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 .

Friday, July 30, 2010

Autoimmune Diseases, Bacteria and GALT (Gut Associated Immune System)

Celiac, Oxidative Stress, Peroxiredoxin, Alopecia
Grain/gluten intolerance, celiac is an immunological attack on the small intestines with increased risk for numerous autoimmune diseases.  Hashimoto’s thyroiditis is a common sequela of celiac and the two diseases share the same autoantigen, tissue transglutaminase (tTG).  Thus, the development of celiac and the production of antibodies to the tTG produced in the intestines, results in a subsequent immunological attack on other tissues that produce lots of tTG, e.g. the thyroid.  Gluten intolerance, because of its attack on the intestines and the proximity of a major part of the immune system (GALT), may play a major role as the foundation for autoimmune diseases.
Gluten Intolerance First Step in Autoimmune Diseases
Celiac may also lead to herpatic lesions of the skin, dermatitis herpetiformis and loss of hair, alopecia.  In these cases, the autoantigen is peroxiredoxin, an enzyme that eliminates hydrogen peroxide produced as a result of accumulation of reactive oxygen species, e.g. superoxide, associated with inflammation.  Peroxiredoxin is also implicated as an autoantigen in periodontal disease, suggesting that celiac may also contribute to dental gum inflammation.
Peroxiredoxin 5 Gene Associated with Alopecia Risk
A recent study (see ref. below) of genes associated with alopecia identified genes involved in Treg and Th-17 development, as well as peroxiredoxin 5 as contributors.  As expected, several genes involved in antigen presentation (HLA-DRA, HLA-DQA)  were also identified.  Th-17 lymphocytes are involved in immune attacks on self tissue, i.e. autoimmune diseases, such as alopecia, in which hair follicles are attacked by the immune system.  Tregs control immune attacks on self tissues.  Peroxiredoxin is an autoantigen and is produced in elevated amounts around hair follicles attacked in alopecia.
Basic Amino Acids of Peroxiredoxin as Expected for Autoantigen
I checked the amino acid sequence of human peroxiredoxin 5 and found an alternative (-nrrlkrfsmv-) to the triplet of basic amino acids that I expect for an autoantigen.  In this case there are two adjacent pairs of basic amino acids (blue rr and kr) that I think precipitate immunological presentation of peroxiredoxin.  Peroxiredoxins are produced in response to oxidative stress at sites of  inflammation and the presence of celiac compromises the gut associated immune system (GALT) that provides Tregs to restrict autoimmunity, so celiac sets the stage for peroxiredoxin presentation to the immune system and for subsequent production of anti-peroxiredoxin antibodies, autoimmunity and destruction of hair follicles, alopecia.
Anti-Inflammatory Diet Should Avoid and Treat Autoimmunity
Control of autoimmune diseases mediated by peroxiredoxin should benefit from a reduction in the conditions that spawned the diseases:
  • Th-17 elevation -- celiac inflammation stimulated by grain/gluten
  • Treg loss -- GALT inactivation due to inflammatory diet and inappropriate gut flora
  • Autoantigen (basic amino acid concentration) presentation -- oxidative stress stimulation of peroxiredoxin
Treatment would be supported by dietary changes:
  • anti-inflammatory diet to control gut inflammation and minimize celiac symptoms (vitamin D, low carb/high saturated fat, high omega-3 to -6 fatty acid ratio, no grains)
  • probiotics and soluble fiber (e.g. pectin, inulin) to re-establish gut flora (cure dysbiotic constipation) and GALT function, and development of Tregs
  • supplements to compensate for depletion of vitamin C and glutathione by oxidative stress, e.g. vitamin C and acetylcysteine (NAC)
Th-17 and Tregs in HIV Infections
Th-17 cells are also reduced by HIV infection, producing susceptibility to infection, but this infection should also reduce autoimmune disease.  The reduction in Th-17 also may be a consequence of problems in the GALT.  Therapy for HIV infection should also include diet considerations to increase Th-17 and also Tregs to reduce autoimmune diseases due to unbalanced Th-17.
Petukhova L, Duvic M, Hordinsky M, Norris D, Price V, Shimomura Y, Kim H, Singh P, Lee A, Chen WV, Meyer KC, Paus R, Jahoda CA, Amos CI, Gregersen PK, Christiano AM.  2010. Genome-wide association study in alopecia areata implicates both innate and adaptive immunity.  Nature. 466(7302):113-7.


Elizabeth said...

In all of your reading and research have you ever come across the causes of mucus and small amounts of blood tinged mucus in stools? Could this occur in gluten sensitive individuals? Also, do gluten sensitive individuals ever suffer from diarrhea after consuming gluten containing grains?

Anonymous said...

Dr. Ayers,

I found your blog because I read your articles on suite 101

"Bacterial Species Are Made in Intestines" and "Biofilms, DNA Transformation, Drug Resistance"

Do you think that e.coli o157:H7 could be created in someone's gut, from common e.coli, as a result of eating a meal that favored the o157:H7?I have read that this can happen in cattle when they are brought in from the range to a feed lot,switching from a grass diet to grain.Do you think this could happen in our gut too? What sort of food might favor the o157:H7?


Dr. Art Ayers said...

I suspect that there are many ways for the bowels to become inflamed and the epithelial layers shed. I think in most cases the brighter red the stools, the further down the bowels it is produced. Bright red = colon, darker brown = small intestines. Gluten acts up in the small intestines, so would be an unlikely candidate.

I would check with an MD with those symptoms.

Juan said...

I am a male whose hair loss ceased after switching to an anti-inflammatory diet. Also, probiotics eliminated dandruff. So count me convinced.

Do you have any suggestion for a male with low testosterone that does not seem to respond much to an anti-inflammatory diet? I believe my problem is secondary hypogonadism, of the hypothalamic-pituitary axis.

Why do your recommend acetylcysteine instead of taking glutathione directly?

Thanks for any advice, Juan

Dr. Art Ayers said...

The O157:H7 E. coli has picked up shiga toxin on a bacteriophage from a pathogen. That nasty form of E. coli can survive better in antibiotic treated cattle, so the use of antibiotics has selected for it. This toxin producing risk is associated with the use of antibiotics to alter the gut flora of cattle to enhance weight gain. It makes the cattle short lived and sick, but good beef producers. Grass fed cattle do not have these problems.

There is no common source of the toxin carrying phage/virus in humans, so your E. coli can't be converted, even if you take antibiotics.

Thanks for the questions.

Dr. Art Ayers said...

I think that most sex hormone issues are based on general health. Good health means no problems.

Glutathione and NAC can both impact the major anti-oxidant of cells, glutathione. I think that NAC is a better source, simply because the glutathione that you eat is just going to be converted to cysteine and other amino acids anyway and I think that NAC is a lot cheaper. Methionine is also helpful.

You should also check your vitamin C tolerance. If it takes more than 4 grams of vitamin C to loosen your bowels, then you are right about oxidation stress. But most oxidation stress is the result of inflammation, so the anti-inflammatory diet should also be a benefit.

What "anti-inflammatory diet" are you using? Does it have all of the parts that I recommend?

Let me know how you do.

Juan said...

Thanks for the response.

I am on a paleolithic diet, but it seems to be nearly identical to what you call an anti-inflammatory diet, so I was just using your preferred terminology. I follow all major aspects of your diet, although I probably eat less fruit than you do.

I didn't follow the comment about vitamin C and bowels. What question of mine was this a response to? Can you give more background about the rationale behind testing vitamin C tolerance through its laxative action?

Is CRP the main test to get to check for inflammation? Do you suggest other tests?


WilliamS said...

Re: evidence of gluten sensitivity

I'm severely hypothyroid, and my holistic doc believes leaky gut was the probable cause. He thought gluten sensitivity was a not-unlikely part of the problem.

I did a GI Effects test (stool analysis by Doctor's Data), which came out quite well, surprisingly. No bacterial or other pathogenic overgrowth or other gross abnormalities (just a bit of nutrient malabsorption that could be the result of mild HCL, pancreatic enzyme, or bile insufficiency). Interestingly, the measure of gut inflammation (lactoferrin) was the lowest my doc has ever seen (and the WBC and mucous tests were negative).

With no sign of gut inflammation, and the overall undramatic GI Effects test results, he thought it was extremely unlikely I am gluten sensitive. He still believes a leaky gut *caused* the autoimmune thyroid disease at some point, but that I've since healed my gut and am not currently gluten sensitive. He thought that I could safely eat a little wheat and that a formal gluten-free diet trial was not indicated for me (though he frequently does this with other patients).

I'm curious if his conclusions make sense to you. Is a lack of gut inflammation, and other signs of gut dysbiosis or pathology, a pretty clear indication that one's current diet, including a bit of wheat now and then, is unlikely to be a cause of illness? Or can wheat cause trouble without signs of gut inflammation or dysbiosis?

Anonymous said...

DR. Ayers,

People do suffer from o157:H7 infections.Do you mean that the source of the infection must always be a food or at least an external source?Wouldn't our commensal e.coli take up any DNA in it's surroundings when it is subjected to stress?How can we know that the toxin producing DNA is not part of some other type of bacteria in the gut?

Is it an out of balance terrain that is the cause of disease or is it an invading parasitic bacterium that is the cause of disease?

againstthegrain said...


Have you considered testing for anti-gliadin (gluten) antibodies, etc. with Enterolab? Enterolab uses also uses stool samples to test for antibodies to common food allergens as well as to tissue transglutaminase, but the genetic tests for HLA genes that predispose to celiac and gluten sensitivity are done with cheek swabs.

www dot enterolab dot com if you want to learn more about their testing service. No affiliation with Enterolab, except I my son and I used their tests about a year and a half ago.

Tests can be ordered by individuals without a doctor's order (unless you are in NYS), which is convenient, though some insurance will pay and some won't (we have HMO so it didn't, but it was worth it anyway, IMO).

Anonymous said...

Sorry, this is off topic.
I recently discovered your blog and read most of the posts.

I read here and elsewhere about the benefits of getting natural sunlight. Makes total sense. I would love to do so, but as soon as I'm in the sun for any length of time, I get more age spots (I'm 49). Seems like a sign that something isn’t functioning correctly in the body. I'd love to understand the mechanism behind it and stop or reverse the process.
Is there a connection to inflammation?
Interestingly, I made a lot of dietary changes and the pigmentation on my forehead, but not elsewhere, very gradually faded. Then, when I taking using apple cider vinegar, my forehead was intensely sensitive for a few days (the touch of my bangs was insufferable) and the pigmentation came back. I am taking ACV again, but doesn’t seem to do more. On the other hand, even while the forehead was clearing up, I got lots of new spots.
I stopped using seed oils about 4 years ago. I eat no processed food. Some rice, potato, and very little sourdough bread (less than a slice a day), grass fed beef, regular chicken (still working on that one), pastured eggs, a little fish, and lacto-fermented veggies daily, almost no dairy.
My D level is 38 ng/ml. I had been taking 1000ui, and upped it to 2000. I take cod liver oil.

Any thoughts?

Dr. Art Ayers said...

I think that you can benefit from increasing your vit.D3 supplement until you test at 70 ng/ml. I was asking about which anti-inflammatory diet you were following, because some people think that adding plant anti-oxidants to a typical modern diet of processed foods makes it anti-inflammatory.

The reference to vit.C comes from the response to excess dietary vit.C, which is to dump it into the gut, where it loosens the bowels. If you have extra oxidative stress, then your vit. C is depleted and it takes more dietary vit.C to reach an excess. Even spending a lot of time in the sun depletes vit.C.

I don't think that most measures of inflammation are much better than checking one's own inflammatory symptoms, such as sore joints, acne, depression, etc. I guess high sensitivity CRP is as good as any to pick up gross sources of inflammation. Of course it can't tell you if it is from dental infections, an inflammatory diet, or obesity.

My only problem with some paleo diets, is that they sometimes lead to a narrowing of gut flora, by the absence of a diversity of veggies. It is also easier to rely on dairy for probiotics. What about omega-6 vs. omega-3?

The only improvements seem to be increasing vit.C, D3 and fish oil.

Keep in touch.

Dr. Art Ayers said...

Autoimmune diseases indicate to me a history of gut inflammation combined with GALT disfunction, as I indicated. Once the autoimmune symptoms are appearing, the gut inflammation is no longer needed to maintain the disease, but the GALT disfunction is needed to prevent Tregs from stopping the tissue attack. Antibiotic treatment is a typical antecedent.

I don't think that the gut flora tests that were done could test for the integrity of the gut flora vis-a-vis GALT function and Tregs. Do you have any food intolerances, constipation or other signs of gut flora problems? Have you used NSAIDs that can cause leaky gut?

How is the leaky gut supposed to have produced the thyroid problem? Is it autoimmunity? Are you on a high carb/low saturated fat or a high sat. fat/low carb diet? How does your diet compare to the anti-inflammatory diet that I recommend?

There are lots of possibilities.

Dr. Art Ayers said...

Thanks for the useful suggestions for evaluating gluten intolerance. Celiac is supposed to have an incidence of a couple of percent, but I think that the detection is way off and most people respond to grain gluten.

Dr. Art Ayers said...

Age spots -- My take on these spots is that the skin is a clonally-produced patch work of cells with slightly altered genes. That means that some of the patches respond to light differently, because the patches of cells are already different. That's history.

The ease with which all of your skin becomes damaged and responds by increasing pigmentation can be changed. Chronic dietary inflammation makes the skin more easily damaged and decreases vit. D production in response to sunlight.

The anti-inflammatory diet that I recommend should reduce sensitivity to UV and increase vit.D production by the skin. The other part of the equation is gut flora.

I would recommend switching from cod liver oil to fish oil capsules to increase your omega-3s and decrease the -6s. You might also increase your saturated fats vs. carbs for your calories. Your vit.D is low and your supplement at 2000 IU/day may be too low to bring it up. You will need to recheck to be sure.

Let me know what happens.

Dr. Art Ayers said...

O157:H7 is always from an external source, because there is no selection in your gut to produce it. It has to be eaten and then bad luck causes it to increase in vulnerable people.

Cattle use of antibiotics selects for )157:H7, because the normal bacteria that grow in the hind end of the cattle gut are killed off by the antibiotics and the only bacteria that can grow there are E. coli that produce a toxin. That toxin is from a pathogen.

Humans don't have the pathogen that produces the toxin, otherwise they would be dying from that pathogen. Our gut flora can't make the toxin gene from other genes.

Our gut bacteria are stimulated to release DNA and pick it up in the biofilm environment. They are genetically very dynamic, but if they don't reproduce as fast as other bacteria, they are replaced. There is constant selection for the most productive in the numerous niches of the gut. Stress is just another selective environment.

I think that there are two problems. The cattle industry is making pathogens by abusing the use of antibiotics, and modern diets are making people very susceptible to pathogens and toxins.

Thanks for your comments/questions.

Anonymous said...

Thanks. I'm pretty much already doing the anti-inflamatory diet + improving gut flora.

While I think some existing spots have lightened, I'd say the rate of new spots has increased, if anything, since I've made dietary changes(about 8 months). Of course, there an age/hormone factor.

I'll increase the vitamin D as you suggested.

Could you explain why fish oil capsules would be better than cod liver oil. I always prefer a traditional food, where possible. Maybe it's time to add fresh salmon to my diet.


Jason said...

I'm a male in my 30's that developed raynaud's on my fingers and feet 1 year ago and have later tested with positive ana of 1:1280 with + RNP auto antibodies. There is no history of autoimmune disease in my family and was perfectly healthy before.

My only symptom is the cold fingers and I'm trying everything to stop it progressing to a full blown connective tissue disease. RNP auto antibody has some scary disease associated with it.

Based on your recommendations, I have been taking vitamin D 5000 UI for the last few months and raised my level from 28 to 55 ng/l,I'm taking 5 capsules of epa(400mg)dha (200mg) omega 3's every day.

I've also started eating an anti-inflammatory diet for the last few months.

My symptoms have slightly improved and my finger get less cold than before. I also had some gut issues before (heartburn, feeling of fullness) which has healed since starting my new diet and supplements.

Do you recommend I higher my vitamin D levels ? Take more fish oil? or add any other supplements?

The only prebiotic in my diet is keffir and kimchi. Do you think the dairy in the keffir is risky ?

Is there anything else I could do from your experience that would halt or help stop a possible progression to a connective tissue disease? Is there any chance of lowering my ANA and RNP?

thanks, jason

Anonymous said...

Gut Bugs and TH17

Then the researchers decided to see what would happen if bacteria were reintroduced to the germ-free mice. But not just any bacteria. They inoculated mice with one specific organism, an unculturable bug from a group known as segmented filamentous bacteria. In prior studies, these bacteria had been shown to lead to intestinal inflammation and, more intriguingly, to induce in the gut the appearance of a particular immune-system cell known as Th17. Th17 cells are a type of T helper cell—cells that help activate and direct other immune system cells. Furthermore, Th17 cells induce the inflammatory cascade that leads to multiple sclerosis in animals

Byron said...

Hi Dr. Ayers,
thanks for another great article.
As I mentioned often enough I´ve Hashimoto´s, asthma, eczema and lots of allergies and intolerances. Everything except the "real" allergies were deeply improved even resolved by a very strict version of trial and error and heavy supplementation. Just want to mention how important patience is. It took 8 month of a nearly only meat diet with lots of SFA, fish oil more than 4g, D3 10000, pro- and prebiotics. Vitamin C is a good example for the importance of high quality. If I take any kind of ascorbic acid I´ll have diarrhea at very low dose. But with buffered ascorbic acid I can go up to 6-10g!In my experience the huge improvements were made with prebiotics/gut restauration or/and vitamin D3/sunshine. Greetings.

WilliamS said...

Againstthegrain and Dr. Ayers, thanks for your responses!

againstthegrain said, "Have you considered testing for anti-gliadin (gluten) antibodies, etc. with Enterolab?"

The GI Effects test included an anti-gliadin test, which was negative. My doc didn't feel the more comprehensive Enterolab test was warranted once he saw the excellent GI Effects inflammation results and the lack of any other sign of major gut dysfunction or dysbiosis. He didn't believe I could have gluten sensitivity or leaky gut without gut inflammation; and as I mentioned, my lactoferrin test result for inflammation was the lowest he'd ever seen.

Dr. Ayers said, "Do you have any food intolerances, constipation or other signs of gut flora problems? Have you used NSAIDs that can cause leaky gut?"

No food intolerances I'm aware of, and no constipation. My bowel function, overall, seems quite excellent, as judged by my elimination habits. I do have some chronic problems with belching and gas, and, I'm told, some bad breath that neither my dentist nor my docs can find a cause for but could be digestive in origin I imagine.

As for NSAIDs, for years I took a baby aspirin once a day, as is the fashion, but I stopped some months back after learning more about it. No other regular NSAID use, and no antibiotics.

"How is the leaky gut supposed to have produced the thyroid problem? Is it autoimmunity?"

Yes, my holistic doc believes that many years ago I probably had a leaky gut that caused an autoimmune reaction, hence my Hashimoto's. He thinks I healed my gut at some point along the way but that the autoimmune disease continues, much as the immune response to some vaccines can last for decades after the exposure.

"Are you on a high carb/low saturated fat or a high sat. fat/low carb diet? How does your diet compare to the anti-inflammatory diet that I recommend?

Yes, I'm on a high sat.fat/low carb/sugar free diet, my Vitamin D levels with supplementation are always well over 50, and I take both 1 gram of EPA + DHA from fish oil plus 4–6 krill oil capsules a day. I've drastically reduced grain consumption and eat them only now and then when my girlfriend insists on pizza, pasta, etc. (That's why I was interested in whether my doc seems right to say a little wheat now and then is unlikely to be a problem for me given my GI Effects test results.)

I do follow your other guidelines as well, including avoiding vegetable oils as much as possible, eating real kefir, kimchi, sourkraut, pickles, etc. daily, and high-intensity Nautilus strength training. I'm very lean, eat lots of non-starchy vegetables and moderate fruit, and take 2 grams of Vitamin C. Also some probiotics suggested by my doc to try to correct some minor gut flora imbalances indicated by the GI Effects test (Bifidobacter sp. a bit lower than Lactobacillus sp.). The only part of your program I think I haven't tried is the glucosamine and the vagal nerve stimulation.

One oddity is that I have quite a bit of stiffness in my fingers, which has progressed to chronic tendinitis on my primary index finger (complete with the classic palpable knot in my palm along that tendon). My docs suspect that's related to the hypothyroidism, which so often causes joint problems. They're not swollen, just stiff. I've been experimenting with your suggestion of Castor Oil, and also ice baths, but so far at least the problem hasn't resolved.

I have considered upping my Omega 3 dose even more, with either more fish or krill oil, but am a bit hesitant to keep adding polyunsaturated fats, even the good kind.

If there are other reasonable ways to encourage those tregs to make my immune system behave itself I'd be interested. I've even considered some of the more exotic ideas out there for autoimmune disease, such as low dose naltrexone and helminths, but so far at least they feel a little beyond my comfort zone.

Thanks again.


Anonymous said...

i've always felt that i've had issues with gluten, but a serum antibody test and biopsies from a recent endoscopy did not show any problems. for someone like me, how important is it to follow a wheat free vs a gluten free diet. i've had issues with chronic diarrhea. thanks doctor!

Anonymous said...

Dr. Ayers,

This is such an important post – you could be speaking to my husband! While he doesn’t have alopecia, he does have psoriasis on his scalp and he has dental issues which complicate the situation. We went from a low-fat to a high fat diet almost 10 years ago and haven’t eaten gluten for even longer. I suspect leaky gut, and he may even be celiac prone though he's never been tested for it. He had hepatitis (A, I believe, from sewage contaminated water) over 30 years ago when he lived in China so his liver has issues, and he is fastidious and fussy about bacteria as a result.

The only thing that has caused a big improvement in his psoriasis is eliminating nuts from his diet. He resisted doing this which only convinced me he should. He doesn’t eat any fruit due to his dental issues (fructose). A little fruit would seem beneficial in the diet so I wonder how he can add foods that may adversely affect his dental situation but are still needed for gut health.

He is very logical about things and seems to come up with numerous reasons why something won’t work, but I’m pretty good at persuading him.

We've read your article on psoriasis, but given the complexity of his condition, do you have any advice for us on how to proceed?

Thanks for your blog and your generosity!

Anonymous said...

To the person talking about psoriasis. I had it on my scalp, elbows, ears, and above my lip for 6 years. Minor in summer, major in winter. (I love the sun).

Last summer I began taking low dose naltrexone for something else. I kept waiting for psoriasis to arrive in winter. It never did. It is now a year later and it is gone, gone, gone. It finally dawned on me that it was the ldn and I googled it and found out that yes, it works on psoriasis because it works on the opioid receptors and the immune system. This stuff is great - non toxic, cheap, normalizes the immune system. I tried every natural thing for psoriasis and got nowhere until, without trying, it is gone.

Anonymous said...

Ms. Age Spots here (what a name!)

Just wanted to add that besides the vanity aspect, I am assuming that the age spots are a sign that something is not yet right in the diet. The reason I think that is that I've seen the spots come and go to some extent along with dietary changes. Also, I'm getting spots in areas that don't get exposed to the sun, so it isn't just "sun damage". I don't know if I should get more sun exposure to up my D levels, or just rely on supplementation. There is sun almost 365 days a year where I live.

I also suffer from a relatively mild case of chronic fatigue syndome.

Thanks in advance,


María said...

Buenas noches Dr. Hace poco tiempo me diagnosticaron la enfermedad celíaca. Tengo 45 años y me gustaría que me diera algunas pautas para regenerar un poco mis órganos, ya que han sufrido mucho hasta saber qué me pasaba. Ya estoy siguiendo una dieta antiinflamatoria, pero me gustaría hacer algo más para restablecerme, por ejemplo qué suplementos, o consejos me daría? Tengo mucha artrosis y deseo que a partir de ahora no progrese y mejoren mis articulaciones. Muchas gracias y disculpe que no le escriba en inglés, pero no sé. Su página la leo mediante el traductor, gracias

Anonymous said...

To "naltrexone",

I can't thank you enough for posting this information. My husband thinks it would work because he had hepatitis so we'll definitely be giving it a try.

You're a god-send!

Anonymous said...

some information might suggest that in certain autoimmune diseases (crohn's, etc) small intestine bacterial overgrowth may be to blame. as a result, some experts advise avoiding anything that contains bifidus bacteria (mainly various probiotics) as this species is more likey to form biofilms that in turn contribute to the sibo. do you think there is any rationale behind this?

Jason said...

Hi Dr Ayers

I have hashimotos. Is taking levothyroxine good for the thyroid?

What is Treg?

What kind of vegetables i need to eat to diversify my gut?

My diet is always sweet potato, beef liver, egg, sirloin steak. Seldom vegetables.

Dr. Art Ayers said...

Levothyroxine doesn't do anything for the thyroid that is damaged in Hashimoto's immune system attack on the thyroid. It just replaces the missing thyroid hormone.

Hashimoto's usually result from celiac, which is an autoimmune disease of the intestines that is triggered by gluten in grains. The thyroid gland has the same target antigen as the intestines, tissue transglutaminase, so it gets involved in the immune system attacks and thyroid hormone is not produced properly.

Autoimmune diseases are based on inflammation and disruption of the intestines around the appendix. This is where the Tregs, lymphocytes that suppress immune system attacks, develop in response to gut flora, and it is the same area where celiac happens. Reversing Hashimoto's would require fixing the gut with diet and attention to restoring gut flora.

To develop gut flora, you need a source of hundreds of different species of bacteria, many of which are in soil or on the surfaces of plants grown in soil. To have diverse gut flora, you need to eat diverse plant material, i.e. vegetables. They need to be fresh, local and not too clean, to supply lots of different bacteria. All types are good. Herbs and spices also help.

Studies show that food preferences require about three weeks of persistent exposure to change. Preferences are solely the result of experience and are not inherited, although women who eat diverse food the last trimester of pregnancy and while nursing help there nursing offspring to develop diverse preferences.

Thanks for the questions.

Dr. Art Ayers said...

Unfortunately, it is 40 years since I had my training in high school Spanish. I can understand your writing, but find it too difficult to find the correct words in Spanish.

Celiac is difficult to treat, because the intestines damaged by the attack on gluten in grains is also responsible for normal function of the immune system. The cause of the celiac is a previous infection in the intestines combined with a diet that reduced the gut flora needed to prevent the infection from turning into autoimmunity.

To reverse celiac, which is a true food intolerance that cannot be reversed by only adapting gut flora to digesting gluten, gluten/grain must be avoided until the gut is repaired. The damage to the gut also limits absorption of nutrients to produce numerous vitamin deficiencies. Damage to the immune system also eventually leads to a string of autoimmune diseases and allergies.

I would recommend switching to the low carbohydrate diet that I outline on this blog, because it already suggests limiting or eliminating grains. That means meat and vegetables, with most calories from saturated fats and no grains. You will have to supplement for poor vitamin absorption. This will probably also include the sulfur amino acids (NAC) and vitamins (vit.C) depleted by oxidative stress. This will avoid triggering celiac reactions and help the gut to quiet down. Glutamine would also be helpful for repair.

To rebuild the gut flora will require a combination of probiotics, esp. Bifidobacteria and then vegetables and fruits with soluble fiber (pectin, inulin).

This approach should also help your inflammation symptoms of arthritis and joint pain.

Let me know how you do.

María said...

Gracias por su respuesta Dr. Intentaré llevar una dieta lo más saludable posible para compensar tanto daño, es usted muy amable, gracias

Medjoub said...

Dr. Ayers-

I have had a good deal of success dealing with poor digestion using your protocol. Raw vegetables, occasional raw fruit, fermented vegetables, and yogurt supplement my otherwise high-fat, grain free diet. However, I've had little success in treating my rhinitis symptoms (nasal/sinus swelling, mostly) through diet alone.

For the last two or three years, I have not taken any medicine for my allergic symptoms. Are there any that you are aware of that are safe? Aspirin? CLO? Any off-the-wall suggestions or things I might not have considered? I want to avoid the obvious antihistimines and decongestants, but I need to find a way to get some relief while I continue to work on my health through diet. Daily headaches and sinus pain are at very least frustrating and, at worst, prevent me from being productive in any way.

Interestingly, despite having this problematic immune response to molds, dust, etc, and nuts (anaphylaxis, here), I don't get sick often -- I just feel more or less steadily crappy.

I'm considering testing for Celiac's, as it's possible I need to be more stringent about avoiding gluten. I can't imagine that that could have much to do with it at this point, though, as I don't often eat out so am at a low risk for contamination.

Thanks for any suggestions.

tanya said...

Medjoub...I'm going to jump in here and let you know that Mayo did a study and much of the sinus issues are fungal related. They even patented a nasal spray based on the antifungal foot sprays. I would recommend you try Xlear nasal spray, or another brand that contains grapefruit seed extract. The fungal issue could be what is making you feel generally icky too, as Dr Ayers reminded me of recently.

Anonymous said...


I've been exerimenting with various things to improve my health. I recently put a stop to years of daily sneezes and nose blowing.

I cleaned out the filters in my central air conditioner/heater. I washed all the sofa covers and cushions that are washable. I now vacuum my mattress once every two weeks and let all my pillows and sofa cushions sit in the sun every few days. I don't have a lot of carpets in the home, but I washed two small area rugs in my bedroom.

My sneezing is down to almost zero. I have no idea if it would help with sinus trouble, but it's one of those harmless things that are worth a try.

Hope that helps.


Medjoub said...

Tanya, Anon -

Thanks for the recommendations. I'm looking into Xlear and, in general, I try dust-mite avoidance by the suggested methods. Unfortunately, I have had little success with the latter procedure. I *feel* that if I could somehow reduce my general nasal inflammation, I could afterwards maintain that healthy status through diet. However, *treating* it through diet has been a bust -- thus far. I have been able to improve my digestion with "dirty" veggies/fruits, but my nasal response and sinus pain is virtually unaffected. It'd be wonderful if some of the standard over-the-counter meds were safe, but as I said, I don't use them. I just wonder if there is something obvious I'm overlooking...

Dr. Art Ayers said...

Have you tried humming? In sinuses the circulating immune system can't reach the source of the inflammation, the bacteria in mucus. Humming disrupts the layer near the surface and provides nitric oxide that dilates the blood vessels. Studies show that it is more effective than antibiotics.

You should see results in a day and your improving immune system should contribute.

Let me know how it works for you.

Anonymous said...

I have been suffering from sinus congestion for last 7 years and tried 100 different things. I found immediate reliefs from following
1.Pancreatin Enzyme tablets before meals.
2. 1-2 tbs vinegar after each meal.
3. Pineapple and bromalain suppments with meal or on empty stomach
4. Sniffing cayenne and eating very spicy food.
5. Very low carb diet with high coconut oil consumption. It takes few days to get used to this oil.

Unfortunately I have a very sensitive stomach and i cant follow none of these methods for more than few days.
If you can tolerate you can try these. Vinegar can he harsh on teeth.

Currently i am getting good results following Dr Ayers diet.
5000 IU Vit D, 2-3 gm fish oil, 1gm Vit C, 200 IU Vit E, Humming, Lots of soluble fiber(onion garlic carrot ripe banana), 50-100 gms of carb, yogurt lassi. Ayurveda suggests that yogurt should be consumed with salt,water and spices added.
I hope you get quick relief from this terrible suffering.
-- Rashed

Anonymous said...


Have you tried a neti pot to wash out the sinuses? I haven't tried it personally, but have read that it made a dramatic difference for some people.

Let us know if it helps.

Medjoub said...

@ Dr. Ayers -

I am trying humming as we speak.
:-) I will report back on its helpfulness. Are there ANY safe over-the-counter medicines (I'm thinking of aspirin or guaifenesin...) for reducing nasal inflammation?

@ Rashed -

Thanks for the numerous suggestions. I will try some of those. Do you typically use those remedies simultaneously, or at different times?

@ Anon -

Neti pots are pretty ineffective for me, as have been most attempts at avoiding allergens (dust, mold, etc.) and potential allergens (milk, eggs, etc.).

Anybody with other suggestions, throw 'em at me. Things couldn't get much worse. :-)

Medjoub said...

@ Rashed -

One thing I forgot: does the type of vinegar matter?

Medjoub said...

@ Dr. Ayers -

I apologize for taking up so much space on the board -- if I had thought this stuff through, I'd have asked everything at once. I recently moved to CZ, and many Europeans use Bioparox (fusafungine) to treat rhinitis and sinusitis, along with Sinupret. Do you have any insight into the safety or efficacy of these supposedly "natural" treatments? (Hopefully this isn't starting to sound like I'm hoping for a quick fix -- dietary measures have been such a let down, that I'd just like to find SOMETHING helpful).

Anonymous said...

I mostly used apple cider vinegar and sometimes i used white vinegar. I did not see any difference in result. I never tried all of those method at one time, i am afraid if i try all of them together ill get severe stomach pain. I have problem handling acidic food. Enzyme pancreatin is not acidic but i feel nauseated after taking this, but i get excellent result with it.
One thing i have just noticed that all my cures are suggested by Dr Ayers in disrupting biofilms. Protease, vinegar, spices, low carb all disrupts biofilm. Please check his posts on biofilm.
I also avoid dust mites as much as i can. Good air conditioner and regular filter change help a lot.
I had major improvements after totally cutting off gluten.
Good Luck

Medjoub said...

@ Dr. Ayers and Rashed -

I have tried an hour of humming each day for several days, but it has had no effect on my nightly nasal/sinus swelling. Unless I am not properly doing it, I assume that it isn't "speaking to the problem," as it were.

I've also been trying a tbsp of apple vinegar after some meals, but this appears to be resulting in loose stools, etc. The symptom *could* be unrelated, but as I've not changed my diet in other ways, I can't imagine what the problem would be.

Re fusafungine - I did some research and found out that is a local antiobiotic (non systemic) used to treat sinus infections and throat infections. It is over-the-counter here in Europe and apparently originates in France. It seems unuseful, of course, for my current concerns (unless maybe there is some lingering bacteria or fungus in my sinuses that I haven't addressed, but without a diagnosis it seems unwise). I wonder if it is preferable to systemic antibiotics (which I have not used in years and refuse).

I take vitamin D daily and have decided to start taking 500 mg vitamin C. I doubt I get enough vitamin C from my diet, so we'll see if this measure has any effect.

Thanks for your suggestions and commentary.

Medjoub said...

Dr. Ayers -

If I continue on a gluten-free, "dirty" veg, high-fat diet - like that which you recommend - and still find little to no relief from nasal allergies and sinus pain, is there a "next" step? I have not been tested for celiac's, but as I've heard that testing is inefficient, I don't know what good it would do to go to the trouble (particularly when I don't eat bread anyway -- maybe it could tell HOW careful I should be). I have also never completely eliminated dairy to gauge its impact on my sinuses, but doing so would leave me cream/butterless (god forbid).

I apologize again for my repeat posts, but my lack of improvement is VERY frustrating and I read enough of your posts (and Peter's, Stephan's, Kgh's, etc) to know what I should be doing and what should work. My digestion has improved, though still with some constipation. I assume that is related to my allergies, but conventional doctors certainly don't make the connection.

Thanks for your time...

Dr. Art Ayers said...

I would guess that the missing piece is immunological. You still indicate that your gut flora is dysfunctional, i.e. the basis for your continuing constipation. That would indicate a corresponding dysfunction in your immune system, e.g. deficient Tregs. Deficient Tregs are characteristic of the establishment and persistence of allergies and autoimmunity. Swelling from allergies will involve mast cells and histamine.

As I see it, that leaves two choices:
1) Check to see if an antihistamine eliminates your symptoms.
2) Check to see if you symptoms can be suppressed by increasing fish oil supplements. (This would check for some other source of inflammation.)

Let me know what happens.

Medjoub said...

Dr. Ayers -

I tried experiment (1) to basically no effect. As a child, I regularly treated my allergies with antihistimines and decongestants. Neither have much impact on my current, chronic nasal inflammation. A single Benadryl did little beyond make me very sleepy and reduce some mucous production -- but none of the swelling or pain.

What is curious about this situation is that allergens (dust, animals) make my nasal pain worse, but antihistimines don't completely eliminate or cover up the symptoms. I feel like it is allergic in origin, but its expression has become close to constant.

I am now going to try experiment (2): increasing fish oil. I eat absolutely no seed oils, as I am following your diet protocol, so what gradation should I use to increase the fish oil? Is there a ceiling?

Thanks so much.

Dr. Art Ayers said...

Fish oil capsules typically have about 350 mg each of DHA and EPA in a 1200-1500 mg capsule. I wold start with 4 capsules twice a day with meals containing plenty of saturated fats. Make sure that you have adequate saturated fats for absorption of the omega-3 oils and to decrease possible production of lipid peroxides at sites of existing inflammation.

Start with 8 capsules/day and increase 2 more per day after watching for several days. Increase up to 12 per day if needed and continue for a week.

You history points strongly toward Treg deficiency that will only be improved by reestablishing your gut flora as demonstrated by normal bowel movements and no food intolerances.

Let me know what happens.

Greg Davis said...

Dr. Ayers,

First off I have to say thanks for your time spent on this blog. I have been mining it for information for a few months now and find your insights fascinating, worth more than any good book on these subjects.

I have a bit of a puzzling (for me and my doctor) situation that manifests itself most acutely by the fact that I awake early in the morning, which is stopping me from getting more than 5-6 hours of sleep. I sleep like a log from about 10-11 to 4-5 a.m. But wake up feeling "wired" and I feel this is causing my other health symptoms of low weight, testosterone, and hemoglobin (not iron). Doctor is totally puzzled as I otherwise seem like a healthy, fit, and well androgened 28 year old.

I've been investigating this for almost 2 years now and it seems like I'm showing symptoms of some sort of autoimmunity. But I've been eating "paleo" for close to 5 years now, but with occasional starchy meals especially when engaged in sports of much intensity.

When I saw this blog post of yours it triggered me to remember that about 3-4 years ago I had a short bout of alopecia, not unlike the picture you show here. Lasted about 2 months and then went away. Never considered this to be possibly linked to my issues..

I am trying my best to assume inflammation/autoimmunity could be an issue and so sticking to a paleo diet with some kefir and cheese. Going to try ratcheting down fruit intake (already quite low), increasing good fats, and keeping exercise moderate to the point where starch is not needed in significant amounts. Had vit D tested last summer and came out at 65, so I am continuing with supplementation of that and some other things in line with your recommendations.

Do you have any thoughts on the symptoms I am describing and if the alopecia could be related?

Dr. Art Ayers said...

I am puzzled by your mention of possible autoimmunity, but no mention of your gut flora.

My view of a typical treatment for anything autoimmune/allergic focuses on the gut flora. That means, in brief, probiotics, soluble fiber and muddy veggies.

The paleo diet fixes problems of inflammation from the typical high carb/high omega-6 diet, but it doesn't address immune system problems based on deficient Tregs. Tregs are the immune cells that regulate the attack of the immune system. Tregs develop in the GALT in response to gut flora and those gut flora grow in response to plant polysaccharides, i.e. veggies. Probiotics can contribute marginally and temporarily, but you need to recruit a hundred different bacterial species from your environment (other people, animals, soil-laden veggies) and then maintain that gut flora with diverse veggies.

Paleo is great, but it thins out the gut flora. You are short on gut flora and are trying to treat that shortage by paleo. Doesn't make sense. You need more diet/veggie diversity, rather than less. Any intolerances will reveal bacterial deficiencies that should be remedied by slowly increasing that food in your diet.

Let me know of your progress.

Greg Davis said...

Dr. Ayers,

I will definitely implement some of your ideas for improving gut flora and report back on progress.

You've mentioned the lack of diversity in a paleo diet before, and I don't quite understand how it differs from what you recommend. What specifically is left out that you would recommend?

I include all sorts of fruits and veggies, some tubers/root veggies, minimal nuts. Small amounts of dairy in the form of kefir, cheese, and cream.

I haven't seen you refer to anything specific that wouldn't be captured by my approach?

Dr. Art Ayers said...

I am probably just guilty of generalizing from impressions that I have from lurking on paleo site, that bowel transit times are slower on paleo diets. That suggested to me that some of those diets were low on plant polysaccharides/soluble fiber and hence were potentially low on gut flora populations and gut flora diversity. I also had the impression that many on paleo diets found it difficult to adjust to new veggies, another indication of restricted gut flora.

If you have normal bowel movements, i.e. no constipation issues, no food intolerances and respond to apples and leeks with just a modest bowel output, then you should be on the mend, if you do have autoimmunity/allergy problems.

Let me know how you do.

Tanya said...

Concerning Tregs, I've been looking up stuff on the Thymus gland...some food for thought "A study done by PESIC and LAWNICZAK, entitled "Immune correction with the help of thymus extracts under negative influence of some antibiotics upon the phagocyte", clearly reveals that the application of THYMEX-L after treatment with antibiotics or cytostatic agents, leads to a correction in the level of enzymes.

According to clinical examinations the regular application of thymus reduces the susceptibility to infection. Moreover a visible improvement in the general condition of most patients can be detected. The treatment with thymus extracts in cases of chronic, recurrent infections must be regarded as a causal therapy. It leads to a fundamental restoration of the immune system. " from and also there was this

Anonymous said...

Dr Ayers
I have been following your diet and suggestions for few months now. I am seeing major improvements in my severe allergy,sinus and polyp problems. I also have autoimmune Hashimoto, subclinal hypothyroid. I increased my intake of soluble fiber, mostly apple,carrot, banana. Traditionally we use lot of onion and garlic in our curry. I assumed that i was getting enough inulin from those two sources. Then i read many articles on Inulin and oligofructose and how they totally alter the gut flora in a short time. This article showed that in vivo 15 gm inulin in two weeks changed bifidobacteria from 20% to 70% and reduced bacteroides from 65% to 26%. ( Gibson, Gastroenterology , 1995), To achive that i started taking large amounts of raw garlics and onions. After few days of stomach upset im seeing huge improvements in my allergy/sinus. I am extremely happy about it and i have to thank you for your suggestions. I am curious how much of inulin in onion/garlic gets destroyed in cooking.
After reading all these inulin articles it seems like inulin alone can bring balance in gut flora. Im curious why do you suggest diversity in vegetables? Should i assume that we all have fewer species of gut bacteria? In that case,to have soil laden vegi i need to start growing my own veggies. After living in usa for 12 years now i am living in a not so sterile 3rd world country. Is it ok to eat small amount of soil to get new bacteria? Is it scientifically proven that most bad gut bacteria, other than Klebsiella, thrives on sugar and starch? Im also curious how do spices alters gut flora.

Thank you for all your help

Medjoub said...

@ Dr Ayers-

Re your fish oil dosage recommendation -- are you saying start with 8 capsules, each containing 350 mg TOTAL of EPA + DHA, or 8 capsules each containing 700 mg (350 x 2)EPA/DHA? There are no capsules in Europe with anything close to the latter strength, so I'm trying to make sure I understand you correctly.

Thanks again --

Dr. Art Ayers said...

You are correct. I have been a little casual about my suggestions for omega-3s. I tend to buy based on quality (EPA and DHA analysis, not omega-3, which frequently includes other short chain fatty acids) and price. Most recently, I got a good deal on some "professional strength" capsules that are 400 mg EPA/300 mg DHA. Most are roughly 120 EPA/ 280 DHA. I should have cut the number of capsules in half for the doubled content, but alas I forgot that I had changed capsules and just wrote down an approximation of the content, since I remembered that the analyses were varied.

The point of the use of omega-3 fish oil supplements is that they should be temporary (used to determine if inflammation is the source of symptoms) and empirical (gradually increase the amount until the symptoms are minimized.) Since omega-6 fatty acids compete with omega-3s, and are stored for years, history of vegetable oil use will change the amount of fish oil needed to block inflammation symptoms.

Thanks for persisting to make sense of my nutrition advise.

lightcan said...

Hello Dr. Ayers,

I would like to continue the discussion related to fish oil. You say intake should be temporary and empirical to see if the symptoms of inflammation subside. OK. However, we say we should try to keep the balance between omega 6 and omega 3 at around max 2:1 and also that total PUFA should not go over 1% of calories (Chris Masterjohn) and should be taken with enough saturated fat. So I see it as more of an ongoing issue, relative to omega 6 consumption. If for years previously one has consumed omega 6 in excess it takes about 2 years of supplementing omega 3 to change the ratio in the cells. After that if omega 6 is low (present in meats, nuts, olive oil) omega 3 can be low too and intermittent.
If inflammation is present, a higher dosage per day is acceptable but then it needs to be taken for a short period only until the symptoms improve. Is this correct?

Anonymous said...

dr ayers,
wondering if you or any of your bloggers have had any experience with Enterolab. i'm considering have their stool test for celiac disease, but was hoping to get some feedback from someone regarding the benefits.

Anna said...


I used Enterolab just over 1.5 years ago to test my son and my self. We did the entire gluten test package for antibodies, plus the genetic testing. They included the milk (casein) test with the full gluten panel.

After I received the results, I decided to do the other tests for yeast, soy, and egg (they keep the sample for about 6 weeks - imagine their freezer ;-) - so it's easy to add extra tests within that time frame.

I thought it was a good service, and I consider it money well spent.

mtflight said...

Dr. Ayers,

What is your take on autoimmune disease and naltrexone at low dosages.. I wonder what the mechanism is. A Hashimoto's patient I am going to have a TPO autoantibody test before and after low-dose naltrexone to see if the autoantibody levels drop any.

In the meantime, I was wondering if you have any input as to how blocking opioid receptors in the immune system (?) helps reduce autoimmunity and supposedly cancers etc. Sounds like a leap, but it's working for many, especially with MS and Crohn's.

Love your blog, btw.

lightcan said...

Dr. Ayers,
I looked in your archive for posts on periodontal disease and this one came up so I hope you don't mind if I ask you about it here. What is your take on periodontal pockets resistant to repeated scaling and cleaning? I understand that pockets deeper than 3 mm can't be cleaned by the patient and that the anaerobic bacteria population reestablishes itself after 3-4 months hence the regular visits. I was also told that I might suffer from some kind of immunity problem that might cause chronic periodontal disease at such a young age (they don't know exactly what) but there was no blood testing done.
I've read about possible IL4 dysregulation as a cause.
Can you please share your ideas? Is there anything that can be done?

Anonymous said...

Hi Dr. Ayers,
I discovered your blog after googling all my diagnosed ailments ie Hashimoto's thyroiditis, SIBO (causing fructose and lactose malabsorption), Raynaud's, alopecia areata and discoid dermatitis. I need to periodically have antibiotics for the SIBO. I have tested negative for gluten allergy. Do you think eliminating gluten from my diet, despite the negative result, might help alleviate autoimmune symptoms?

Medjoub said...

Dr Ayers-

Update on my fish oil/chronic nasal swelling battle --

I'm up to about 5 g DHA/Epa (which means about 3x times that in terms of total g of fish oil). Unfortunately, I've had no reduction in my nasal inflammation symptoms.

Do you think I should reduce my fish oil intake? It is quite expensive continuing with such high doses -- I've increased the amount over 2 or 3 weeks to what I estimate your maximum suggested does to be.

I don't want to resort to conventional allergy medicine (which seems virtually ineffective anyway). Is there any other route I should pursue? I hate to throw in the towel and just accept my condition.

Thanks for your continuing advice and support.

Dr. Art Ayers said...

My impression from your experiments with fish oil and the minimal impact of antihistamines, is that you have developed some type of chronic inflammation and the anatomy of your sinuses has changed, e.g. like lung tissue adapting to asthma or the esophagus adapting to GERT.

I read back through your previous comments and it seems to me that your immune system is stuck in a chronic sensitivity to antigen/allergen, because of your defective gut flora. Are you still constipated? Do pectin and/or inulin-rich fruits and vegetables yield normal stools? Do any food intolerances persist?

A normal, healthy gut flora is needed for a normal immune system. Since your immune system is still dysfunctional, your first step is making sure that your gut flora is normal.

Have you confirmed by test that your serum vit.D is over 50 ng/ml?

I would reduce fish oil to 2-4 capsules per day.

You should be pleased that you are addressing many aspects of your diet that will contribute to long term health. I am confident that your condition will respond. It probably took decades to reach this state and the return to full health will takes some time.

Medjoub said...

@ Dr. Ayers-

I feel comfortable saying that my digestion has improved, with considerably less constipation (often none) in response to *most* foods. Occasionally, I'll have a strange reaction to certain foods, but I can't really trace a pattern. Pectin and inulin containing foods generally seem fine. Of course, my range is usually limited to leeks, apples, onions, and tomatoes.

I just had my vitamin d levels checked (again) after my initial check and supplementation, but don't have the results yet. It's interesting to me that my immune system seems very strong -- since supplementing with vit. D, I have had nary a cold in a year and a half. Living in a new city with an elementary school teacher wife, this is no small feat. But this doesn't translate to a healthy response to allergens -- particularly dust, dander and cigarette smoke, along with whatever lingering foods to which I'm still intolerant.

I appreciate your advice and will let you know the results of my vit. D tests.

Oh -- I also asked before about the local antibiotic fusafungine (bioparox) that Europeans seem to favor. It is non-systemic (nasal spray), but do you see it is an equal threat to systemic antibiotics? I personally don't use any of them at all, following your advice, but I'm interested in how the body response would be different...

Thanks --

Viktor said...

Dr. Ayers

In order to restore gut flora you mention eating a vast number of vegetable, ideally locally grown without pesticides etc.

What are the options if you live in a large city with not readily access to these kind of vegetables?

Is it still a good idea to eat them them unwashed?

Anonymous said...


re washing veggies

You might find this article interesting:

Adelle said...

I see mentions to gum disease throughout your site, however I can't quite get the connection. Is gum disease a cause of other illness symptoms, or a result of overall illness? How would I find the cause of, and how should I treat, gum disease?

I'm worried about my badly receeding gums as I'm only in my early 30's, but I don't know what to do about it. I'm trying to treat other things I have (gut problems, gluten intolerance, CFS, heavy metals, and later on I'll try and treat lyme, too), but it's my gums and the fear of ending up with a toothless smile that worry me the most!

Medjoub said...

Dr. Ayers-

I have posted here frequently in search of some relief from allergies. Recently, I was diagnosed with mild hypothyroidism. I had my antibodies checked and they were well within acceptable range, so there appears to be no problem with autoimmunity. However, constipation is a common symptom of hypothyroid that often resolves when a proper dosage of hormone is reached. It seems to me that those with hypothyroid could have trouble "fixing" constipation through diet. Do you have any thoughts on this?

Dr. Art Ayers said...

I missed you post. Sorry.
Gum disease is autoimmune in some cases. It can start as many autoimmune diseases with celiac or a derivative autoimmune disease, e.g. Hashimoto's thyroiditis, and then as a result common autoantigens, in this case peroxireductase, the gum tissue is attacked.

That means that gum disease is both a disease of inflammation and autoimmunity. Inflammation is fundamentally an issue of diet and autoimmunity is fundamentally an issue of gut associated lympoid tissue and hence gut flora and diet.

The anti-inflammatory diet that I recommend, supplemented with special effort to establish diverse gut flora via veggies and probiotics, addresses both inflammation and autoimmunity. Also see my articles on capsaicin, menthol and castor oil for temporary relief from pain/inflammation.

Thanks for your question.

Dr. Art Ayers said...

Hi Medjoub,
I think that it is the other way around. I think that most people start by messing up their gut flora with antibiotics and/or an unhealthy diet. This compromises their immune system and makes them prone to allergies and autoimmune diseases. Many also have celiac and in response to gluten go on to Hashimoto's thyroiditis. Hashimoto's is a classic autoimmune disease with tissue transglutaminase as the autoantigen.

So, I think that the constipation precedes the thyroid diagnosis. If the constipation abates in response to thyroid hormone, then there is still a problem with the gut flora, but it is not severe enough to change stools.

There are of course, several types of constipation, including simple dehydration. I am talking about the predominant type that is typically inappropriately treated with laxatives and is misunderstood. It is a disruption of the gut flora.

Thanks for your comments.

Dexter said...

Dr Ayers,
The following question was asked at Paleohacks:

Since you are the inulin guy that I refer people to on Paleohacks for gut dysbiosis problems, I thought I would forward the question. Perhaps you could answer directly or pass along to me to post a response.


I listened to Robert Lustig's episode on Jimmy Moore's show, Living the Low Carb Vida. Lustig was strongly against fructose consumption above 50g/d. This started my thinking about inulin which composed of chains of fructose. Conventional wisdom on inulin is that it passes undigested through the stomach and small intestine and gets eaten by gut flora in the large intestine. I wondered if inulin could break down into fructose and provide a large amount of fructose to the body.
I searched and found this: "The most dramatic reductions in inulin content, however, are obtained by slow cooking. Another inulin-rich plant, the camas lily (camassia spp.), was traditionally pit cooked by Native Americans. This involved burying the camas lily bulbs in a pit and covering them with dry wood and stones and, once the fire had been established, earth and grass. The food was cooked for 12 h to 36 h. This method was also possibly used for Jerasalem artichoke tubers, over a 12 h period. Cooking by this method eventually turns all the inulin to fructose, leaving a sweet and soft textured food." from Biology and Chemistry of Jerusalem Artichoke: helianthus tuberosus L. by Stanley Key and Stephen Nottingham, page. 108.

So my question is: If Lustig's warnings about fructose are correct, is slow cooking inulin rich plants a good idea? Is there something as too much slow cooking?

Onion has an inulin content of 2-6 g / 100g. Jerusalem artichoke 14-19 g. Garlic 9-16g. Artichoke 3-10 g. Camas 12-22 g. Chicory 15-20 g.

Anonymous said...

I have wondered about this issue and did my online research. I have read abstract of several articles that states dry heating changes inluin to a different kind of fructose. One of this article claims that these heated inulin are better prebiotic than regular inulin in vitro. I think wet cooking effect will be different since inulin is water soluble. I would like your comment on this abstract. I am curious will these "low-molecular degradation products, most likely di-D-fructose dianhydrides" be digested in our intesttine before reaching colon?

"Effect of dry heated inulin on intestinal bacteria"
by A Hohm , B. Klessen T Henle
"Abstract : Degradation of a sample of high-molecular (degree of polymerisation, DP, between 13 and 30) and low-molecular (DP below 12) inulin from Jerusalem artichoke during dry heating for 30 min at 165 and 195 °C was analysed using high-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD) and thin layer chromatography. Dry heating at 195 °C induced complete degradation of the fructan chains and the concomitant formation of low-molecular degradation products, most likely di-D-fructose dianhydrides. In vitro fermentation studies using mixed faecal samples of eight human volunteers for 24 h at 37 °C showed significant stimulation of the growth of bifidobacteria and Enterobacteriaceae and a significant decrease of possibly pathogenic bacteria of the Clostridium histolyticum and C. lituseburense group by inulin samples heated at 195 °C compared to unheated samples and samples heated at 165 °C. This preliminary data may point to the hypothesis that heat-treated inulin or its degradation products may cause improvements of the gut microflora superior to native inulin. "

Rashed Hasan

Dr. Art Ayers said...

Heating inulin or other carbohydrates to high temperatures results in carmelization, browning and flavor changes. That is what happens when you toast a marshmallow made of sugar.

Digestion of inulin and its impact as a probiotic, depends on how adapted the particular gut flora are to inulin.

The article that you cite of significance only for baking at high temps. At these temperatures, in contact to boiling or cooking when water is still present, covalent bonds can be broken and rearranged to make new molecules, such as the anhydrides (water removed) molecules produced from inulin in the paper.

Inulin is just fine as a probiotic, soluble fiber to feed gut flora, as it is normally prepared in food. It doesn't have the impact of fructose in sugar or HFCS.

Thanks for the question.

Conner said...

Dear Dr Ayers,

I've just stumbled across your blog and love it - wish I'd seen it before!!

I'm a nutritionist based in France, with a special interest in dietary/lifestyle cancer-prevention. (I write a blog on this:

I was wondering whether you could share your thoughts on the latest study out of the UK showing that long-term aspirin use significantly reduces cancer mortality. Could a similar effect be achieved through anti-inflammatory foods, without the risks of brain & stomach bleeding or gut permeability (which can increase inflammation risk, right?).

I'd love to quote you in a piece I am planning to write about this and look forward to hearing from you!

Many thanks and best regards, Conner (you can reply to me at conner AT nutrelan . com)

Theresa said...

Hello doctor.

I just got one question about my stools.

Lately my stools became very very dark in color but still soft and all. Basically "good" in all cases besides color, which is somesort mixture of very very dark green and black.

Also sometimes I get a hard brown stool amongst the others. Why so ?

Do you have any idea about this ?

Thank you

Dr. Art Ayers said...

Remember, I am a PhD, not an MD. Black stools can indicate bleeding in the digestive tract. I would suggest that you see a physician. It can also result from iron-rich supplements, etc.

Anonymous said...

"Th-17 elevation -- celiac inflammation stimulated by grain/gluten"
I am bit confused about this statement. Did you mean all grains( rice, lentil, corn etc) including gluten stimulate Th-17. I have Hashimoto and my TSH is slowing going up, its 5.7 now. Do you know anyone who has been able to control their Hashimoto using your diet. Do you think i should give up all grains. I stopped gluten and now i only eat rice.
Thank you
Rashed Hasan

Anonymous said...

Hi Dr Ayers,

Any thoughts on "homeostatic soil organism (HSO)" probiotics vs regular probiotics--something along the lines of Primal Defence. i have crohn's and have been following your suggestions and my MD's with no improvements. i read something that these type of probiotics may form spores which can eventually be problematic? no other amount of fermented foods/probiotics have seem to make a difference.

Anonymous said...

Dr Ayers
I was wondering if there is any connection between Lipopolysaccharides (LPS) and auto immune thyroditis like Hashimoto.
I came across few articles about LPS and Autoimmune thyroditis. I didnt understand the basic concept. Here are the links

www. ( Fulltext)

Is it possible to control autoimmune thyroiditis by changing count of gram negative bacteria in gut flora by restricting starch and increasing probiotic.
I greatly appreciate all your help and inputs.
Rashed Hasan

Dr. Art Ayers said...

Hi Rashed,
The articles that you cite show that LPS from bacteria cell walls can serve as an adjuvant to stimulate presentation and antibody production against a self antigen involved in Hashimoto's Thyroiditis. This is an artificial mouse model system and says little about the establishment of the disease in humans.

The typical progression to Hashimoto's in humans is celiac or EBV infection, which result in antibody production against a self antigen, e.g. tissue transglutaminase, which is abundant in the tissue initially involved, e.g. the intestine compromised by grain gluten.

After autoimmunity is established, then the initiating events are irrelevant and all that is needed to perpetuate the autoimmunity is to continue to compromise the tolerance system, i.e. disrupt normal gut flora in the colon by diet.

Curing autoimmune diseases required repairing the tolerance part of the immune system and then preventing the recurrence of the conditions that initiated autoimmune presentation of self antigens. In most cases of Hashimoto's, that means fixing the gut flora and eliminating celiac attack of the gut by gluten.

I don't think that restricting starch and adding probiotics is enough, because it does little to alter the anaerobic gut flora of the colon, e.g. Clostridium species, that are needed for immunological tolerance. People with Hashimoto's need several dozen missing species of bacteria that are not present in probiotics, but are present in soil.

Thanks for your questions.

Andrea said...

Dr. Ayers,

I have been suffering with chronic constipation for 4 years now. It began after a 3 week period taking antibiotics. Since this time I have developed many health issues including insidious weight gain, insulin resistance, PCOS, Crohn’s Disease and oestrogen imbalance (16α-hydroxyoestrone dominance).

I have been following a strict paleo diet (grains, legumes and dairy avoidance) for the last 10 months, while I feel better and have noticed an improvement in insulin sensitivity. I have not experienced any change in constipation, oestrogen imbalance or weight loss. In the last few months I have been following a paleo autoimmune diet and eliminated eggs, nuts and nightshades, this seems to have made the constipation worse.

I am taking several supplements (for the last 2 years)…Vit D, Fish oil, Chromium, Selenium, Magnesium, several probiodics.

My stool tests show bifidobacterium are nonexistent. Thyroid antibodies, TSH and T4/T3 are within normal range.

I would really appreciate your opinion on where to go from here. I feel my health is rapidly diminishing at 26 years of age. Should I try to diversify my diet a little more (within the parameters of the Anti-inflammatory Diet?)? My doctor has suggested an IgG food allergy blood test. What is the accuracy of this in someone with leaky gut?

Thankyou for your time,


Dr. Art Ayers said...

Constipation indicates that you are lacking most of the species of bacteria needed to handle food and for the normal function of your immune system.

To fix your gut and gut flora, your need to eat the anti-inflammatory diet that I have recommended, but equally import, you have to eat new bacteria to reconstitute the complex bacterial community of the gut. Probiotics,as in live yogurt, can supply a few different type of bacteria, but a healthy gut has more than a hundred different species of bacteria to supply enzymes to digest the complex polysaccharides in different foods.

You just keep eating different foods, but you aren't taking in the bacteria that you need to grow in your gut to be healthy.

So, check your serum vitamin D, avoid starch/sugar/vegetable oils, and increase the veggies. Hygiene is you enemy, since you need to eat new bacteria to develop the complexity of your gut flora. Bowel stools are made of bacteria that grow on soluble plant and animal fiber. If you lack the bacteria needed to digest a food, you just produce the dehydrated stools of constipation. The bacteria that you lack can be obtained by eating fresh, lightly rinsed veggies.

Some of my friends only have healthy guts when they are intimately in contact with their "friends."

Tell me how you do.

Ruth Almon said...

Wouldn't eating a wide variety of homemade lacto-fermented vegetables (pickles, sauerkraut, etc.) on a daily basis do the trick?
What about drinks like kombucha?

Dr. Art Ayers said...

The fermented veggies would provide a narrow range of bacteria, which would be even less diverse if they were typical branded products.

The fact is that most people treated with antibiotics do not recover their normal gut bacteria by eating typical commercial foods in developed countries. The result is the suite of autoimmune and degenerative diseases. Antibiotics and processed food lacking contaminating bacteria that would normally repair damaged gut flora is a lethal combination.

It is a serious mistake of modern medicine to assume that modern diets can produce healthy gut flora. Modern disease patterns clearly show this assumption to be false. Most people are simply too clean and excessive hygiene is preventing the spread of healthy gut flora.

Anonymous said...


Dr. Ayers encourages his readers to share their observations so here are mine:

According to Dr. Ayers, some gut bacteria requires other bacteria to already be present in your gut before it can establish itself. That is why a diverse diet is so important. Allergy tests and resulting elimination diets may help you establish a balance that relieves your symptoms, but you will still have a weakened immune system if you restrict strong sources of nutrition such as eggs and nightshade vegetables. A weak immune system is your real enemy not food allergies. If you are sensitive to a particular food, don’t give up on it, instead eat a diverse diet and keep trying it (in my experience, it takes a week or two at most for the necessary gut bacteria to be available for the problem food to establish itself).

Nightshade vegetables: Dr. Ayers says peppers are very strong plants (resistant to insects and disease) and strengthen your gut flora. Unwashed herbs are also strong and easy to grow. Foraged foods and wild berries in season would also be a good source especially as they require exercise to obtain them. Exercise is equally important even if you can only walk short distances at first (2000 steps = 1 mile). When your gut is healthy, you want to move about and exercise so it will become effortless.

In my personal experience, too little saturated fat causes stools to “pellet” so it’s a good gauge of balancing nutritional needs. After all, a low-carb diet is mostly saturated animal fat, secondly protein and lastly carbs. When hungry (and it’s important not to let yourself be hungry or too full), I first seek saturated fat which usually means bacon - I keep it pre-cooked in the fridge.

Gary Taubes explains estrogen’s roll in women’s weight issues in his most recent book “Why We Get Fat and What To Do About It” which could explain why you are having so much trouble with weight.

Good luck!


Andrea said...

Thankyou Dr Ayers and Mary for taking the time to reply to my post, I really appreciate your help.

Since my post last week I have begun reintroducing some of the foods I eliminated from my diet. This was a little daunting at first but I think I am doing ok. I found a small amount of heavy cream caused me a lot of discomfort to begin with but 5 days later I tried it again and I did much better…baby steps!

Dr Ayers, I have done quite a lot of reading of your very informative blog over the last week and I have a few questions I am hoping you can help me with….

1) I have been using Lactulose as a laxative on and off over the years to address chronic constipation. I am in Australia and here it is sold as a really sweet tasting stool softener. I have read on your blog that Lactulose is used as a prebiodic – is this the same stuff? Also, am I going to cause any long-term damage by using this occasionally, as needed while trying to re-establish gut flora?

2) The anti-inflammatory diet advises avoiding starch. As I have been on a Paleo diet for the last 10 months I have eliminated all grains and legumes and feel much better for it. Is there a place for ‘fermentable fibre’ in the form of sweet potato in the anti-inflammatory diet? Where do root vegetables fit in (carrots, parsnip, beetroot ect)? Are they ok in moderation or best to be avoided given weight loss is necessary for me at this stage? Is starch to be eliminated on the anti-inflammatory diet because of its effect on blood glucose levels or gut flora?

3) I have read Gary Taubes new book, it seems the role of oestrogen is certainly contributing to my weight gain. Once my gut flora is re-established is weight loss and an improvement in oestrogen levels likely to occur? I have been on a low carb/high fat diet for 10 months and had very little change in weight loss or oestrogen levels.

Thanks again for all your help.


Kerry said...

Andrea, there is a wide range of "normal" for thyroid tests. Make sure you educate yourself as to what is optimal so you don't wake up 10 years from now, realizing that you've been hypothyroid all along. This happens way more often than it should.

dave said...

Dr Ayers.
First off I'd like to thank you for your wonderful blog.

I have a question about digestive enzymes. Is it good to take digestive enzymes in supplement form? If so, does it make sense to take a probiotic with digestive enzymes? Finally are certain digestive enzymes better then others and is there a limit to what you can take?

timekeeper said...

I recently started to have Rhematoid arthritis symptoms (mcp pain and swelling- 2 months now)after beginning to take arginine supplement for cold hands/feet. I have been concerned with autoimmune issues as both mother and father expressed autoimmune diseases at fairly young age. My question is could Arginine or Citrulline contribute to Rhematoid arthritis. I don't quite understand the mechanisms but i inferred that proteins bind to citruilline and become antigenic. Im male and 32 and in pretty good health but have been diagnosed with empty sella and bouts of low testosterone. I have also had many other symptoms that could be associated with "autoimmune" conditions. thanks in advance

Bibi said...

I found your site while researching Galt. My 11 year old son has been diagnosed with itp after a severe reaction to a fall with zero platelets that put him into the hospital for a fees days. My first thought was that it was related to us putting him back on gluten and dairy (for testing purposes) after gluten free for a year. None of the doctors we've seen at ucsf (pediatric hematology) think there could be a connection. My acupuncturist does, and so do I. I'm getting the gist of your dietary and supplement recommendations. Do you have any other leads for me?
Thank you!

Dr. Art Ayers said...

IPT precipitated by injury

Platelets have a surface protein that interacts with heparin. The implication is that protein will be strongly exposed to the immune system during injury, if there is already chronic inflammation present. Your son's use of a gluten restricted diet suggests that gut involvement and inflammation were already present. I would expect antibiotics were also used. In any case, your son's gut flora was compromised, and that is what led to a predisposition to the development of autoimmunity to platelets.

The typical medical approach is to further compromise the immune system to stop autoimmune attach on platelets, because there is not a good medical approach to stimulate regulatory T cells. This part of the immune system is dependent on gut bacteria (Clostridium sp.)' which have been killed off in your son. (H. pylori and Helminths may also contribute.)

The long term solution is to replace the missing gut bacteria and repair the gut-based immune system. In the mean time, you might examine low dose Naltrexone, and the established treatment for C. diff, which is a hospital-derived infection facilitated by antibiotic removal of the Clostridium spp normally residing in the gut: fecal transplant.

It should also be obvious to support all treatments with the Anti-inflammatory Diet that I recommend on this blog.

Let me know how it turns out.

Anonymous said...

This is all so interesting. My 16 year old daughter is coming up to the 2 year anniversary of starting with what is now chronic ITP. A recent food intolerance test demonstrated reactions to cows' milk, eggs, cola nut(?), gluten, wheat and slightly to hazelnut, rice and yeast. This seems such a wide range of foods (and very difficult for a teenager to exclude) that I felt the problem must lie with her gut rather than the foods themselves. As a young child she always suffered with excessive flatulence and frequent threadworms. She was tested as a baby for lactose intolerance (negative) because of stomach pain and loose stools - she tested negative recently for coealic but I still feel the answer to all this lies in the gut (call it a gut instinct!)Probiotics don't seem to have helped with the ITP but she is less flatulent now. Any suggestions?

beachbirdie said...

I am grateful to have stumbled into your site.

I was diagnosed with Hashimoto's Thyroiditis almost 10 years ago, and though hormone supplement helped somewhat, I've never been as energetic or healthy as I was before getting this condition.

I was "subclinical hypothyroid" for some time before developing antibodies.

I wish I had known all those years ago about the connection of gluten to Hashimoto's, I might have been able to save my thyroid.

Forewarned is forarmed, and my daughters who have been descending into hypothyroidism are now gluten-free paleo eaters. All because last year my daughter-in-law developed a c.diff infection that she could not get over. We thought we were going to lose her!

Because of research we did on her behalf, we discovered the Specific Carbohydrate Diet, and in researching further to help my mom with her pre-multiple myeloma/pre-B-cell lymphoma condition, I discovered you.

Thank you for your work, and for your patient responses to all who ask questions. I have learned so much here!

Christyn said...

Hi Dr. Ayers,

I am hoping you can shed some light on a few topics for me. Approximately 4 years ago I had an emergency appendectomy and within 6 months developed alopecia areata. Around the same time, I was receiving allergy shots that were causing awful allergic reactions post injection (intense nasal congestion and swelling). I had this once as a child(alopecia), but it spontaneously resolved. Today, I have lost around 80% of my hair on my head and body and it seems to get slightly better and then decline. I have started on your anti-inflammatory diet and am trying my best to get my hands on as many organic vegetables as possible (we live in South Texas, basically on the border so organic is hard to come by). I am taking the following: New Chapter wholemega fish oil 3 per day (1000mg), Zyflamend, 2000IU D3 on its own and then I get another 2000IU D3 from my calcium and multi vitamin. Do you have any suggestions on what I am missing and how the appendectomy could have triggered the autoimmune? I have just done the Enterolab test as well and am awaiting results. Any guidance would be greatly appreciated. Thank you!

roton11 said...

The B-complex vitamins include vitamin B1, vitamin B2, vitamin B3, vitamin B12, vitamin B6 help us
performs a important function in your body.

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Harbor Compounding Pharmacy said...

Hashimoto’s thyroiditis is the most common cause of hypothyroidism due to dysfunction of the autoimmune system leading to chronic inflammation and destruction of the thyroid gland. Interestingly, there are also many other patients whose thyroid blood tests display normal ranges but experience the same Hashimoto’s hypothyroid symptoms.