Histamine Producing Gut Bacteria

November 28, 2017  |  Blog, Histamine Intolerance

Histamine producing gut bacteria is one of the leading causes of histamine intolerance in my clients.

It is well established that histamine can be produced by bacteria in fermented foods, but there is an emerging body of research, showing that the microbes within the human gut can also produce, regulate, or degrade histamine.

We can therefore no longer assume that mast cells are the sole source of histamine in the human body.

Indeed, one of the key sources within my client base is dysbiosis. Once the histamine producing bacteria is addressed the histamine intolerance reverses.

Despite this clinical experience, the research is still emerging. Here is what we know so far.

Histamine Producing Gut Bacteria Study 1

There has long been a hypothesis that there is a link between the microbiota and asthma.

A recent study found the amount of histamine producing bacteria in asthmatics was significantly higher than non-asthmatics.

Interestingly, the type of histamine secreting bacteria was Escherichia coli, Morganii morganii, and Lactobacillus vaginalis commonly associated with fish-related food poisoning. Furthermore, the higher the levels of Morganii morganii the more pronounced the symptoms. 

As a result is hypothesized that increased levels of histamine producing gut bacteria, interact with histamine receptors, to cause the asthma symptoms.

Histamine Producing Gut Bacteria Study 2

It is well established that the immune system is heavily dependent on how the gastrointestinal tract handles histamine.

Histamine can have both pro-inflammatory or anti-inflammatory effects on the immune system depending on which histamine receptor is activated.

There are currently four known histamine receptors. H1R and H4R are thought to be pro-inflammatory and initiate an immune reaction. H2R and H3R are thought to be anti-inflammatory and halt an immune reaction.

However, in one study, it was demonstrated that a moderate histamine producing bacteria, stimulated the inflammatory H1 receptor. Whilst in two other studies, it was demonstrated that higher histamine producing bacteria blocked the anti-inflammatory H2R.

Interestingly, increased histamine levels are increased in patients with irritable bowel syndrome and inflammatory bowel disease, and it was recently shown that inflammatory bowel disease patients have decreased H2 receptor function. Could this be due to very high levels of histamine producing gut bacteria?

It is hypothesized that the amount of histamine produced by the bacteria determines whether the immunoregulatory effects is pathological versus protective. This hypothesis is consistent with research into the progression of mast cell activation.

Histamine Producing Gut Bacteria Study 3

A recent 2017 study, identified that the production or degradation of histamine and other biogenic amines was a common function of microbiota inhabitants. That is it was a key not incidental function.

A small number of strains could produce histamine at levels well above the maximum safety limits, however, the number increased dramatically when incubated with other biogenic amines (particularly cavedeine and putrescine).

This led researchers to conclude that histamine appears to have a complex system of regulation with other biogenic amines. For example, Escherichia coli, a histamine producing bacteria well linked to histamine food poisoning, is only toxic because of the presence of other biogenic amines.

Histamine Producing Bacteria Study 4

Another 2017 study, of 51 saliva samples, collected from patients with respiratory problems, were tested for 255 bacteria. 50 strains of Klebsiella pneumoniae were identified, and 11 of the 50 strains, were histamine producing. Histamine concentrations were at levels sufficient to cause histamine poisoning.

Klebsiella pneumoniae was found to be able to be treated with the antibiotic Triemethoprim. In my experience, Klebsiella pneumoniae is also able to be treated with herbs.

A List of Histamine Producing Gut Bacteria

There needs to be a fair degree of caution in relying upon the lists that follow. This list will emerge and be refined in line with further research.

Firstly, these lists are of species, not strains, and it is the strains that determine the histamine reaction. I have not listed the strains as the gastrointestinal tests do not currently report them.

Secondly, there are no large-scale studies, of the 10,000s of microbial species. Most major studies look at no more than 125 strains.  Given what seems to be a complex interplay between the microbiome these types of studies are needed.

Thirdly, many of the earlier studies, are not of the human gut biome. I have included high histamine strains where there is a high degree of consensus. I have also included all strains tested with human samples. This is imperfect. A more conclusive list will emerge in time.

With those caveats here is a list of what we know to date.

The histamine producing gut bacterial strains in their own right:

  • Morganella morganii (also high tyramine) – this is able to be tested on the GI-Map
  • Hafnia alvei
  • Lactobacillus vaginalis
  • Lactabacillus saerimneri strain 30a
  • Klebsiella pneumoniae – this is able to be tested on the GI-Map.

The tyramine producing bacterial gut bacteria in their own right:

  • Most enterococcus species
  • Escherichia coli (also mast cell activation ) – this is able to be tested on the GI-Map
  • Klebsiella pneumoniae (also mast cell activation) -this is able to be tested on the GI-Map
  • Morganella morganii (also high histamine) – this is able to be tested on the GI-Map

The putrescine and cadaverine producing gut bacteria that increase histamine levels:

  • Most gram-negative bacteria – some of which are able to be tested on the Gi-Map including Klebsiella pneumoniae, Escherichia coli, Proteus mirabilis, Helicobacter pylori, and Salmonella
  • Escherichia fergusonii
  • Enterobacter cloacae
  • Serratia liquiefaciens
  • Serratia marcescens

Other strains strongly linked to histamine food poisoning:

  • Proteus vulgaris
  • Proteus mirabilis – this is able to be tested on the Gi-Map
  • Entrobacger aerogenes
  • Raouletella planticola
  • Raulella ornithinolytica
  • Citrobacter freundii – this is able to be tested on the GI-Map
  • Pseudomnas fluourescens
  • Photobacterium damselae

The 2017 study highlighted for the first time that many microbial strains can become histamine producing in the presence of other biogenic amines. The significance of these findings is not yet fully understood particularly as some of the strains have not been implicated in histamine food poisoning. Nevertheless, the strains which were identified as problematic were:

  • Bifidobacterium adolecentis
  • Bifidobacterium longum
  • Bifidobacterium pseudocatenulatum
  • Enterococcus species (including faceium, faecalis, and avium)
  • Lactabacillus crispatus
  • Lactabacillus fermentum
  • Lactabacillus gasseri
  • Lactobacillus salivarius
  • Streptococcus vestibularis


Research into the role of histamine producing gut bacteria is still in its infancy. Never the less there is mounting evidence that one of the hidden sources of histamine intolerance is the gut microbiome.

In the absence of conclusive research, much progress can still be made even in the most sensitive people.

Whilst it is not proven that food poisoning causes the change in the microbiota, the fact that many of the infections are linked to histamine food poisoning, suggests that good food hygiene should be a key preventative strategy.

Furthermore, many of the key offenders can be tested on DNA based gut tests, such as the Gi-Map. This is an easy first step, to test for pathogenic bacteria, clearly linked to chronic symptoms, and which are easily treated with herbal remedies.

Improved techniques are also making it possible to sequence the microbiome including the richness, evenness, and diversity of the species present.

I am increasingly using the Viome gut test, to start to work with the whole gut biome. I suspect that these types of sequencing will ultimately hold a lot of the answers to histamine producing gut bacteria.

In addition to histamine producing bacteria, there is also a range of species which act to degrade histamine, which can be found in my e-book The Insider’s Guide to the Therapeutic Use of Probiotics for Histamine Intolerance.


Almayah, A. A., and A. H. Issa. “Ibrahim Hk “Virulence factors and antibiotic susceptibility patterns of Klebsiella pneumonia strains Histamine producing bacteria isolated from sputum”.” Sci. J. Med. Res 1.4 (2017): 103-109.

Pugin, Benoit, et al. “A wide diversity of bacteria from the human gut produces and degrades biogenic amines.” Microbial Ecology in Health and Disease 28.1 (2017): 1353881.

Barcik, Weronika, et al. “Immune regulation by histamine and histamine-secreting bacteria.” Current Opinion in Immunology 48 (2017): 108-113.

Colombo, Fabio M., et al. “Histamine food poisonings: A systematic review and meta-analysis.” Critical reviews in food science and nutrition (2017): 1-21.

Pugin, Benoit, et al. “A wide diversity of bacteria from the human gut produces and degrades biogenic amines.” Microbial Ecology in Health and Disease 28.1 (2017): 1353881.

Barcik, Weronika, et al. “Histamine-secreting microbes are increased in the gut of adult asthma patients.” Journal of Allergy and Clinical Immunology 138.5 (2016): 1491-1494.

Feng, Charles, Suzanne Teuber, and M. Eric Gershwin. “Histamine (scombroid) fish poisoning: a comprehensive review.” Clinical reviews in allergy & immunology 50.1 (2016): 64-69.

Ferstl, Ruth, et al. “Histamine receptor 2 is a key influence in immune responses to intestinal histamine-secreting microbes.” Journal of Allergy and Clinical Immunology 134.3 (2014): 744-746.

Björnsdóttir-Butler, Kristin, et al. “Development of molecular-based methods for determination of high histamine producing bacteria in fish.” International journal of food microbiology139.3 (2010): 161-167.

Improved screening procedure for biogenic amine production by lactic acid bacteria, Sara Bover-Cid and Wilhelm Heinrich Holzapfel. Int J Food Microbiol. 1999 Dec 1; 53(1):33-41

Taylor, Steve L., et al. “Histamine production by food?borne bacterial species.” Journal of Food Safety 1.3 (1978): 173-187.

Huang, Yvonne J., et al. “The microbiome in allergic disease: Current understanding and future opportunities—2017 PRACTALL document of the American Academy of Allergy, Asthma & Immunology and the European Academy of Allergy and Clinical Immunology.” Journal of Allergy and Clinical Immunology 139.4 (2017): 1099-1110.

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  • Charlotte Geniez

    Dear Alison, thank you for this (a bit scary) post. You mention that some “can easily treated with herbal remedies”. What do you do at the stage when a client is not able to tolerate herbal remedies? How do you introduce them? I have read your post on foods that heal the gut: is there more that can be done without remedies? Many thanks.

    • You cannot clear infections with food. Some stressors on the body need remedies.

      In my experience, most clients are able to tolerate something. Some very simple well-tolerated mast cell stabilizing herbals can be used to treat infections.

      I also use increasingly using a form of kinesiology testing (ART) to work out what is stressing the body and blocking it and what can unblock it. And also what will support the body to stop hyper-responding.

      Things for this reason also need to be done in order.

      • Charlotte Geniez

        Thank you Alison, for your prompt reply. Yes, there has to be a method to addressing the madness when all comes crashing, and it is hard to follow the steps and go slowly and methodically (and not freak out). I am reading more of your posts and your answers in the comments (which are as instructive) and learning how you work. It is very interesting. I will be starting with a nutritionist who has MCAS soon to help me and I think she knows a thing or two but I don’t exclude working with you in the future; you seem to accommodate overseas clients.

  • Mike Robins

    Candida can also cause histamine release

  • Nia Holtom

    It seems to get more getting ocomplicated. I seem to be making headway but …. boom…..there is an unleashing of symptoms and don’t know why. I have been trying your Megaspore and zeolite but just had another attack. I wonder how long it takes to work. I worked up to 2 capsules of probiotic so now at about 6 wks. Like to come down to visit you from GCoast.

    • Things work in a hierarchy. Simplistically, if something is not quite clearing, then the body might be responding to something higher in the hierarchy. Also, it is possible to increase the dose of zeolite when having an ‘attack”. Its also the full moon and all the buggies are out playing and multiplying.

  • Rosalie Mason

    Hi Alison,

    Thank you for your post.
    I was wondering, Where is the best place to get these gut bacteria tests done? I’ve been dealing with this for around 4 years now and want to try fringe the root of the issue. I’m pretty certain I have Candida.
    I’m based on the Gold Coast.

  • Heather Huerta

    HI Alison,
    I have a question about the megasporebiotics. Is it possible to get a sample of it?

    • Unfortunately, they do not do samples.

      • Heather Huerta

        Thanks for your response!

  • I always treat H. Pylori. The Th1 and Th2 theory is not as black and white in practice. I use ART to work out what the body will tolerate. Also it is often the case that things need to be treated in order or the immune system will kick in.

    • Edwina Astley

      Thank you Alison. I am seeing someone here in Switzerland that is using ART on me also but my body gives me a different reading to what I can actually tolerate. Perhaps this is a practitioner issue? I am guessing you cant use ART remotely?

      • ART is an art, not a science (lol). There are several reasons for this. Firstly the two people doing the testing need to be in tune. If they are not on their remedies then they will not pick things up properly. Also, this still needs to be done within body systems and an order of treatment framework and in conjunction with testing. In some respects, the most important part is the order of treatment which is what makes the difference.

  • Eve

    Thanks for the article, it put some pieces together. You mentioned you always treat H. Pylori – which I think is the root of all for me. Is this possible to do this while nursing a 2 month old? Or does it have to wait until one is down breastfeeding?

    • I am not sure but I suspect it would have to wait. I would not like to take the risk.

      • Eve

        Thanks for your thoughts 🙂 I’ll look you up at that time then!

  • Yogaguerilla

    I find that the megaspore biotic gives me an upset bowel and the runs- is it worth persevering? I have histamine issues that result in hives, rashes, headaches, insomnia and diahorrea.

    • What dose are you taking? You may need to start much lower and build from thre.. See instructions here: http://alisonvickery.com.au/wp-content/uploads/2016/06/MegaSporeBiotic_Dosing_2017_2_.pdf . You can start lower too.

      • Yogaguerilla

        Thanks. It’s whenever I take take even one. I have blasto ( with not particularly bad digestive symptoms compared to others but it probably doesn’t help the histamine issues at all ) so maybe it’s got to do with that

        • yes, blasto is a troublemaker but go down even lower – 1/3 capsule even. It’s likely causing a die-off.

          • Yogaguerilla

            Thanks Alison, you and your knowledge are very appreciated!

  • mulufka

    I need test from Viome. How can I get it in Australia?

    • its not available in Australia yet but you can go on their wait list.

  • Mike Robins

    Hi Alison. What are your thoughts on cromolyn? i personally have tried it (few drops ) and it actually made my histamine flare worse. I read it can have this affect before it starts working but for me the inflammation wasnt worth sticking it out. Have you seen this with patients and what do you recommend usually? Thanks

    • No that is not what I have seen. I don’t have a ‘standard’ recommendation. It would depend on what is happening.

  • Jesse Bruce Uern

    Hi Alison,.. im suffering with gut and histamine issues,.. but i dont know whats causing it,.. is there any good “available” tests in australia that will tell me whats going on? Thanks

    • You can get the Gi-Map in Australia (Via the UK). Unfortunately, the other tests are inferior in my opinion.

  • Pingback: RFR 152: Gut Health, Histamine & Food Intolerances with Alison Vickery - The Wellness Couch()

  • Anna Olsson

    If one suspects histamineintolerance and mastcellactivation disorder due to bacteria
    in the intestines could an nonabsorable nonsystemic antibiotic like xifaxan , rixifamin help take the overgrowth away ?

    Very grateful to your replies!

    • It needs to be the right antibiotic for the type of pathogen BUT it will significantly deplete good bacteria which can take up to 16 months to two years to rebuild. Herbal formulas don’t do that. However, if the medication is all that is tolerated, then that is all that is tolerated. I have never needed to use antibiotics to eradicate pathogens.

      • Anna Olsson

        Dear Allison, thanks a lot for your reply. The herbs is broad-spectrum and not dependent of patoghen right ? Also they are absobed by the whole system….Is it the SIBO herbal treatment :Allicin from Garlic, Oregano,Berberine Oregon Grape, Barberry, Coptis, Phellodendron
          Neem and Cinnamon that you mean as herbal alternative ? Neem makes me worse and oregano oil is very strong for me . . I am not a fan of AB at all but desperate since I have become very ill and developed severe histamine intolerance and my functional Dr . Prescribed xifaxan. But I just read a new medical article that xifaxan also developes resistent bacterias.There is different theories of why I got this but after reading your text I will ask if my functional Dr caN order Gi-Map (he is one of only 2 Dr in the whole Sweden who recognises thi’s issues). I have resistent E.coli after a trip and stomach issues in Asia … and sadly also a story with SSRI that destroyed my system alot. .

        Again very grateful to your reply regarding the herbal alternative treatment.

        Thanks again !
        Kindest regards /Anna

        • herbs are tailored to the pathogen also.

          • Anna Olsson

            What herbs? Could you give some examples against histamine producing bacteria’s ?
            Really grateful to your response cause no one knows these things here in Sweden and I am trying my best as a medical student and being sick …
            Thanks again

          • I canot give generic answers sorry.

          • Anna Olsson

            Ok. What about probiotics – could that also be an alternative way to fight the “bad ” bacteria?

          • No. Megaspore can play a supporting role but not on its own.

  • Your liver/gallbladder was not properly supported. Heavy metals, viruses, parasites love the liver too. Oregano oil is incredibly intense. I dont make generic recommendations I am sorry.

    • Shana Ross

      Alison, could u let me know what would be needed to work w/u?? I have done so much testing in the past, spent so much money, that I am reluctant to “start all over again”. But I’d be happy to pay u for yr input… could there be a consult, possibly??

  • Ken Lassesen

    You may wish to checkout this site which will give suggestions on how to alter some of the above bacteria.


  • Anna Olsson

    Could NAC have any effect in the histamine producing gut bacteria?

    • No nac is about the liver and detoxification. Everything that goes through the gut ends up in the liver and sensitivity can definitely be about the liver. In addition, viruses and heavy metals love the liver. Parasites too!

  • Anna Olsson

    GI-MAP latest research : http://pca.st/5SRV
    Comments?/thoughts ?
    You use it ?

  • Ellie Ali

    Hi Alison, where can u do the cyp450 profile?