People often assume that if they react to a particular food, it must be an allergic reaction. But if symptoms appear after foods like red wine, aged cheese, fermented foods, cured meats, or leftovers, histamine intolerance may be worth considering.

Histamine is a compound released by the body during immune and inflammatory responses. Histamine intolerance occurs when the body struggles to break histamine down efficiently, allowing it to build up and trigger symptoms.

Traditionally, this has been linked to low diamine oxidase (DAO), the enzyme that helps metabolise histamine in the gut. However, emerging research suggests the gut microbiome may also play a role. That’s why many patients are seeking specialist gut microbiome analysis.

What Is Histamine Intolerance?

Histamine is a chemical that’s released as part of the normal inflammatory response. But it’s also found in certain foods. Usually, there’s no issue. Histamine levels temporarily spike until DAO has a chance to break down the compound. If DAO levels are low, however, histamine can accumulate, affecting normal bodily functions.

Common symptoms include:

• Bloating

• Diarrhoea

• Abdominal pain

• Headaches or migraines

• Flushing

• Itching or hives

• Runny nose or congestion

• Palpitations

The condition can be difficult to diagnose. Many symptoms overlap with other conditions like IBS, food allergies, coeliac disease, and IBD.

The DAO Problem

Low levels of diamine oxidase (DAO) are the primary cause of histamine intolerance. If DAO activity is low or overwhelmed, symptoms begin to occur. Even in people with low DAO, mild spikes in histamine are fine. It’s only when they have a severe release or consume histamine-containing foods that problems begin to occur.

DAO activity is regulated by many factors, including genetics, gut inflammation, certain medications, alcohol, and intestinal disease.

Experts aren’t sure about what exactly causes low levels of DAO. Some research has pointed to bacterial overgrowth as a potential explanation.

Can Gut Bacteria Produce Histamine?

Gut bacteria may not reduce DAO directly. Instead, they may increase histamine load, meaning even normal DAO levels can become overwhelmed.

That’s the theory, anyway.

Most people have histamine-producing bacteria in their gut. They convert the amino acid histidine to histamine. That’s fine if your gut has a careful balance of different bacterial species. But if that balance becomes disrupted, certain strains like Enterobacteriaceae, Proteus, Staphylococcus, or Enterococcus can proliferate.

As a result, histamine production suddenly spikes, leading to the characteristic symptoms. People may notice changes after taking antibiotics, eating ultra-processed foods, or periods of increased stress.

What Does the Research Show?

The research is still early, but there are a few clear signs that the gut microbiome may matter in histamine intolerance.

• People with histamine intolerance may have different gut bacteria. One 2022 study found lower levels of bacteria linked with gut health, including Faecalibacterium prausnitzii, and higher levels of several histamine-secreting bacteria.

• Some gut bacteria can produce histamine. A large genomic study identified many potential histamine-secreting bacteria across human gut microbiome datasets, making the microbiome link biologically plausible.

That said, the evidence is not complete. Gut bacteria are highly likely to be part of the picture, but they’re probably not the only possible cause.

Why Fermented Foods and Probiotics Can Be Tricky

Fermented foods are often used to promote gut health. They contain helpful bacteria and can replenish levels after a course of antibiotics or other causes of gut dysbiosis.

There’s just one problem: fermented foods often contain histamine.

Foods like kefir, kombucha, sauerkraut, kimchi, and natural yoghurt can spike histamine levels, worsening symptoms rather than providing relief. That doesn’t mean all probiotics are bad. But people with histamine symptoms should follow a more targeted approach.

What Can You Do If You Suspect Histamine Intolerance

If you suspect you’ve got a histamine intolerance, it’s best to keep a track of your symptoms. You’ll want to know what you ate, when symptoms occurred, and how removing those foods from your diet affected how you felt.

Don’t just focus on histamine intolerance.

Factor in other potential causes like IBS, SIBO, allergies, and IBD. For example, immediate symptoms such as hives, swelling, wheezing, or throat tightness may suggest an allergy, while persistent diarrhoea, blood in stool, weight loss, fever, or night-time symptoms require urgent medical assessment.

Find Out What’s Happening in Your Gut

Whether you’re dealing with a histamine intolerance or another gut-related condition, understanding your gut microbiome could help relieve symptoms.

The Functional Gut Clinic provides specialist gut testing, including microbiome testing and SIBO breath testing, to help investigate possible causes of ongoing digestive symptoms to help you get back on track.

Learn more about microbiome testing and how it can help get to the bottom of your symptoms.

Check out the next article: The Gut–Thyroid Axis: How Your Microbiome Affects Thyroid Health