November 27, 2017 9:00 pm


Histamine producing gut bacteria are one of the leading causes of histamine intolerance I observe in my client base.

In fact, it is well established that bacteria produce histamine in fermented foods.. However, research shows that the microbes within the human gut can also produce, regulate, or degrade histamine.

Therefore, we can no longer assume that mast cells and basophils are the sole sources of histamine in the human body.

Indeed, an imbalanced microbiome is one of the root causes of histamine intolerance, autoimmunity and mast cell activation in my client base.

Therefore, histamine intolerance can be reversed once the histamine producing gut bacteria are addressed and the microbiome is balanced.

Here is an outline of the key research.

histamine intolerance, mast cell activation, histamine producing gut bacteria, alison vickery, health, Australia

Key Research

Here is a summary of some essential research on the role of our microbiome and histamine intolerance.

Study 1: The Link Between Histamine Producing Gut Bacteria and Asthma Severity

Firstly, a hypothesis about a link between microbiota and asthma has long been suggested.

In fact, a recent study found that the amount of histamine producing bacteria in asthmatics was significantly higher than in non-asthmatics.

Specifically, the histamine producing gut bacteria identified were Escherichia coli, Morganii morganii, and Lactobacillus vaginalis, commonly associated with fish-related food poisoning. Furthermore, the higher the presence of Morganii morganii, the more pronounced the symptoms.

Consequently, histamine producing gut bacteria interact with histamine receptors, causing asthma symptoms.

Study 2: Understanding Histamine Producing Gut Bacteria on Immune System Regulation

Next, it is well established that the immune system heavily depends on how the gastrointestinal tract handles histamine.

Depending on which histamine receptor is activated, histamine can have pro-inflammatory and anti-inflammatory effects on the immune system.

Furthermore, there are currently four known histamine receptors. H1R and H4R are thought to be pro-inflammatory and initiate an immune reaction. Conversely, H2R and H3R act as anti-inflammatory agents and halt an immune reaction.

However, one study demonstrated that moderate histamine producing gut bacteria stimulated the inflammatory H1 receptor. Additionally, two other studies demonstrated that higher histamine producing gut bacteria blocked the anti-inflammatory H2 receptor.

Interestingly, patients with irritable bowel syndrome and inflammatory bowel disease have increased histamine levels and inflammatory bowel disease patients had 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 the bacteria produce determines whether the immunoregulatory effects are pathological or protective.

Study 3: The Complex Interaction Between Histamine and Biogenic Amines in Gut Microbiota

Then, a 2017 study identified that the production or degradation of histamine and other biogenic amines was a key function of the microbiome.

Specifically, researchers identified a few strains that produce histamine at levels well above the maximum safety limits. However, the number dramatically increased with other biogenic amines (cadaverine and putrescine).

As a result, researchers concluded that histamine appears to have a complex regulation system 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.

Food Reintroduction, Histamine Intolerance Histamine Producing Gut Bacteria

Study 4: Histamine Producing Bacteria In Respiratory Patients

Next, in another 2017 study, researchers tested 51 saliva samples collected from patients with respiratory problems for 255 bacteria.

Specifically, they identified fifty strains of Klebsiella pneumoniae, 11 of which produced histamine. The histamine concentrations were at levels sufficient to cause histamine poisoning.

Therefore, this study further reinforces the link between histamine producing bacteria and histamine intolerance in respiratory patients.

Study 5: Intestinal Dysbiosis and Barrier Dysfunction in Histamine Intolerance

Then, a 2018 study examined the intestinal bacterial composition in patients with proven histamine intolerance compared to healthy individuals.

Namely, The study included 64 participants, with 8 having diamine oxidase (DAO) deficiency and 25 having histamine intolerance (without DAO). The study found that DAO deficiency was not the sole driving factor.

Moreover, the microbiome analysis revealed that the histamine intolerant group had dysbiosis and intestinal barrier dysfunction.

Therefore, this study further reinforced the link between histamine producing gut bacteria and histamine intolerance.

Study 6: Impact of Gut Microbiome Imbalance on Histamine Intolerance

Next, a 2022 study compared the microbiome composition of histamine intolerant individuals with that of healthy individuals.

Indeed, the histamine intolerance group had dysbiosis, with a significantly lower proportion of beneficial bacteria, including butyrate-producing bacteria, compared to the healthy individuals.

Additionally, they had a significantly higher levels of histamine producing gut bacteria.

As a result, more histamine producing gut bacteria lead to high levels of histamine even in individuals without DAO deficiency.

Study 7: Histamine Producing Gut Bacteria and Irritable Bowel Syndrome

Finally, a 2022 study also identified Klebsiella aerogenes as a hyper-producer of histamine.

Additionally, the study linked histamine producing gut bacteria to irritable bowel syndrome.

Specifically, the study, histamine-producing bacteria activated histamine receptor 4, attracting mast cells to the colon and leading to irritable bowel syndrome.

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The Importance of Overall Composition Over Individual Strains

Significantly, the 2018 study raised the issue of whether the overall composition of the gut microbiome is more relevant than specific strains, suggesting we might be missing the forest for the trees.

That is, our knowledge of the gut microbiome has significantly increased with the introduction of whole microbiome sequencing tests.

As a result, researchers have concluded that the gut microbiome, acts synergistically.

Previously, the focus was on individual strains being good or bad. However, it is now evident that a healthy microbiome can naturally balance itself.

Therefore, the issue is not whether an individual bacteria is present but rather whether there is dysbiosis.

Balancing the Microbiome for Histamine Producing Gut Bacteria

Previously, the focus was on individual strains being all good or all bad for people with histamine intolerance, but this is no longer our understanding.

Now, much can be achieved by giving the microbiome what it needs to balance itself. This includes the four Ps of good gut health: prebiotics, probiotics, polyphenols, and postbiotics, most of which can be obtained from our diet or supplements. 

However, when there are significant histamine imbalances, particularly with hyper-producers of histamine, antimicrobials are typically needed.

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In conclusion, research into the role of histamine producing gut bacteria is still ongoing.

However, there is compelling evidence that the gut microbiome is a hidden source of histamine intolerance.

From a practical perspective, I have consistently reversed histamine intolerance within my client base by manipulating the microbiome.

We can effectively manage and potentially reverse histamine intolerance by focusing on maintaining a balanced microbiome.

To learn more about bacteria that activate mast cells, check out my blog post, Bacteria and Mast Cells: Rethinking Mast Cell Activation.

Follow me on Instagram and Facebook to continue the conversation.

Additional Reading

Sánchez-Pérez, Sònia, et al. “Intestinal Dysbiosis in Patients with Histamine Intolerance.” Nutrients 14.9 (2022): 1774.

Ray, Katrina. “Bacterial histamine and abdominal pain in IBS.” Nature Reviews Gastroenterology & Hepatology (2022): 1-1.

Tsimmerman, Y. S. “Study of intestinal dysbiosis (“dysbacteriosis”): state of problem and new trends.” Herald of Pancreatic Club 45.4 (2019): 44-53.

Barcik, Weronika, et al. “Bacterial secretion of histamine within the gut influences immune responses within the lung.” Allergy74.5 (2019): 899-909.

Folkerts, Jelle, et al. “Effect of dietary fiber and metabolites on mast cell activation and mast cell-associated diseases.” Frontiers in immunology 9 (2018): 1067.

Schink, M., et al. “Microbial patterns in patients with histamine intolerance.” Journal of Physiology and Pharmacology 69.4 (2018).

Almayah, A. A., et al “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.

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.

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.

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.