Histamine intolerance and gastrointenstinal issues are connected in so many ways. The root cause of histamine intolerance can often be traced back to an issue or imbalance in the gut, including dysbiosis, SIBO, leaky gut, food sensitivity, or intolerance.
Beyond this, histamine intolerance can also contribute to and worsen gut problems, creating a vicious cycle. Achieving a healthy gut is arguably the most important step to take while working towards the root cause of histamine intolerance or mast cell issues. Here we will break down some of the correlations between histamine intolerance and gut health.
How does Histamine Intolerance Impact Gastrointestinal Symptoms?
Histamine intolerance can be difficult to address because it comes in different forms and every individual shows a different set of symptoms. Most people with histamine intolerance often experience gastrointestinal symptoms such as constipation, bloating, stomach pain, diarrhea, or abdominal cramp.
In some known cases, these symptoms are more severe and may lead to a gastrointestinal diagnosis (like IBS) before uncovering histamine intolerance. While in other cases, GI symptoms are present but do not interfere with everyday life as much as other symptoms.
You might not even realize that your mild or moderate gastrointestinal symptoms are related to your histamine intolerance. Issues in the gut (like histamine intolerance) can also be behind symptoms in many other areas of the body.
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How do Gut Imbalances affect DAO Levels?
Histamine is broken down in the gut by the enzyme DAO. The most common cause of histamine intolerance is insufficient production of the DAO enzyme which means the body is not able to break down the intake of dietary histamine. This could lead to a buildup of histamine in the body. When I’m trying to get to the root cause of this problem, I start by asking “why would your DAO levels be so low?” The major causes of low DAO involve gut imbalances or gastrointestinal disease. Imbalances such as SIBO (Small Intestinal Bacterial Overgrowth) and dysbiosis are closely associated with inflammation in the gut wall. This can lead to damage of the cells that produce DAO.
Leaky gut, IBS, food intolerances and sensitivities (including to gluten), Crohn’s disease, and colitis also affect the impaired DAO production and histamine intolerance. Medications such as antibiotics and NSAIDs, alcohol, and other substances that cause inflammation in the guts can block DAO production.
Genetics are also known to play a role in DAO levels. There is an interaction between genes and your environment. Those with a genetic predisposition towards impaired DAO production may be more susceptible to dysfunction as a result of the same environmental risk factors (i.e., inflammation in the gut). Did you know that you can experience worsening gastrointestinal symptoms after eating high histamine or histamine-releasing foods?
Relationship between SIBO, Dysbiosis, and Histamine Intolerance
SIBO and dysbiosis which create inflammation in the gut can reduce DAO activity and boost the activation of mast cells. Even though so many factors can lead to inflammation in the gut and other parts of the body, SIBO and dysbiosis are a result of an overgrowth of bacteria.
In some cases, this could be the root cause of histamine intolerance. Gut bacteria can produce histamine. They can also break it down or leave it as it is. Some bacteria strains are more likely to produce histamine. And if there is an overgrowth of these bacteria strains or any form of imbalance in the production and degrading of histamine, symptoms of histamine intolerance will show up.
The connection between IBS and Histamine Intolerance

There is a strong relationship between IBS and histamine intolerance. Most people with histamine intolerance are first diagnosed with IBS. And it might not be discovered in the early stage that histamine is part of the problem. Research from experts has shown that gastrointestinal symptoms could worsen when individuals eat high histamine or histamine-releasing foods. Recent research also shows that SIBO is often the root cause of IBS, as well as commonly being behind histamine intolerance.
Managing Histamine Intolerance in the Gut
Checking and improving your gut health is a necessary step if you have histamine intolerance or mast cell issues. I will also recommend a low histamine diet. Avoiding high histamine foods is necessary to reduce overall histamine load. I’d advise you to focus solely on fresh, whole, and nutrient-dense foods.
You should also avoid alcohol as much as possible. While boosting gut health, it’s also important to remember that some of the foods we typically think of as gut health superstars (like fermented foods) are problematic when it comes to histamine intolerance.
Final Thoughts on Gastrointestinal Issues and Histamine Intolerance
There are so many strong connections between histamine intolerance and the gut. Addressing the root cause of histamine intolerance can often be traced back to gut issues such as SIBO, IBS, leaky gut, dysbiosis, or food sensitivity.
It is necessary to check gut health and work towards a healthy gut in order to win your health back. When it comes to histamine intolerance, gastrointestinal symptoms may be mild, severe, or not present. Dietary histamine is broken down in the gut by DAO. And a deficiency in this enzyme is often the cause of histamine intolerance. Inflammation in the gut can damage the cells that produce DAO. SIBO and dysbiosis are common causes of gut inflammation and low DAO.
An imbalance or inflammation in the gut may lead to both reduced DAO production and increased mast cell activation & histamine release. Gut bacteria can also produce histamine; an overgrowth of histamine-producing strains may occur with SIBO or dysbiosis. Avoiding high histamine foods, alcohol, and fermented foods is helpful in managing histamine intolerance.