually indicates food intolerances that result from missing gut bacteria. Fix your gut flora and you will eliminate the food intolerances.

The dermatitis would not occur without damage to your immune system and the immune defects are based on missing gut bacteria.

All pharmaceuticals impact gut flora, so it is difficult to repair gut flora and take pharmaceuticals.

The reason that minocycline relieved your symptoms was that it killed off the gut bacteria responsible for the remaining part of your immune system. With a thoroughly compromised immune system, your aggressive immune attack symptoms were reduced.

People typically pick up new bacteria in their gut by constantly swallowing inhaled bacteria, or bacteria on the surface of fresh vegetables or from significant others. A friend of mine with significant inflammatory disease would go into remission every time he had a new girl friend. He probably would have also benefitted from an outdoor pet, gardening, tending a floor sweeping toddler or generally being less hygienic. Hygiene is typically an enemy of healthy gut flora.

I would suspect that swimming may also reduce your overall microbiome by killing off everything with chlorine and showering. Showers also reduced vitamin D uptake from solar exposed skin.

Also, note that one of the best treatments for sinus infections is humming.

Let me know how you progress.

van Nieuwstadt said...

Many thanks for your reply prof. Ayers.

What do you think about medicaments such as fluconazole, which is supposed to treat fungal and Candida infections? It was not my idea, but my doctor’s, and I remember I took it for couple of days/weeks, but with no noticeable improvement.

I studied the matter before and I am aware of importance of vitamins and minerals. My daily supplementation is multivitamin (chelated) and additionally 10.000 IU in a pill form if I am not exposed to the sun for at least 20 minutes over the course of the day.

Same with omega-3 oils, I eat considerable amount of fish almost every day (150-400g per day), plus I take 2x1000mg of fish oil (18% EPA, 12% DHA) per day.

What’s your view on taking large doses of vitamin C in a form of ascorbic acid? I am considering adding this to my daily supplementation, though I do not have a problem with flu/fever – I haven’t been sick in the winter for 12 years. But perhaps it is beneficial to repairing gut flora?

An interesting point is the link between being exposed to dirt and animals and gut flora, since I lived on a countryside until the age of 9, and my problems with dermatitis started when I was 13… I already heard about the hygiene theory, but now I am seriously considering implementing some ‘dirt’ changes to my life. What changes do you think are the most crucial here? When it comes to my skin, I have already learned that my eczema goes worse if I stopped using soap. The good news is that I managed to reduce my cosmetics to baby soap and no-fluoride toothpaste. No shampoo, no antiperspirants etc.

My current diet looks is the following:

- Breakfast: couple of fruits and vegetables (salad, celery, cucumber, apple, lemon) mixed in blender. I used to eat 5-6 boiled eggs with walnuts, but I stopped 10 days ago to check if it doesn’t cause any inflammatory reaction. Do you think it’s a good move?

- 2nd breakfast: banana

- Lunch: meat or fish with raw vegetables (usually beetroot, carrot, tomato, raddish)

- Dessert: apple and avocado (not regularly)

- Supper: meat or fish with grated 2-3 gloves of garlic, plus sauerkraut/pickles/okra.

- Extras: green tea, 1-2 pieces of dark chocolate (85% cocoa), aloe vera juice (2x60ml daily on empty stomach) and apple cider vinegar (2 tablespoons with a glass of water 1-2 times a day, before a meal). What do you think about having a glass of red, dry wine several times per week? I don’t do it more for health reasons rather than pleasure (but ok, there is some pleasure in it too).


Thank you in advance for your comments, that’s greatly appreciated. You've just gained a new faithful reader!

Dr Alyson Murray said...

Hi This is fantastic information. I work with babies and see many with signs of immune function imbalance. I fully appreciate the benefit of breast milk on the immune system development however am seeing mothers who have compromised immune systems/gut flora and their babies are getting ill. My question is, apart from implementing the strategies you discuss into a breast feeding mothers diet, what is the best and safest treatment for formula fed babies from birth up until the introduction of solids? The concern being that their systems become overwhelmed with bacteria and it becomes a cause of disease instead of health?

Shalin Siriwaradhana said...

What is the software you used to create this infographic type diagram? Is it creately ?

Kelly said...

This is in response to 'Professor Lars'' comment that one can find bacteria that break up oxalates on certain vegetables, provided they hadn't been washed or sterilized in some way.

Sorry, but that's not true from what I've read, because the bacteria that degrade oxalates are anaerobic.

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JPOM said...

Hi

I am a bit confused about Short Chain Fatty acid production being stimulated by RS. Autism has recently been shown to be linked to excess SFCAs. Permutter says Clostridia have been shown to be linked to Autism.

I realise there are different species, but if RS is given to Autistic people will it not make things worse.

John

Anonymous said...

Dear Prof Ayers,
I suffer from LTP allergy, or allergy to a protein, LTP, found in all plants. Many fruit and vegetables, herbs, nuts and seeds, the sacred foods that are supposed to nourish and heal us, actually make me ill. The allergy is confirmed by RAST test. I was wondering if you have an advice for me too :), something that can help lower my IgE or help me tolerate foods better perhaps. The symptoms are constant gastritis, bile reflux, and I am waaay underweight. The problem is I cannot avoid completely this LTP or my diet would be very unhealthy. My cabinets are full of digestive enzymes, amino acids and more, providing only a temporary relief. Thank you for your precious help- Angela R

Dr. Art Ayers said...

Angela R, LTP allergy,
LTP is a lipid transfer protein that is related to the alpha amylase/trypsin inhibitor of wheat that causes celiac. You can see a post about it on my site. I would guess that an allergy to LTP is just the early stage of celiac, before it is converted to an antibody reaction to gluten and gut transglutaminase, before eventually attacking the thyroid.

The point here is that this is an autoimmune disease in the early stages, posing as an allergy. Autoimmune diseases and allergies all have an origin in gut dysbiosis/damaged glut flora that produces an immune system problem, defective immune tolerance mediated by regulatory T cells, Tregs. Tregs mature in the lining of the gut in response to gut flora, which means that your problem fundamentally is a lack of bacterial species in the gut needed to produce immune tolerance.

Vegetables are important nutritionally to supply prebiotic polysaccharides, e.g. resistant starch, inulin, pectin, used to feed specific gut bacteria to produce short chain fatty acids and other components to control development of immune cells in the gut. Without those immune cells, some of which suppress aggressive reactions, autoimmunity and allergies develop. That is your case.

My initial impression in summary, is that you have an early stage of celiac, probably precipitated by antibiotic killing of gut flora. You need to replace the missing bacteria, by somehow eating those bacteria. Many of the missing species are in the group of Clostridia, so most probiotics, thou temporarily of benefit in helping to develop the missing parts of your immune system, will not repair your gut flora. A few have C. butyrica, which may help.

In addition, you need to eat prebiotic polysaccharide fiber to feed your missing gut bacteria. It is clearly a good idea to not fan the flames of your LTP (ATI) allergy, so you would be wise to avoid whole veggies and stick to rendered soluble fiber, e.g. potato resistant starch, inulin and pectin. You might also be able to eat fermented vegetables, since the fermenting probiotic bacteria should have digested some of the problem. I would stay away from seeds and especially grains/wheat, since they are rich in ATI and you are heading toward gluten intolerance.

Let me know it this is a helpful explanation of your situation.
I would also guess that you already or will develop SIBO. Obviously, any drugs that you take will be a problem, since most have strong antibiotic activities that will exacerbate your problems.

How do you tolerate potatoes? The Potato Hack would be a good tool for gut repair, if you can tolerate it. You might also look into Probiotics-3.

Anonymous said...

Wow Professor Ayers, I've been studying LTP for 4 years now but this is all new information to me. Thank you, thank you so much. I never stop learning. My LTP allergy started during my teenage years but only got the worst symptoms after my pregnancy. A few months after giving birth, I gradually became allergic (IgE allergic) to every plant based food, with symptoms like diarrhea, heartburn, bile reflux and severe joint pains. A nightmare. I recently started an immune modulating therapy that allows me to tolerate foods better. Yes, I can tolerate potatoes and other root vegetables. I can now eat berries, lettuce, brown rice, coconut, mushrooms and others. I have to stay clear from peach and fruits of the peach family (apples, pears, cherries etc) as I had a severe reaction to Pru p3, the LTP of peach which cross reacts to many other LTPs. I am IgE positive to gluten too and I have not been eating gluten for the past 4 years. Dairy, even from goat products, despite not containing any LTP, is a struggle to digest and can trigger heartburn. I'm trying to heal my esophagus, inflamed after years of bile reflux, so I have to avoid that too. So you think that everything generated from gluten? That is most interesting to me. But my first reaction was to peach, was that generated from wheat allergy? And how come I'm not "cured" after years of avoiding gluten? I'll try Probiotics-3. What is the potato hack? I'm really trying hard to heal. Look forward to your comment. Angela

Dr. Art Ayers said...

Angela,
Most doctors don't keep up with the biomedical literature and haven't studied enough science to understand the background cell biology and biochemistry. They haven't noticed the broad applicability of insights into the gut microbiome.

I don't think that bile reflux is anything other than another form of GERD, which is stomach and intestinal contents pushed up the GI tract as a result of gas build up in the small intestines due to SIBO, small intestine bacterial overgrowth. The stomach valves open in response to low stomach acid and the GI pressure forces the contents up to the esophagus. Celiac commonly results in SIBO.

Celiac starts with antibodies to ATI/LTP and then spreads to include antibodies to gluten and other intestine proteins. Avoiding a target antigen does not eliminate the antibodies to that antigen. Avoiding gluten lessens symptoms, but does not cure celiac. Celiac is the most complex of the autoimmune diseases to cure, because it also compromises the lining of the gut and further disrupts gut bacteria and the gut based development of the whole immune system.

It is possible to cure autoimmune diseases, but not through immune modulating therapy, which just shifts the types of antibodies produced. It is not good to shift from allergies to autoimmunity.

Antibodies to wheat ATI also bind to LTPs and gluten. The immune presentation of gluten requires binding to intestinal transglutaminase, and that causes full blown celiac and thyroid problems. Your problems started with damage to your gut flora and reduced Tregs/deficient immune tolerance, then exposure to wheat ATI, which typically results in antibodies to ATI and gluten, led in your case to antibodies to related LTPs. You are probably already getting attack on your thyroid, which can produce either elevated or low thyroid hormones. After the antibodies are produced and broadened to include other antigen targets, it doesn't matter if wheat is discontinued, because the new antigen targets maintain the allergies and autoimmunity. The only solution is to fix the root cause, deficient immune tolerance due to low Tregs caused by damaged gut flora.

Do a Google search for The Potato Hack and the author, Tim Steele. Also read up on phytoalexins, natural antibiotics produced by plants. Natural antibiotics have the same impact as commercial antibiotics. Also read up on live, fermented vegetables.

Read up on SIBO and realize that antibiotic treatments will further damage your immune system. You need non-antibiotic approaches. Also note that increasing your gut acidity is necessary and starving your SIBO while feeding your colon bacteria prebiotic fiber may be a major goal. Your immune system is not overactive, but rather it is deficient in immune tolerance. SIBO kills immune system development in the gut.

Why don't you mention meat/fish/eggs, soy and dairy? It seems that many of your problems may stem from vitamin deficiencies associated with celiac and damaged gut bacteria. The reflux is clearly SIBO. Have you had your serum vitamin D measured? I would be amazed if you weren't highly inflamed from vitamin D deficiency.

Anonymous said...

I am speechless. First of all, thank you. Your help is so precious to me. I have been studying and asking hundreds of doctors over the years for an answer to this LTP allergy, and only now I have an explanation. I remember having an IgE test pre-pregnancy, about 10 years ago, it showed I was allergic to wheat, tomatoes, corn, rice, onions, garlic, peach, nuts, seeds, over 50 plant related foods. My allergy specialist dismissed it saying "it is not possible to be allergic to all of this". Since I did not have any symptoms he told me to keep eating everything. Maybe this has inflamed and damaged my gut flora during the years. Celiac, SIBO.. Gosh. I just ordered Probiotics-3 on Amazon and the potato starch. I'll start with that and keep my diet. I do not eat any form of processed food or sugar. I do eat eggs, fish and meat, some fruit and those few vegetables I tolerate. Would that be a good start for now? If you think I could benefit from other supplements please let me know. I do not tolerate dairy very well unfortunately, as it sometimes triggers my heartburn. I am still very underweight! I avoid drugs/antibiotics etc as I know they don't treat the root cause of my condition. I was deficient in vitamin D yes. I took 5,000 daily for a few months, I'll check my levels again soon. In my family nobody has food/pollen allergies but both my father and my sister have thyroid disorders. Professor Ayers, I know this is just another thank you comment from an ill person, but to me this means the world! I passed this LTP condition to my little daughter and now I have an even bigger motivation to find a way out. Thank you for passing your knowledge on this to me. Angela

Anonymous said...

I have read on SIBO and natural antibiotics. I feel you might be right in my case and SIBO could be my underlying cause. In the diet there are a few restrictions. My daily diet consists of chicory coffee (no coffee), baked potato, lamb, poultry, salad, beetroot, cucumbers, fish, brown rice pasta/crackers, blueberries, figs. I use coconut oil coconut butter, jam (no sugar added) and raw honey. Not sure what I need to eliminate out of this for the SIBO diet as from what I read there should be NO carbs at all? Any advice would be truly useful. I am currently taking probiotic-3 (they have been a miracle as they helped me to put weight on, don't know how!!) and saccharomyces boulardii. I also take magnesium and elderberry syrup (homemade). Thank you Professor! Angela