Got Allergies? Your Microbes Could Be Responsible | Chris Kresser
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Got Allergies? Your Microbes Could Be Responsible

by Chris Kresser

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Every mucosal surface on your body is colonized by a distinct group of microbes, including your gut, lungs, and nasal passages. Far from causing harm, these microbes “teach” your immune system to tolerate dietary proteins and other harmless allergens in the environment. Read on to learn how disruption of your resident microbes might be associated with your allergies, and learn what steps you can take to alleviate your worst symptoms.

You may have noticed that microbes have been a key focus of my blog lately. The microbiota is a rapidly growing field of research, and disruption of the microbiota, or “dysbiosis,” has been implicated in many chronic diseases (1). The ability to manipulate the microbiota using dietary and lifestyle interventions makes it a prime target for a functional approach to disease treatment.

Recently, I have written on the dangers of antibiotic use in children and also discussed the relationship between gut microbes and the thyroid. Here, I tackle the connection of gut, lung, and airway microbes to allergic diseases.

The Hygiene Hypothesis

As the microbiota has gained more attention in the media, you may have heard the term “hygiene hypothesis.” Originally proposed in the late 1980s to explain the decreased prevalence of chronic hay fever in larger families (2), the modern hygiene hypothesis has evolved to suggest that our insistence on cleanliness and lack of exposure to environmental microbes in the developed world deprives our bodies of immune stimulation, disrupting normal immune development and thus increasing the risk for allergic disease.

Several epidemiological studies have provided support for the hygiene hypothesis. People who own indoor pets have been shown to have lower incidence of allergic disease (3). Children who grow up on farms (4,5) or those that consume raw, unpasteurized milk (6) are also less likely to have allergies. On the other hand, early-life environmental influences that are known to disrupt the microbiota increase the risk for allergic disease. Antibiotic use (7), cesarean birth (8), and formula feeding (9) are all associated with increased susceptibility to asthma and allergies later in life.

Recent advancements in sequencing technology have allowed researchers to compare the gut microbiotas of allergic and nonallergic children. Children with allergies tended to have increased abundance of Staphylococcus, Clostridium, and Escherichia species, while numbers of Lactobacillus and Bifidobacteria are significantly reduced (10,11) compared to healthy children.

Taken together, these studies suggest that exposure to a diverse array of microbes early in life effectively “trains” our immune system, teaching it which substances in the environment are harmful (pathogenic microbes) and which are harmless (friendly microbes, dietary proteins, and many environmental allergens). We’ll see next that the mucosal environment in the gut and lungs is crucial to this “education” of the immune system.

Food Allergies: All Roads Lead Back to the Gut

Food allergy has become an epidemic in our modern world. Whereas a food allergy was considered an anomaly just a few decades ago, today one in 13 children in the United States suffers from a life-threatening anaphylactic food allergy (12). And this figure does not include those with celiac disease, non-celiac gluten sensitivity, lactose intolerance, or any other type of food intolerance. As the major site of dietary absorption and the home to 80 percent of your body’s immune cells, it makes sense that the gut is a key player in the pathology of food allergies.

Your gut is lined with millions of epithelial cells that are responsible for maintaining a barrier between your gut contents (the intestinal lumen) and your bloodstream. In a healthy gut, small nutrients are absorbed, but large dietary proteins are unable to cross this barrier and enter the bloodstream. However, when the intestinal barrier becomes compromised (i.e., “leaky gut” syndrome), these large dietary proteins are able to enter the blood, stimulate an immune response, and produce symptoms characteristic of various allergic diseases (13).

So how does this relate to microbes? Studies in mice have shown that disrupting the gut microbiome with antibiotics or a low-fiber diet is capable of causing this increased barrier permeability. On the other hand, certain strains of bacteria in the genus Clostridia are able to protect against intestinal permeability to food allergens (14). Researchers are looking into developing probiotics containing these strains as a potential treatment for food allergies.

Allergies of the Airway: Leaky Lungs?

The incidence of allergic airway diseases has also risen dramatically in recent decades, with allergic asthma and allergic rhinitis now affecting around 20.3 million Americans and 50 million Americans, respectively (15,16). Many more people suffer from less severe allergies of the airway and sinuses. For quite a while, it was thought that the lungs were completely sterile (17). Only recently, with the development of culture-independent techniques, has a distinct community of microbes in the lungs been identified.

Interestingly, the epithelium of the gut is structurally very similar to the lung endothelium, and inflammation tends to happen in both areas in people with allergic airway diseases. While not many studies have assessed lung permeability, it seems plausible that the mechanisms that lead to leaky gut may also cause “leaky lungs.” Like in the gut, microbial communities likely have a major impact on the integrity of the lung tissue.

Unlike the gut, however, reduced diversity seems to be associated with better health. Asthmatics have been shown to have a greater diversity of microbes in their lungs compared to healthy individuals (18). They have increased levels of Proteobacteria and reduced levels of Bacteroides species compared to healthy controls (19). Though characterization of the bacteria, viruses, and archaea that make up the “lung microbiota” is still in its infancy, it represents an important frontier in the field of allergic airway diseases.

The Histamine Connection

Histamine is an extremely important compound in the body. It acts as a neurotransmitter and regulates production of stomach acid, blood vessel permeability, and contraction of skeletal muscle (20). It’s also a major component of the immune response and thus a key mediator in allergic reactions.

While we all need a certain amount of histamine for proper physiological function, some people have a condition called histamine intolerance, in which they produce excess histamine and/or have a deficiency in diamine oxidase, the enzyme that breaks it down.

Many microbes that reside in the human gut are capable of producing histamine.  These microbes produce an enzyme called histidine decarboxylase, which converts the histidine present in various proteins into histamine. The more of these microbes you have, and the more histidine you consume, the higher the amount of histamine that can be produced in your gut. Histamine can be then be absorbed by epithelial cells and traffic to various sites of the body, exacerbating allergic symptoms (21).

Histidine decarboxylase-producing bacteria are also present in the guts of animals like fish. When a fish dies, its gut bacteria start to breakdown the histidine in its tissue proteins and produce histamine. This is why many people with histamine intolerance can only tolerate fish that is immediately processed and frozen.

Some have speculated that individuals with SIBO may have an overgrowth of histamine-producing bacteria, such as Lactobacilli, in their small intestine. Although Lactobacilli are an important genus of beneficial bacteria in the gut, they are also major producers of histamine and can cause problems when overrepresented in the small intestine. Restoring a healthy balance of gut flora is the best long-term solution to resolving a histamine issue.

7 Steps You Can Take to Improve Allergy Symptoms

So does this mean that I can throw away my EpiPen or inhaler? Not exactly. Severe allergic reactions are not something to mess with, and most people with anaphylaxis will always have some degree of sensitivity. However, there are several things you can do to reduce the severity of allergy symptoms and improve your overall quality of life.

  1. Take probiotics or eat fermented foods
    Fermented foods and probiotics can help bring the microbiota and your immune system back into balance. If you are sensitive to histamine, try histamine-degrading strains such as Bifidobacteria infantis and Lactobacillus plantarum.
  2. Eat plenty of fermentable fiber
    Complex fibers like plantains, cassava, or sweet potatoes are fermented by gut bacteria, resulting in the formation of short-chain fatty acids (SCFAs) like butyrate, acetate, and propionate that regulate the immune system. Butyrate has been shown to reduce intestinal permeability to dietary antigens in a mouse model of food allergy and induce regulatory T cells, which suppress immune responses. In mice, propionate has been shown to reduce allergic airway disease (22).
  3. Get tested for sensitivities and avoid inflammatory foods
    Continuing to eat foods you are sensitive to can cause low-grade inflammation and impair gut healing. Look into getting a Cyrex panel to identify sensitivities. For more information, check out my podcast episode on allergy testing. Consider keeping some activated charcoal on hand for those times that you accidentally eat something you are sensitive to. Many people find that it can provide quick and safe relief for food allergies.
  4. Try a low-histamine diet
    A low-histamine diet can often reduce the severity of allergy symptoms. Foods high in histamine include fermented foods, aged cheese, citrus fruits, fish, shellfish, avocados, spinach, cocoa, and leftover meat, to name a few. Consider taking quercetin (a natural antihistamine) or diamine oxidase (the enzyme responsible for breakdown of histamine) in supplement form, and use antihistamine herbs like thyme and holy basil in cooking. Check out my article on histamine intolerance for more information.
  5. Get tested/treated for SIBO or intestinal pathogens
    SIBO and parasites are both common, but often overlooked, causes of allergies. SIBO is also a common cause of histamine intolerance.
  6. Try local raw honey for seasonal allergies
    Raw honey contains both beneficial bacteria and trace amounts of pollen picked up by the bees from local plants. Consuming raw honey produced in your area can help to “educate” your immune system to tolerate these local pollens. A randomized controlled pilot trial published in 2011 showed that allergic patients who consumed birch pollen honey had 60 percent reduced allergy symptoms and twice as many asymptomatic days during birch pollen season (23).
  7. Take further steps to heal your gut

Many people find that just switching to a nutrient-dense diet can significantly improve allergy symptoms.

Now I’d like to hear your thoughts. Did you know that the microbiota was associated with allergies? Have your symptoms improved at all by healing your gut or reducing your histamine consumption? Let us know in the comments section!


Join the conversation

  1. Hi, I actually have just developed seasonal allergies. This after eating a clean diet. I had been 8 months eating basically a whole30 diet and now this spring have allergies, which are miserable, they are to pollen and dust mites. I staryed eating clean to help with anxiety and depression, I was able to get off my ssri in December and got the allergies late February, I live in Illinois. Any help would be greatly appreciated!!!

  2. I have taken probiotics on and off for a number of years – honestly without much noticeable difference until about 2 1/2 years ago when a friend introduced me to the one I’m taking now. Combining that with many of the foods noted in your article along with some other supplements that support balance in the body and gut health I have seen MANY of my seasonal and food allergies go away completely. For example, 3+ years ago – even with taking an over-the-counter daily allergy medicine, I would still wind up in my doctor’s office every Spring and every Fall for a steroid injection and sometimes a course of oral steroids as well. Little did I know at the time how that was working against gut balance.

    After 4 months of being on my current protocol, I no longer needed daily allergy medicine and haven’t had a steroid injection in almost 3 years. In addition, foods that used to send me running for antihistamines I can now eat with no noticeable reaction at all. It’s changed my life. I haven’t had a cold or flu in over 2 years and each year that I continue focusing on supporting my gut, I see that I’m getting more and more healthy. My doctor is amazed every year at the improvement at my annual physical. Keep spreading the good word.

    • Very interesting, thanks for sharing your experience! May I ask which probiotic you used and what dosage you took? Thanks!

    • Immune: Hyperbiotics is a good probiotic with histamine degrading bacteria (including plantarum and infantis), minerals, echinacea, and brewers yeast. To the contrary of what this article states, brewers yeast has been shown to reduce seasonal allergy symptoms. Hope this helps.

  3. There’s also research to support the fact that exposure to pathogenic bacteria increases risk of allergies and asthma, especially if that exposure happens in the womb or during the birth process (vertical transmission). I read a study recently that found that of a cohort of children with severe asthma, something like 60-70% of their sputum samples tested positive for Chlamydia (both C Trachomatis and C Pneumoniae).

    The proposed mechanism is that the body mounts an immune response to the bad bugs (Chlamydia, staph, or whatever) and other harmless allergens that happen to be ingested at the same time are mistakenly identified as invaders. It makes sense to me that allergies are not a “mistake”, but a response to something that is genuinely harmful. (Does the body really make mistakes??)

    The other compelling piece is that pathogenic bacteria pave the way for other pathogenic bacteria, which eventually will crowd out the good flora. So it makes perfect sense that allergic people would have higher levels of staph and other bad guys, and fewer “good” species. It could be that they were exposed to something nasty at some point, maybe something we’re not even able to test for yet, and have never truly recovered from it.

    Chris, let me know if you’re interested in reading some of this research and I’ll dig up the links. It’s truly fascinating—and a bit scary, since allergies and asthma are just the tip of the iceberg. Cancer, heart disease, diabetes, PCOS, you name it.. are all associated with Chlamydia and other pathogens.

  4. An extensive review of clinical trials was presented in the North American Journal of Medical Science in 2013. The review focused on the treatment of allergic rhinitis with a wide range of lactobacillus and bifidobacterium probiotic strains.

    Researchers have concluded that each of the examined strains has the power to offer a specific immunity modulating effect that reduces the severity of reaction to allergens.

  5. I have been told I have allergic fungal sinusitis. I have had 5 surgeries, and the problem is worse! I know it is a gut related allergy. I have had this problem for 7 years, and been on antibiotics to kill bacterial ifections that are constant. Foods seem to eniciate the problem. Can you help me?

    • When I removed carbs and sugar from my diet all my (lifelong) allergies went away. I have objective proof….I had been visiting my allergist every 3 months for a check up (and medicine). Every time I visited I had to blow into a machine that measured lung inflammation. I had been seeing this allergist for over 3 years and every single time I blew into the machine he would tell me that I had bad inflammation in my lungs (allergies). I also had bad sinus allergies as well. Around the same time I was diagnosed with diverticulitis (inflammation of the intestines) and gave up sugar to decrease the inflammation. But carbs turn into sugar so I also had to give up carbs as well.
      Low and behold, all my allergies disappeared!!!! On my next visit to the allergist I blew into the machine and was told that my lungs were free from any inflammation. My sinus allergies had also disappeared and my diverticulitis is GONE!!!
      Sugar, in the human body, causes inflammation. The human body converts carbohydrates into sugar. Inflammation aggravates and exacerbates allergy symptoms. I guess I’m still allergic to the same things but I get no reaction (inflammation). I haven’t been back to the allergist for over a year and will probably never have to go back.
      So before to try any medications or remedies I would try living without sugar and carbs for a month to see what happens. If you do a little research you”l find (like I did) that sugar is a major cause of inflammation in humans. But since we have the ability to convert carbs into sugar you have to also give up carbs.
      I’m finding that a few carbs are acceptable but no more than 30-40 per day.

      You wrote:
      “I have been told I have allergic fungal sinusitis. I have had 5 surgeries, and the problem is worse! I know it is a gut related allergy. I have had this problem for 7 years, and been on antibiotics to kill bacterial infections that are constant. Foods seem to eniciate the problem. Can you help me?”

      I’d be willing to bet that fungus LOVES sugar???? Just like Cancer cells LOVE sugar!!!!!

      Good Luck,

  6. I developed strong, respiratory allergies as a child. I was breastfed, had an indoor cat and lived on a farm, drinking raw milk. So personally, I don’t believe that a sterile environment is necessarily a good hypothesis as to why folks suffer from allergies, both considering my situation or when thinking of the high rates of asthma in inner city youth.

    Interestingly, when I was treated for Lyme disease etal, and took antibiotics for 22 months, I was prescribed rotating types of antibiotics and was also on a probiotic called Floragen. A surprising thing happened, my allergies went away! I was allergy free for nearly two years after I stopped the antibiotics. Now, slowly over months, the allergies have returned. I am now back to taking antihistamines daily and suffer from burning lungs and nasal / sinus symptoms.

    I suspect that the antibiotics killed out the bacteria causing the allergic reactions, and good bacteria from the floragen replaced the bad. Contrary to everything I had heard about the dangers of taking antibiotics long term, I felt better than I had in years.

    I have yet to read anything about a bacterial connection to allergies in medical papers online, but because of my experience, I now strongly suspect that bacteria in my body has a direct connection to my allergic reactions. I look forward to more research in this region of study, to help all of us who suffer from allergies.

    • Just saw your comment after I posted mine.. but I wanted to say, YES! Check out Dr. Attila Toth’s research – his work links pathogenic bacteria to asthma and all kinds of other terrible health outcomes.

    • Wheezy, your story is fascinating! I was breastfed and spent my childhood barefoot and outside, yet I have worse allergies than anyone I know.

      I’ve never heard of the allergy/antibiotic connection. So interesting!

      Thanks for sharing. I hope both of us can find a permanent solution to our misery.

  7. I’m from New Jersey I struggle with blepharitis & allergies been relentless in
    My journey for healing …. I also am trying
    To find a functional Doctor in the New Jersey or Philadelphia area.
    Thanks so much .

  8. I have a 15 year old son that was diagnosed with Oral Allergy Syndrome and cannot (and has not) eaten raw fruits or raw vegetables since he was 4 years old. He can eat cooked fruits and vegetable and can eat peanuts but avoids all other tree nuts. Does anyone have any experience with this and can a probiotic treatment or cleanse help him? If so, I would appreciate any reference in the Philadelphia area for a doctor to consult with.

  9. This is amazing information. Accurate and well organized for the average human to understand. Goes right along with all of Dr. Mark Hymens research findings. Keep it up!

  10. Hi Chris, you write that the epithelium of the gut is structurally similar to the endothelium, and that inflammation tends to happen in both areas in people with “allergic airway diseases.”
    I find this a very interesting point and have some anecdotal evidence for this. Do you have a reference for this correlation between lung and gut inflammation?
    Many thanks for this interesting post!

    • I know I’m butting in here but I have real world evidence of the relationship you’re asking about…but it is more than just lung and gut. I say it’s all internal organs that have mucosa!! I have had allergies since I was 11/12 years old, I’ve also had asthma and lung inflammation most of my life.
      It wasn’t until I developed diverticulosis that I was able to figure it all out. Diver is an inflammation in the gut that causes bleeding, pain and many times worse. I eventually found that many things that I eat and drink aggravate the Diver giving me much pain and discomfort. When stopped eating carbs and sugar all my Diver symptoms went away. But as it turns out…the next time I went to my allergist, I found that my lung inflammation had also gone away. My nasal allergies had also disappeared. All these internal organs have a mucosal layer!! I haven’t been back to my allergist in well over a year because I no longer have allergies, I also no longer have asthma or the inflammation that comes with it.
      As far as proof….each time (bi-annually) I visited my allergist he would make me blow (forcefully) into a machine that measures lung inflammation. After I had been on my no sugar, no carb diet for 6 weeks when I visited my allergist and found that the lung inflammation had gone away. None of the inhalers that I had been given had made my lung inflammation lessen nor had any of them make it go away.
      My only dilemma is this….I don’t know if the gut inflammation, lung inflammation or sinus inflammation disappeared because of the Ketones released naturally by my body OR if the inflammation went away because I stopped eating carbs and sugar. Sugar causes inflammation in humans and the body turns carbs into sugar. Ketones are released by the body to be used as fuel in the absence of carbs and sugar. Ketones are also found in Blueberries and other foods. Ketones have been found to fight inflammation in the body.
      So, there it is!! The machine that my allergist uses proved that my lung inflammation had gone away after 50 years of allergies and asthma. My allergies have disappeared. I no longer take allergy pills (daily), NO inhalers for me and most important…my diverticulitis is nonexistent!!! I’m just sorry that it took me decades to figure it out.

      My appologies for butting in and I hope this helps….

      • I have had a similar experience with asthma and allergies and diet. Whenever we travel, and there isn’t healthy options, I won’t feel well. I don’t have diverticulosis, but my mom does. I do have Celiac disease. I have wondered about lung micro biota for years.

  11. Well where do I start!! My husband has hayfever and Allergic rhinitis. He is chronic — MSG – peanuts — etc. We can’t eat out much as gravey’s, condiments and anything unnatural will send him into full blown rhinitis inflammation – live a severe cold. We have worked out what some of his trigger are but now looking at getting a leaky gut test. He also has Meniere’s Disease and has had this since 2003. We manage this through low salt diet, caffeine free, stress management low alcohol consumption. We are hoping that the leaky gut test will give us some answers – any suggestions??

    • Andrea, I’ve had allergies/hay fever since I was 12 years old (I’m 64 year old now). It gets really bad quite often. I’ve also had asthma all my life. I also have diverticulitis. After a routine blood test my fasting blood sugar was 102 my Doctor told me not to worry about it. I worried about diabetes so I stopped eating sugar, sugar substitutes, and carbs in any form. As everyone knows carbs and sugar raise you’re blood sugar level. Sugar causes inflammation which is the thing that keeps the sinuses/lungs inflamed. Now remember, sugar/carbs is in fruits, vegetables and the great majority of foods sold at the super market.
      After many weeks of research I started a no sugar/ no carb diet. I ate only meats (chicken, beef, sausage, tuna, eggs, etc). I also substituted EVOO for all the fats/oil that the human body needs. I take a long list of vitamins and minerals to compensate for the lack of vegetable and fruits.
      After about 3 weeks all my allergies disappeared, my lung inflammation went away and (most importantly) my diverticulitis completely vanished.
      I had no idea that the things I was eating were causing all my problems. I had no idea it would fix my diverticulitis. My gastroenterologist told me to eat plenty of fiber but most fiber foods contain carbs/sugar. That didn’t help me at all, it actually made it worse!!!. Now I take Citrucel for fiber and I’m allergy free….NO MORE nasal sprays twice a day, No MORE inhaler, No MORE abdominal pain.
      My allergist had given me an allergy test (skin test and blood test). They gave me a long list of things to avoid (peanuts, Oak trees, etc, etc). So yes, I have allergies but without the “inflammation” the allergies can’t get “a hold” on the mucus membranes (lungs/sinuses/intestines)
      I’m not saying that this diet is for everyone but I will NEVER get off this diet as long as I live so I can enjoy life without all the pain, bleeding, sneezing, wheezing!!

      GOOD LUCK!!

    • Andrea have you considered mould toxicity or Staph infection? Staph can affect anywhere in the body but it lives in the Sinus passages. Tea tree oil on a cotton bud may initially cause it to flare but when continued, helps to kill it off. If looking at Moulds, cut coffee and alcohol as both contain high micotoxins and start on Chlorophyll and 1/8 teaspoon Borax 5 days a week.

      • Thank you – I will check those avenues out. My husband has Seasonal Allergies also. I have booked him in for an Intestinal Permeability test. He reacts to stoned fruit, most crumbed things unless I make my own home made. We are currently changing from wheat to Spelt flour and hoping to move to buckwheat flour as it is not a grain as we believe. The reaction my husband has is up to sneezing 500 times a day, watery eyes, inflammation so bad in his nose that he can’t breath through is and can’t smell anything — we go through boxes and boxes of tissues on a daily basis. I have a suspicion that it is his gut health as he was on alot of antibiotics as a child. His inflammation seems to be getting worse every year — we had him go through a desensitization program a few years ago for his seasonal allergies but after 2 years we gave up. Also one other thing I did not mention — he has Meniere’s Disease and has had since 2003. We have managed that through low sodium diet and a mood stabilizer called Pristiq desvenlafaxine. This has helped remarkably and he has not had an attack for nearly 2 years. We run out own business which can be quite stressful at time.

        • I too believe that many of these allergy symptoms go back to the gut and intestinal permeability. My partner suffers from allergies so badly he can go into anaphylactic shock from a perfume or around cats. These allergic reactions are known as Multiple Chemical Sensitivity. He was recently diagnosed with H.Pylori and I believe he has intestinal permeability but he did the Tea Tree Oil up the nose once a day for months and all his sinuses cleared up and his allergies got better. He thought he didn’t need the Oil anymore and stopped it only to have everything return. There is a symbiotic relationship between Staph/Mould/Candida/and the gut bacteria.
          Wow 500 sneezes a day. That must be horrible for him. Have you tried going completely gluten free? What about fermented vegetables and drinks? The Medical Medium, Anthony William says that Menieres Disease is due to inflammation of the Vagus Nerve by Epstein Barr Virus. He recommends drinking a cup of Thyme Tea daily to reduce viral load.

          • Thank you — We are heading towards gluten free. I’m trying to ease into it as feeling a little overwhelmed atm. I eat/eat kombucha, Kefir, saurkraut and blue cheese as it has helped me alot gut wise as I have digestive issues but are far much better now. I am wanting my husband to get onto this but his taste buds need some training. He has his doctors appointment tomorrow for referral re Intestinal Permeability and also a Complete Digestive Stool Analysis. I think if we do this first that will give me the grounds to start at – well I hope.

            I will definately look at the suggestions you have made and keep you posted as to our results.

            thank you for your prompt response to my letters.

  12. Hi Chris,

    Love your work, thank you. I know you have talked about Cyrex labs being the best, because of the methods they use when testing for allergies. Do you know of a good one in Canada that meets the same stringent requirements please?



  13. Very helpful! I’ve also been looking at this other article to see if I can tweak my probiotic consumption to be heavier on the histamine breakdown side of the : equation and wound up buying two to supplement my prescript-assist brand…adding bifido breve to the two strains Chris has listed here. We’ll see how it goes! I’ve gotten a lot of mileage out of the bromelain/quercetin supplements. Way less mucous, but sometimes bothers my tum a bit. Will be good to balance out the bacteria a bit, I think.

    • Update: Quercetin did a number on my progesterone levels (research confirms this effect), and I’ve stopped using it a month ago, though I think it helped with allergies for awhile. I’m experimenting with colostrum (lactoferrin) …there’s a study indicating it’s helpful for mast cell activation disorders. That plus the Fast Tract diet for addressing SIBO. Also have tried histidine…paradoxical treatment for excess histamine…and it sure seems to work, though I’m afraid to use it long term.

  14. Hi Chris, I want to know if eating eggs is bad for those with histamine intolerance or is it only the white of the egg that causes the allergies , and eating only the yolk of the egg alright for them?

    • I have read that raw egg whites are to be avoided by those with histamine intolerance but cooked eggs, white and yolk is fine.

  15. Hi Chris, I put my daughter on Herpanacine for her son after reading some feedback on one of your skin articles recently. Her hayfever has vanished this year! I’m assuming it’s related or possibly she has grown out of it?

  16. I eat a low histamine diet and avoid dairy in the spring and fall when my seasonal allergies are the worst. This seems to help me and I also take a Histaminum Hydrochloricum 30 c homeopathic remedy and Antronex a natural antihistamine from Standard Process. And I also use some massage to unblock my sinuses. I have avoided Gluten and Nightshade foods for years but I don’t think those foods are at all related to my allergies. I am sure gut flora has an impact on all health. Hope this helps someone the way it has helped me.

  17. Very interesting! This would definitely be something worth considering now that my allergies are at their worst. Me and pollen aren’t on good terms right now!

  18. I will be going in for my periodic colonoscopy and was wondering whether this will be bad for the gut flora or an opportunity to start over at ground zero.

    Prior to the exam it’s no food just a laxative and water in huge amounts to flush out the intestines.

    So what is the state of the gut after going through this preparatory procedure? Has all bacteria of all types been transported out?

    If this were so, it would be a chance to build up the system from scratch and I was wondering what would be the best way to do this.

  19. thanks for the good information. i am in the early stages of autoimmune paleo diet to fix leaky gut and get relief an allergies/nasal polyps/asthma-like condition. however, some of what i read in this article conflicts with what i’ve read about the autoimmune system. for example, TH1 and TH2 dominance in white blood cells is an important consideration because, if you’re TH2 dominant, quercetin will produce an allergic reaction.

  20. Super interesting write up. Many of my nutrition clients are blown away when we discuss the allergy and gut connection. This was a great blog to help me understand more behind it.

  21. Vit c, vit e, selenium and magic4.havent had a down day from even the nastiest cold bugs in 7 yrs. Any plain c works, zinc take zinc glycinate u only need one 22 mg,any e works (but I prefer multispectrum with all 8 components – all 4 tocopherols and all 4 tocotrienols).any selenium amino chelate works but i also prefer to use the 3 forms of selenium which will also Ward off cancer cells in their three phases as an added benefitm

  22. Allergy testing a decade ago revealed that I was allergic to every item tested except for ragweed (ironically enough). Acupuncture, Chinese herbs and an air purifier in my bedroom were very helpful. Starting a Paelo diet about 3 years ago really helped with allergy symptoms and I now no longer need the acupuncture, herbs and bedroom air purifier. However, last year hives developed on my face that I have self-diagnosed as histamine sensitivity. Cutting back on histamine food has even further eliminated nagging allergy symptoms (inflamed sinuses and ear canals) along with the hives, plus I feel great. Next is SIBO testing. I grew up on a farm, was breast fed but did have antibiotics as a child for an ear infection (formerly an ongoing issue for me pre-Paleo).

  23. Hello, something in your suggestions is not consistent: in 1. You advice to take probiotics or fermented foods then in 4. You suggest to avoid high histamine foods among which fermented foods???
    To my knowledge, everything has to do with the amount of things you have to take in order to keep a balanced amount of the good bacteria in the guts. The gradual exposition to bad bacteria would help teach the body how to get rid of that particular bacteria not all bad bacteria. Too much probiotics might trigger the same symptoms than bad bacteria. Too much of something is bad enough! If someone has no vitamin defficiency and decides to take supplements he triggers imbalance in his systems and possible intoxication. So I think the same applies to probiotics. Nevertheless, other factors contribute to autoimmune problems: vitamin defficiency, stress and sedentary life.

  24. Thank you for such articles. They always create new insights on health and how we can take more proactive steps in our personal health care. I think it is also very important to learn ‘to listen’ to your body when incorporating new dietary measures. I say this because we are all different and react in different ways after taking regular diet or dietary supplements.

    Chris, there are those people who over-react to insect or other stings. Some even get anaphylaxis from this. Could this also be linked to gut issues or does it follow a completely different pathophysiology? Have you covered this subject in past articles?

  25. I am very surprised that many of the articles I read about that mention leaky gut and its causes, don’t mention the one I find most critical and that’s Helicobacter Pylori. I started having food allergies 20 years ago and they progressed into severe Fibromyalgia, Chronic Fatigue, Hashimotos, and ElectroHypersensitivity to wireless frequencies. My detox pathways were barely working and I was becoming more and more sensitive to environmental toxins. Recently after hearing a talk by Dr Amy Yasko on the hidden symptoms of H.Pylori, I began researching it and had to demand a test from my Doctor who didn’t believe I had it as I didn’t actually have the most common symptoms of heartburn and stomach pain. The test was positive and I had extreme levels of Urease which suggested I’d had this bug almost my whole life (55 years). This bug is present in 75% of the population and is contagious through saliva. Most people don’t know they have it but it still does the same thing in the body. It drills holes in the intestinal lining, causing ulceration and permeability, which then allows food particles into the bloodstream causing an allergic reaction. Its a very resistant bug to most methods of treatment and has a high reocurrence of reinfestation, possibly due to its contagious capacity or low level reproduction of the bacteria that are not completely eradicated. Levels under 200 are considered a negative result but can mean the bacteria is still reproducing. Medically, most Doctors are unaware of the dangers this bacteria can have and the endless onslaught of symptoms it can present. Dr Amy Yasko has very in-depth videos on Vimeo that explain more about it. I encourage everyone to do their own research into this bug as I think it is the leading cause of gut permeability and food allergies. H.Pylori is also classified as a class 1 carcinogen. If left untreated, this bacteria causes Gastric Cancer.

  26. I only started getting food allergies AFTER taking milk kefir. I read on here and many other Paleo sites that we need more probiotics, so I obtained some kefir grains and began drinking one small glass a day. Within 3 weeks I was gassy, bloated, full after 1 bite, and running to the toilet every time I ate. SIBO? I stopped kefir, took peppermint pills, did everything natural to try and stop the diarrhea… nothing worked. For a month it continued. I resorted to antibiotics which killed it. Then I developed food allergies and breathing problems/mucus. My issues started with probiotics, I’m now loathe to add them back in (scared!) I follow an autoimmune paleo diet that is extremely limited… and take HCL/licorice/coconut and colostrum powder (the only dairy I’ll touch since kefir!) Hoping to heal my leaky gut that I think the SIBO caused. Not working with a practitioner (due to my geography) so dealing with this on my own, researching and following articles like this even though that was what got me into this trouble! I wish I’d never touched kefir! The couple of times I’ve tried kombucha I’ve had instant bloating and gassy reactions with constipation. Not good. I’m scared to try anything else. I figure as long as I’m eating clean and having a movement every day I’m good. I’ve no idea what else I can do or try. Have I treated the SIBO? Who knows. I clearly have some gut issues going on mostly, i think, because i was never beastfed. 🙁

    • Hi Lucy,
      It sounds as though you may have a Candida overgrowth that produces all the symptoms of bloating and diarrhoea. I’ve been making and drinking milk Kefir for a few years now and I know there are cannibalistic Candida probiotics contained in the Kefir. This strain of probiotic actually digests Candida Albican that can be the cause of a lot of issues with bloating, diarrhoea, leaky gut etc. You may have experienced a die off while drinking the Kefir. If you don’t feel safe trying it again long term, it might be wise to look at treating Candida with other means such as Pau d’Arco (in tea or supplement form) or Caprylic Acid.

    • I have had a long history of constant congestion. Not to bore you with all the details, the bottom line is that I eliminated fermented foods, probiotics, kombucha and other high histamine foods and feel miraculously better. This was after totally cleaning up my diet and only eating real food. I also am afraid to take probiotics. I have made note of the strains that Chris and others recommend for histamine intolerance. I need to do more research. For now I am grateful to be on the right track. I hope the same for you.

      • I read somewhere that a very low carb diet can stimulate histamine intolerance. I’m not sure why. But I suspect this may have been the case with me. I was eating very low carb because I thought the carbs were aggravating my congestion. I now eat good carbs including spelt bread that has only 3 or 4 ingredients.

    • Hey Lucy, it’s so difficult trying to figure this all out on your own isn’t it. Unfortunately it takes so much longer & you’ll end up making more mistakes. I’m in the same situation so I totally get it.

      I had a major histamine flare up last year & couldn’t figure out why. I looked into the whole histame intolerance thing a bit more & was surprised to read how high fermented foods are on the scale. I cut out kefir & other fermented foods. I started taking Quercetin & anti-histamine probiotic pills instead and my symptoms haven’t flared up as badly since. I don’t think the fermented foods were necessarily the cause for me but it it all adds up. It could just mean that your not in that place where your ready for fermented foods yet.

    • I’d be interested in your take on this comment Chris – since it resonates with me. Never seemed to have any problems with dairy in the past – then started making kefir and gut issues exploded. Seem to have problems with all dairy since then (was doing Gaps for a couple of years). I have cautiously reintroduced goat kefir – just consuming once every few days, and seem to handle that, though I can wake with glugged up eyes the day after sometimes.

  27. Are there other histamine degrading probiotics beyond Bifidobacteria infantis and Lactobacillus plantarum? Does all other lactobacillus increase histamine levels? Any specific brand of probiotics that are successfully recommended for histamine intolerance?

    As a person that deals with histamine intolerance I find that quercetin along with a low histamine lifestyle helps tremendously. During seasonal changes it can still be a challenge. Probiotics are one of the things that helped make the biggest difference initially several years ago with histamine issues. That was long before we were talking about SIBO, leaky gut, histamine, etc.

    Great article.

  28. Another natural anti-histamine herb that has done wonders for my sesonal allergy symptoms is stinging nettle. A strong cup of nettle tea in the morning and I am almost symptom-free for a good part of the day. Occasionally, on hogh pollen days, I’ll have another cup later in the day. After a couple of weeks of drinking the infusions, my allergies seem to be finished early, whereas before my seasonal allergies would last for 2 months. I really can’t recommend it enough.

    This year I also am trying the local honey remedy in hope of not having symptoms at all, even without the nettle tea, but I won’t know if it works until the fall when my allergies usually kick in.

  29. I have to restrict my diet to low histamine food the best alternative is to eat freshly cooked food(warm) any food eaten cold gives me issues. If i eat a freshly opened packet of chips no problem and if i eat it next day i have an issue. If if eat fresh fruit no issues but if l cut and eat later again Issue.

    Wonder if it is the mold or histamine or it is the same. I can’t tolerate any fermented food even if it has good probiotics.

  30. What are you thoughts on Rosacea? Can it be connected to leaky-gut? I started experiencing symptoms in my early 30’s, a few years ago, and when I avoid triggers that I learned cause it, I have no symptoms.

    However, if I consume caffeine, alcohol, citric acid, cocoa, and various spicy foods, the symptoms come back with a vengeance.

    I also have common IBS symptoms, but don’t think that those are related to Rosacea. So I am talking about two different issues, but maybe they both originate from the same area – a leaky gut…

    Any thoughts that you, or others on here, could share about this would be very much welcome.

  31. Chris, Thank you for this post!

    I have tried low histamine diets but can’t tell if it helps. I have always been confused about whether to eat fermented foods or avoid them due to high histamines. Do you have any recommendations on where to find those probiotic strains?

    I eat paleo/aip most of the time but still have rhinitis, sneezing, runny nose, constantly, although other previous health issues are much improved. I have tried Xclear nasal spray and Nasalcrom with little results. The only thing that seems to help is the steroid sprays, but i would prefer not to use them.

    • Your symptoms sound just like mine! I was eating paleo also and symptoms improved. However, I think extremely low carb consumption stimulated the histamine issue. I eliminated fermented foods, spinach, avocado (I was consuming all on a regular basis). I felt relief within one day. Other supposedly high histamine foods don’t bother me. I can eat nuts and seeds but stay away from citrus fruits. I now have reintroduced some bread/pasta, though in small amounts because they still make me gain weight.

  32. Hi Chris,

    Great to finally get some insight into
    Allergies, I’ve suffered with inflammation to my nasal cavity causing problems with a nasal drip causing constant clearing of the throat.

    I really struggle with itching of the legs. Usually it occurs on a night and when it comes on my legs come out in lumps, it’s only little lumps but the itching gets to the point where I’m scratching as its the only relief and I almost bleed. I use anti histamine but find they make me feel really drowsy.

    Any insights into what maybe the cause/cure?


  33. I have had asthma for 40+ years. I started eating a traditional diet 13 years ago and then went on GAPS 3 years ago. I was treated for H.Pylori (not with antibiotics) and have tested negative for SIBO. Yet after all this I still have asthma. It greatly improved after starting GAPS but it wasn’t till I took fermented foods out as well as left over meats that I got a lot better. Clearly there’s a histamine connection but it’s frustrating as I thought all the ferments would be good for gut healing. I have no symptoms of gut dysbiosis but all the research claims allergies and asthma are linked to a leaky gut so now In trying to figure out how to heal my gut without ferments. Even bone broth is very high in histamine. I’m trying Prescript Assist, bitters, gelatin and cannabis oil which has been proven to help heal a leaky gut. High CBD oil has helped greatly to improve my lungs and my friends seasonal allergies disappeared after he took it for several months. Hoping all of this this will help.

    • You can find an answer at the Institute of Technology web site by listening to an interview conducted by Jeffrey Smith, its founder. Jeffrey Smith is the individual who has warned us about the dangers of GMOs. The interview is available in transcript form also. I, too, have digestive issues and histamine intolerance and I have improved as a result of what I learned from this interview. I apologize for being vague. Best of luck!

    • Hi Tracey,

      Dr Hulda Clarke has had great results with healing Asthma by treating the lungs for the Ascaris worm, a tiny worm that lives and reproduces in the lungs. Anti parasitic treatment may help.

  34. This doesn’t surprise me.

    The problem with a few of the tips is that they will NOT work for everybody. A lot of my clients have trouble with raw fermented food and increased fiber. It depends on WHICH gut bacteria are missing, and the individual’s overall microbiome. There are more types of bacteria in our guts than we have so far researched: there is no one size fits all approach to the infinite guts out there!

  35. I am so grateful for this post. I don’t have allergies — possibly because I grew up on a farm and spent my professional life digging in other people’s cow pastures as an archaeologist. But my poor 17 year old doggie, Roscoe has severe histamine and immune problems. So thank you for the probiotic strains that would relate to histamine. Im still searching for fiber and prebiotics that would be appropriate for dogs. Pumpkin, sweet potato?

    • has a variety of sprouts for people as well as their pets. Sprouts are far healthier than the full grown veggies.

    • Gloria, Whenever my Rupert,my Labbie (Labs will eat ANYTHING!)ate something which disagreed w/him, my vet would say “Pumpkin”.
      And it DID quiet and sooth his stomach.So you are on the right track!
      Good luck!Roscoe is doing great to be 17! I envy you!

  36. I really was surprised to see that magnesium deficiency was not covered in this article. Magnesium, according to Dr. Carolyn Dean’s book the Magnesium Miracle, is “an excellent treatment for asthma because it is a bronchodialtor and an antihistamine, naturally reducing histamine levels in the body.” She goes on to say that drugs used to treat asthma are also magnesium wasters! Just thought I’d share for those who suffer with histamine issues.

  37. Dr. Kresser, my problems seem to be mostly in my upper gut. Primarily in the area of my solar plexus. This is however, an area none of my Drs. will discuss, unfortunately. I know all health, good or bad, begins in the gut. Sadly, I am a very compulsive person and too often my own worst enemy when it comes to good health. Knowledge gives me alot hope and helps me to at least sustain. Thank you for sharing your knowledge and just how smart are you anyway? Listening to you is like listening to a real Dr. for the first time. I thank God our paths crossed.

  38. Hi Chris, great insight as usual. Though it seems there’s much we still don’t know about why specific people have worse allergies than others.

    I’m a generally healthy person, but have had seasonal and certain food allergies all my life (tree nuts, some fruit skins). I was breastfed as a baby and grew up with dogs. I eliminated pathogens from my gut with the help of Dr. Nett in your clinic, and have a healthy amount of good gut bacteria. I can’t remember the last time I took antibiotics. I eat lots of probiotic and prebiotic foods, and generally I eat a modified paleo diet with little sugar. I even have a great allergist in Berkeley and we did 4 years of immunotherapy (shots), which did reduce my allergic sensitivity to most allergens.

    Yet seasonal allergies still persist! Is it possible certain people are just predisposed to allergies and are just “born that way?” Curious what you think. Thanks!

    • I think genetics is a factor in everything. I never had allergies (that I knew of) until I was about 24, when I got out of the Navy and started to develop seasonal allergies.

      Low carb/paleo has helped, but even better is intermittent fasting (IF). IF helps a lot, for reasons I don’t understand. For instance, I started developing allergies when I got sick this spring (whole family got stomach bug), and I was eating daily. When I was able to eat more normally, I started IF again, and my allergies went away. IF for me means not eating breakfast except every once in a while, and doing longer fasts (no bfast/lunch or not eating at all one day) twice per week. Both last year and this year, IF helped with seasonal spring allergies.

      This year, I have been adding resistant starch and probiotics (mainly fermented foods but also some pills lately). I did this to try to correct some irritable bowl type symptoms. Those symptoms are almost gone, but I’m trying to ensure they’re gone.

      By the way, I thought that sweet potatoes had no resistant starch in them? I’ve taken to eating potatoes sometimes (cooked then cooled or raw) to increase my resistant starch.

      • Interesting insight, Bob! I do IF but not drastically or all that often (aside from the usual 9pm to 9am IF). I haven’t really thought about if it’s helped my allergies, but next time I’ll make a note to remember.

        My personally theory that there’s still so much we don’t know about what lives in the gut and what could be pathogenic. Perhaps there’s still something dysbiotic in my biome that hasn’t even been identified yet. Who knows?

  39. I don’t know???? I’ve always had bad allergies (hay fever, asthma, etc). It’s been that way all my life. My allergist used to give me a lung inflammation test every time I visited him (semi-annually). He would always say that my lungs were inflamed. Once I stopped eating carbs and sugar all my allergy symptoms went away. When I visited my allergist he verified that my lung inflammation had greatly decreased once I stopped eating carbs and sugar. I had been on an inhaler for years but now I don’t need it because of my change in diet. I eat 86 percent dark chocolate every day. I eat NO fiber foods, only Citrucel. I can eat fish, cocao and avocados with no problem.

    What this articles failed to address is that Ketosis may be the answer to many people’s problem (NOT EVERYONE)!!!! All allergies are exacerbated by inflammation. Sugar and carbs (which the body turns into sugar) cause inflammation in the human body. If you don’t eat any sugar or any carbs (no more than 30 carbs a day) you go into Ketosis. When in Ketosis your body produces Ketones which have been medically proven to reduce inflammation. It’s natures way of naturally fighting allergies. Without carbs and sugar your body naturally produces chemicals that fight the inflammation (which aggravates allergy symptoms). I have been pretty much allergy free for over two years now because I don’t eat enough sugar or carbs to fuel the inflammation. I still sneeze if certain pollen is in the air but I don’t get the inflammation and days of suffering. My diverticulitis has also went away. I don’t know if it’s because of the ketones or the lack of sugar (inflammation).

    I would be willing to bet $100 that the microbes talked about in this statement:

    “Many microbes that reside in the human gut are capable of producing histamine. These microbes produce an enzyme called histidine decarboxylase, which converts the histidine present in various proteins into histamine.”

    Can not survive in the presence of Ketones and/or in an environment lacking in carbs/sugar!!!!!!!!!!! I know for a fact that many things that can live in the human body can not survive without carbs/sugar…for example “cancer”!!!

    I take NO probiotics!!


    • Hi Treblig,

      Do you have any experience with xylitol (sourced from US birch, NOT corn-based) as a sweetener? Maple Syrup? Honey?

    • Thank you for giving the caveat that the no carb/no sugar diet is not for everyone. Many people are very reluctant to admit that there is no one size fits all diet. I used to be one of them. I was super low carb for three years (never no carb for more than a week at a time). I felt great for about a year, but after that my immune function tanked, and certain hormonal systems went crazy (google hyperprolactinemia). My husband is a carrier for mono, we had been married for years and I’d never contracted it. Suddenly I had it, and then six months later I had a relapse. I also had this weird fungus develop on my hand. I am a nutritionist, and so I was baffled as to what that thing was feeding on, because I was *so* careful about what I ate. Over a years time, I tried nearly everything to get rid of it, and it never cleared. During this time, I was delving into some information for a client, and I found that some people’s bodies interpret a low carb diet to be a starvation situation. I added well prepared carbs back into my diet, and a month later the hand fungus spontaneously cleared. Three months later my immune system was entirely back on track, and a few hormonal imbalances that I’d had cleared up. I had also gained a bunch of weight being low carb (crazy on a low carb diet, right?) and lost a bunch of muscle mass. I haven’t lost the weight entirely, but my muscle mass is steadily improving. I feel confident that as my body recovers from what it took to be starvation, that will rectify itself in time. I agree that ketosis may be a useful tool for some, but it was nearly the death of me. I feel so much better now!

      • I totally agree that low/no carb is for NOT for everyone but everyone who removes carbs and sugar from their diet will go into Ketosis!! Although it is not recommended for some diabetics. I happen to have a robust immune system, the last time I got a cold was 20 years ago. My wife will come down with the flu or a cold and can eat off her plate and not get sick. She says that I’m an alien..LOL!! I have no idea what a no/lo card diet will do to someone with a compromised immune system. That’s why I said (NOT EVERYONE). I stay on the lo carb no sugar diet to keep my diverticulitis in check, if I eat one large piece of cake I’ll be in pain the next day, it’s pretty simple really.
        On another note, did you know that Tea Tree Oil kills many fungi?? I had a toe nail fungus for more than 10 years and used all the EXPENSIVE medication the doctor gave me but nothing worked. Then I read about Tea Tree Oil (very cheap) so I decided to try it. It took 8 months of daily application but it killed the fungus completely and it hasn’t returned (been three years now). I wonder if the oil would have helped your hand??


        • Yes, Tea Tree oil is just one of the many, many things that I tried that was not efficacious. Interestingly, my immune system was very robust until I embarked on my low carb diet. A low carb diet is something I will still recommend to some clients, but I am much more careful with using it as a tool than I was before. Evidence is on the rise (anecdotal) that this kind of diet can even dramatically reduce fertility (I work almost exclusively with individuals and couples experiencing fertility problems, who want to try addressing them with diet before trying more invasive methods). I have seen women who stopped menstruating while on a low carbohydrate diet, who saw the complete reversal of their symptoms one they resumed carbs. You just have to put the clues together for your own body.

          Glad you feel so well on this diet! It is the answer for some, that is true. Diverticulitis is not something to be messed with, bless your heart.

      • Your experience sounds a lot like mine. I was practically zero carb (GAPS diet Intro phase for way too long) for 5 months and though my SIBO cleared up, I developed hormonal problems, insomnia and a rash on my inner forearms. (I too had hyperprolactinemia but it pre-dated my GAPS diet by a couple years. I suspect it was due to stress.)

        After reading Paul Jaminet’s Perfect Health Diet blog, I added white rice to my diet. I felt so much better nearly immediately. Constipation cleared up, rash disappeared (I suspect it was fungal, as I developed thrush around the same time as the rash) and sleep improved. Jaminet talks about how fungi can thrive not just on sugar but also ketones. So the typical advice to go very low carb to treat candida is misguided and potentially harmful.

        Just wanted to chime in that less is not always more when it comes to carb intake, especially for women and the stressed out.

  40. I eat most of the foods that you have listed on your low histamine diet, including avocados, which I eat daily. My stomach feels perfectly fine after I eat these foods. Should I still consider (which I feel reluctant to do) consider a low histamine diet?

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