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 .

Thursday, April 19, 2012

Genetics of Food Intolerance

Food intolerance is based on missing bacteria in the the gut rather than inadequacy of human enzymes, e.g. lactase, or altered immune system.

I make the extreme statement that food intolerance is not genetic, to emphasize that the vast majority of intolerance can be cured by changing the bacterial composition of the gut's microbiological community, the gut flora, rather than attempting to accommodate a permanent deficiency. The two common "intolerances" that are offered by my readers to invalidate my sweeping statement are lactose and gluten (celiac) intolerance.

Lactose Intolerance is Not Due to Inadequate Lactase
Everybody has the same gene for lactase, but some people have altered upstream control elements and continue to express lactase in their intestinal cells after infancy, whereas others don't. The racial pattern of adult lactase expression is an interesting note on human evolution, but is irrelevant with respect to an individual's ability to tolerate the lactose sugar in dairy products.

Lactose is the major sugar present in milk and the ability of the intestines to utilize lactose directly like glucose is a selective advantage for human evolution. Absent that ability, lactose would just pass through the gut without impact. However, bacteria in the colon also have lactose digesting enzymes. These bacteria produce hydrogen and methane gases, and these products in turn can feed other bacteria. If all of the products are consumed, then the lactose has been treated as a soluble fiber and the result is more gut bacteria and a happy gut. If some of the bacteria are missing, then the lactose acts as a laxative, e.g. lactulose, and the bowels are not so happy.

All that is needed to cure lactose intolerance, as in all food intolerances, is to provide the gut bacteria that are missing to fully metabolize the offending sugars or polysaccharides. Just continuing to eat dairy without also eating or introducing new species of bacteria into your gut, will just provide more symptoms, but eating yogurt still containing live probiotic bacteria (Read the label. Any live bacteria listed will work.) that have the enzymes to ferment lactose, will lead to a rapid cure. (See reference below.) As the fermenting bacteria grow in the gut, they transfer their genes to gut bacteria in the biofilms lining the gut and these new species of bacteria keep the lactose out of trouble.

The point is that having a food intolerance means that the aggregate of all of the genes in all of your gut microorganisms is lacking the genes/enzymes needed to completely digest a food component. In the case of lactose intolerance, the missing genes are present in typical probiotics, bacteria that grow on milk/lactose.

Celiac is not a Typical Food Intolerance
Celiac is a complex interaction between major toxic proteins in wheat (gliadin), detox gut enzyme (tissue transglutaminase, tTg) and antibodies. Gliadin is a wheat protein adapted to attack the intestines of herbivores. Herbivores, such as insects and humans, can in turn protect themselves from gliadin and other polyglutamine proteins with the enzyme transglutaminase. tTg binds to glutamines in gliadin and converts them to glutamic acids. Unfortunately, while the gliadin is bound to the tTg, inflammation can predispose the gut to present these proteins to the immune system for processing to trigger antibody production. This is the start of the autoimmune disease.

The major histocompatibility antigens (MHAs) code for the proteins that display fragments of proteins on cell surfaces for antigen presentation and immune response. There is a lot of MHA variation and evolutionary adaptation. Some MHAs favor antibody production to gliadin and tTg. This just shows that celiac and grain/gluten intolerance is not a typical food intolerance, which will be remedied by simply altering gut bacteria, even though establishing gut bacteria that metabolize gliadin or that reduce autoimmunity, may be part of the cure.

Enhancing Gut Flora is Part of the Cure for all Autoimmune Diseases
There are rare food allergies, even though the majority are misdiagnosed intolerances. The production of antibodies to food antigens is a symptom of the breakdown in communication between the gut immune system and gut flora. Particular species of bacteria are responsible for the development of both the aggressive and suppressive components of the immune system, which occurs in the lining of the gut. Loss of the suppressive cells, Tregs, can result from unhealthy diets and exposure to antibiotics, and results in autoimmune disease, in which the aggressive immune system is out of control and attacks self antigens.

Symptoms of all autoimmune diseases can be improved by reestablishing normal control of the aggressive part of the immune system via healthy gut flora. Clostridium species of bacteria normally induce healthy development of the suppressive immune system and these types of bacteria are common in soil clinging to fresh vegetables prior to extensive washing. Which of the bacteria that are eaten become established in the gut flora is unpredictable, because the bacteria interact with each other, food and cells lining the gut. The only safe and simple procedure currently available is the fecal transplant. Some experimental fecal transplants are facilitated by the use of encapsulated freeze-dried gut flora. There is great resistance to this simple, safe, cheap approach from the medical industry.

Almeida CC, Lorena SL, Pavan CR, Akasaka HM, Mesquita MA. 2012. Beneficial Effects of Long-Term Consumption of a Probiotic Combination of Lactobacillus casei Shirota and Bifidobacterium breve Yakult May Persist After Suspension of Therapy in Lactose-Intolerant Patients. Nutr Clin Pract., 27(2):247-51.


Anek Dodl said...
This comment has been removed by the author.
Nigel Kinbrum said...

"Eating dairy alone will just provide symptoms..."
Did you mean "relief from symptoms..."?

Jorge said...

Hi Dr. Ayes,

Interesting post as always.

So, correct me if I'm wrong, eructing or even flatulence after eating is good, unless there is some pain or laxative symptoms?

Dr. Art Ayers said...

Hi Nigel,

Nice to hear your voice.

I mean what I say, usually. Even thou I am frequently terse to obscurity.

Lactose to the intolerant just produces more upset gut. Nothing comes from nothing and that is true for missing genes and the enzymes for which they code.

Intolerance comes from absence of genes in the gut microgenome and this lack can only be remedied by the addition of bacteria carrying genes for lactose digestion.

Normally the missing genes can be found among the extraordinary diversity of soil bacteria, but in the case of lactose digestion, the lactose digesting ability of probiotics can be exploited. Lactose intolerance is the only intolerance than can be fixed with probiotics.

Thanks for your input.

Steve said...

Dr Ayers,

Any thoughts on the role of epigenetics in lactose tolerance. this article references a study that suggests that bacteria can evolve the ability to digest lactose, simply by being in contact with it. thoughts?

Anonymous said...

Dr Ayers,

This blog or yours is fascinating to the point of addiction for me.

I eat a lot of wild food (dandelions, nettles etc.) It seems then, the benefits are not just from the plants but also from the soil bacteria. My question is how much, if any, of the soil bacteria survive when the plants are stored for winter consumption? When I dry leaves of nettle and then steep them as an infusion does any bacteria survive this process?
Dandelion root in tincture form is an excellent remedy for indegestion from eating too much home baked fresh warm bread - is this the action of just the dandelion/vodka preparation or have any of the bacteria made it through?
What of freezing?

Nigel Kinbrum said...

Gotcha! I do the same thing.

When you mentioned dairy, I thought of yoghurt instead of milk.

Endymion said...

It seems to me that eating sauerkraut, then, would aid in the digestion of cabbage in a way similar to eating yogurt for lactose. The bacteria in sauerkraut is naturally occurring on cabbage, but is often referred to as a probiotic.

Would you recommend eating sauerkraut or drinking the juice for a cabbage intolerance?
Also what about probiotics derived from soil bacteria?

Anonymous said...

Great article as always Art!

I tink the biggest problem for most people reading this is that there's not a simple way to get the needed soil bacteria.

Fecal transplant is not something people do if they aren't very sick. Not saying it isn't great

Probiotics and fermented foods can be helpful, but you've discussed several times that it doesn't have most of the needed bacteria for good digestion.

Vegetables with clinging soil is for most people not available. I don't have my own garden, and even when I buy organic vegetables or fruits there's no clinging soil on them since they've probably been thouroughly washed.

You've also mentioned beeing in contact with healthy people and/or animals, but if you're not in a relationshop you're not exchanging that much bacteria(haha). And I donæt even have a pet.

Do you have any other recommandations?

I've found that one solution for me might be to simply mix some soil with water and drink it? Is this something you might recommend or is there a chance of getting som parasites or whatnot?

Thank you so much for a great blog:-)

Endymion said...

I see that I committed a newbie mistake even though I am not a newbie. (I should have searched your blog before asking questions.) I laughed at myself because I used to teach that very aspect of netiquette.

Anyway, thanks for all you work.

Ian said...

Hello Dr. Ayers:

"Some experimental fecal transplants are facilitated by the use of encapsulated freeze-dried gut flora"

Is it possible to provide more details on that? Can you point to someone who is facilitating it?

Thank you,


Anonymous said...

Good article

Anonymous said...

A question on gluten intolerance. Are we so intolerant to gluten because we have to cook it first before consuming it and we therefore kill any bacteria that would help us digest it?

If this is the case what about predigesting the gluten first by fermenting it such as with sour dough bread. What if we were to drink some of this fermenting liquid? Would this help us provide the necessary bacteria?

Also wondering what your thoughts are on Oats. Oats contain the prolamine avenin that can also be an irritant to the GI tract. Is this something that can be overcome by getting the necessary bacteria?

dextery said...

Regarding parasites, I thought you would like this article regarding a researcher introducing hookworms into his own body to study what happens in the gut with hookworms.

"Part of the motivation for the stunt was to use new technology to show how hookworm infection is acquired.
Until now, no one really knew how hookworm entered the body — they are too small to be seen with the naked eye. But, for the first time ever, we used state-of-the-art imaging to watch the worms enter my body. This gave me and the other scientists useful information about how the worms are able to achieve the incredible feat of being able to get through our tough skin,”

Fordley Boy said...

Hi Dr Art

Fascinating as always.

I have followed your suggestions (e.g. unwashed organic vegetables). However, until I supplemented with Natren's Trinity I had chronic constipation. Trinity has provided me with relief supported by Natural Calm.

I have Ankylosing Spondylitis but I am pretty much in remission if I observe a total restriction of starch. (See the website There is a fecal transplant centre in Sydney near where I live but the cost is very prohibitive. Could soil based probiotics provide a solution?



Anna said...

Just the other day I listened to an NPR program discussing the issues of food safety and "remedies" for convenient pre-washed packaged salad lettuce products.

The current food safety trend now is that any produce plant product that is raised outdoors in soil is considered at high risk of pathogen contamination due to contact with soil, birds and other wildlife, and so on - so the "safe" solution is to trend toward growing as much as possible indoors out of soil (hydroponically, I guess) and wash the heck out of fresh produce in tumbling chlorinated water (all I could think of was a heavily chlorinated swimming pool full of lettuce) before packing it in sealed nitrogen flushed bags (to keep the leaves "fresh", aka prevent them from oxidizing and turning brown during the days of storage, transportation, and on the sales shelf). The big debate was whether to rinse the prewashed lettuce or not after purchase.

My thought while listening to this is while the highly technical chemical washes and tumbling action might be armageddon for pathogenic bacteria (though inspectors know from periodic sampling that a little viable pathogenic bacteria does get through this gauntlet), it's also armageddon for the beneficial soil bacteria, so no wonder this is such a huge problem. So no one should expect to get their beneficial soil bacteria from "fresh" produce if is prewashed and specially packaged for a longer shelf life.

The price of convenience is high indeed.

[M] said...

Are there any good bacteria strains in organic garden soil that can be purchased at lowes/home depot? I do garden (and try not to wash too well), but my garden beds are 100% purchased soil. Hoping that my efforts to get good bacteria from soil aren't in vain...

Roger said...

First off, to the poster talking about drinking a soil solution I would imagine that would be dangerous. There's a lot more in soil than just nice bacteria, some of it very un-nice.

Now onto these bagged salads, I took a past-date bag out of the fridge the other day and it smelled just like an early-stage sauerkraut, so perhaps some of those good bugs are surviving the bleach and gas!

Sarah said...

I find it hard to believe that there is one way of eating that is "right" for every human. You seem to indicate that food tolerance/intolerance is not genetic, but that it is based on gut flora. But could it be that a different set of foods are required to properly adjust the gut flora different individuals and that what may be inflammatory for one could be inflammatory for another?

Do you have any thoughts on the GenoType diet? It tries to individualize a diet to some degree by breaking everyone up into one of 6 "types" rather than saying everyone should eat in one particular way for maximum health benefit. You figure out which group you are in based on certain physical measurements, personality and family history traits and patterns with the assumption that each particular grouping of characteristics is common to a particular genetic type.

I'm wondering if you might say that it's not so much the genetic type, but the "gut flora type" that we have in common with a certain group of people, and that each group, then, seems to do better on certain foods.

I bet there are certain common suggestions that are across the board (essentially the diet you recommend here), like the very limited gluten grain, lower starch, plenty of omega 3, no veg oils except olive, possibly flax, and optimal vitamin D suggestions, but beyond that, I'm not sure if everyone across the board is going to do well on mostly meat and saturated fat.

Sarah said...

Sorry, need to edit (in CAPS):

"But could it be that a different set of foods are required to properly adjust the gut flora OF different individuals and that what may be ANTI-inflammatory for one could be inflammatory for another?"

Anonymous said...

To [M],

So-called organic compost sold in stores is anything BUT organic or even safe. I won't even put it on my garden. It's created as cheaply and quickly as possible from all sorts of *waste* products, anything that rots, even pet wastes. Make your own compost.It takes time but it's worth it. And I agree with Roger, above, to the person considering drinking a soil solution, unless you've had your soil analysed for pathogens you are asking for trouble. Unfortunately good,healthy soil is difficult to come by - there are even cases of manure killing the worms/bacteria/fungi in perfectly good gardens etc because the animals had been medicated.

Anonymous said...

Hi Doc,

Yes, who is now doing the freeze dried poop pill? I've been waiting for that.

Jamie said...

I cured my "lactose intolerance" by drinking raw grass fed milk for a few months. Thank you for this extremely informative article.

nancydmiller said...

I would love to know your opinion about casein intolerance and how to cure that. Would eating well-made yogurt also take care of that?

Thanks for your thoughtful research/insight.

steve said...

Dr Ayers:
Some have an intense allergic reaction to certain foods immediately upon the food touching the lips or going in to the mouth before chewing and transport to the gut has taken place. Some can just touch a food and experience an allergic reaction.
Are you attributing this to gut flora imbalance? Uf so, would love to see the evidence. Thanks

Tom said...

Steve, no one is saying true allergies don't exist. Clearly someone who swells up and struggles to breath when they sniff a peanut has more than an intolerance. What I believe Dr Ayers is referring to is that, in the world of healthcare, 9 out of 10 patients who say they are "allergic" to something actually mean that it makes makes them feel a bit sick or gives them diarrhoea or stomach cramps (or other such minor reactions), which are indeed intolerances rather than true allergies. Let's not be silly about this.

Nina said...

Dr. Ayers,
I have been following an anti-inflammatory diet similar to the one you have outlined to manage my ibd. Since I can tolerate very few plant foods, I primarily rely on saturated fats, protein, and a few supplements to nourish my body.

Saturated fats are the largest component of my diet. As such, I have been increasingly anxious that I will be able to manage my disease while continuing this diet, but the high fats would somehow damage my liver and I would end up with another serious health condition.

Does a high fat diet over-burden the liver, even when done extensively?

[M] said...

Are soil based probiotics safe/effective? I have read about lots of people in the autism community that have success with the body biotics brand.

Anthony said...

hey Dr. Art, I have had issues with lactose intolerance for years now although i have only just diagnosed this by cutting foods from my diet 1 at a time for 2 weeks each. I found that all dairy products cause my symptoms, including yoghurt, so obviously the yoghurt i eat is not not one containing live probiotic bacteria.

My question to you then, is where can i find a probiotic yoghurt? and how can i tell a probiotic yoghurt from a non probiotic yoghurt.

Also could a supplement like inner health plus have a similar effect on my gut flora? :

Anonymous said...

good blog!
Mutaflor (1918 poo)has ecoli and is a probiotic, correct me if I am wrong. So, would this be One that is different from the rest?
I know there are trials out there for Maf yogurts. So I don't think it will take long for this info to get out.
Keep writing! Thanks, Heather

Abhishek said...

Hello Dr Ayers,

Came to your blog searching for inflammation and auto immune diseases.

Have done a lot of research on the subject (as am suffering from few) and strongly believe things can get corrected

Am not working in the medical field but by the amount of reasearch I have done over the past 5+ years make me point to inflammation as the cause of auto immune diseases.

Ur posts seem to link things scientifically and what I experience with my body. I have a history of taking strong courses of antibiotics, giving a lot of importance to the fact that no pathogen gets inside me (to the extent that I even wash my toothbrush before getting it into my mouth, wash my hands numerous times in a day), keeping away from social get togethers, having same food day in day out which doesn't comprises much variety.

Fecal transplant is something that needs a lot attention from the medical community.

Am strongly considering fecal transplant as a solution to my gut cures. But I want to know couple of things from you.

I would like to know is that gut bacteria in the large intestine and the small intestine the same?

Can the gut bacteria in the fecal transplant given in the colon slowly move up and colonize the small intestine also.

Fecal transplant is not available on my side of the world, hence the queries above.


brianpatrick10 said...

Hello Dr. Ayers,

I find all of your posts intriguing, as I have been suffering from gut issues for the past 5 years. I am especially interested in the gut flora aspect with special interest on pathogenic biofilms.

My question is a follow up on some previous fecal transplant questions. I am aware of some people who, out of frustration and desperation, decided to do a fecal transplant on their own. However, they only did the colon portion with an enema of a healthy friend. They never stayed well for long. However, they didnt get worse.

If one irrigates (PEG) properly, I dont think you can screw up a fecal transplant too easy, considering you are putting poop where you normally have poop. I would have done this many times over already because I do not believe it to be to necessary to test the donor pooh for pathogens when I already know their flora is healthier than mine to begin with. I will take their bad stuff over mine any day. My reason for not doing it is I know my major issues are in my small intestine. I have biofilm and malabsorption problems due to antibiotic use and non breast fed- flora issues. I dont have the skill to drop a naso gastric tube down into my duodenum or jejunum, and plant the mirobiota pooh where it needs to most help me. I believe all intestinal diseases, including of the colon, all start in the small intestine. Its obvious science and engineering to figure that out. My question is finally then, How does one go about finding a Doctor who will do this for someone. I am willing to pay cash. I just dont see how only doing a colon transfusion is going to permanently help anyone. but I know this will help. to heck with big pharma!!!!!!


Unknown said...

Hi Dr!!! I am from México and i have a 17 years old son who gas intolerance ti many foods!!! I Made him a test called ALIMTEST OR VERITEST Wich tells you to Wich foods you are intolerante and like a quantity!
My son has intolerance yo too many foods and i would like to her your advice of what to do... For now he us quiting ti everything but it is too much!!! I would like to know what to do!!!! O could send you his resulta si you can take a look... Let me know what to do....

Thanks and let me know how to contact you!!!

From México,


Anonymous said...

Doctor Michael B. Edmond M.D., of Richmond, Virginia (USA) does fecal transplants for patients with antibiotic resistant C. Difficile. If you Google him, you will find links to excellent patient information, a list of pre-treatment tests, and links to good articles.

Anonymous said...

What of leaky gut? Will diversifying the gut flora also cure leaky gut?

Sam Marks said...

Food Intolerance - Read about the distinction between food allergies and food intolerances.

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