Can Your Gut Make You Histamine Intolerant? The Microbiome-Histamine Connection

If you have been dealing with histamine intolerance, you have likely been told to focus on avoiding high-histamine foods. While diet plays a role, histamine overload is not just about what you eat—it is about how your body processes and eliminates histamine.

 

Why Gut Health Is the Missing Piece in Histamine Intolerance

Your gut microbiome is one of the most important regulators of histamine metabolism. If your digestion is sluggish, your gut bacteria is out of balance, or your intestinal barrier is compromised, histamine intolerance can become significantly worse.

If you experience histamine-related symptoms such as bloating, nausea, acid reflux, skin rashes, or headaches, your gut may be driving the problem.

Let’s break down how the microbiome impacts histamine levels—and what you can do to fix it.

 

How the Gut Regulates Histamine

Histamine is produced and broken down in multiple areas of the body, but the gut is one of the primary control centers. There are three main ways your gut impacts histamine levels:

 

1. Certain Gut Bacteria Produce Histamine

Some gut bacteria naturally produce histamine as part of their metabolism. If these histamine-producing bacteria overgrow, histamine levels in the body can rise, leading to symptoms such as bloating, headaches, and flushing.

• Histamine-producing bacteria include:
  • Morganella morganii
  • Klebsiella pneumoniae
  • Escherichia coli (certain strains)

If your microbiome is imbalanced—whether due to dysbiosis, SIBO (small intestinal bacterial overgrowth), or low gut diversity—you may have more histamine-producing bacteria than histamine-degrading ones. Stool testing through companies like DSL GI Map can help identify these imbalances.

 

2. The Gut Produces DAO (The Histamine-Breaking Enzyme)

DAO (diamine oxidase) is the main enzyme responsible for breaking down histamine from food. It is produced in the gut lining, which means that if gut health is compromised, DAO production may decline.

Factors that can reduce DAO production include:

• Leaky gut (intestinal permeability)
• Chronic inflammation or gut infections
• Food sensitivities that trigger gut irritation
• Certain medications (such as NSAIDs and proton pump inhibitors)

If DAO levels are too low, even a small amount of histamine from food can trigger symptoms.

 

3. The Gut Helps Eliminate Excess Histamine and Estrogen

Your gut microbiome also plays a crucial role in estrogen metabolism. The estrobolome (a subset of gut bacteria) helps break down and eliminate estrogen. If this process is disrupted, estrogen can recirculate in the body, further increasing histamine levels.

This means that if you have histamine intolerance and your digestion is slow or your microbiome is out of balance, you may also be holding onto excess estrogen—which can further fuel the histamine cycle.

 

Why Some Probiotics Can Make Histamine Intolerance Worse

Probiotics are often recommended for gut health, but not all probiotics are beneficial for histamine intolerance. Some strains actually produce histamine, which can worsen symptoms.

• Probiotics that may increase histamine:
  • Lactobacillus casei
  • Lactobacillus bulgaricus
  • Lactobacillus reuteri

If you have histamine intolerance, taking the wrong probiotic could actually make symptoms worse, especially if your microbiome is already imbalanced.

 

The Right Gut-Health Strategies for Histamine Intolerance

Instead of focusing solely on food eliminations, addressing gut health can help regulate histamine metabolism and improve tolerance over time.

 

1. Support the Gut Lining and DAO Production

• Increase nutrients that support DAO enzyme production, such as vitamin B6, magnesium, and zinc.
• Reduce gut inflammation by avoiding processed foods, alcohol, and excessive caffeine.
• Incorporate gut-healing foods such as bone broth, aloe vera, and glutamine.

 

2. Focus on Probiotics That Degrade Histamine

Instead of taking general probiotics, focus on strains that help break down histamine rather than produce it.

• Histamine-degrading probiotics include:
  • Bifidobacterium infantis
  • Bifidobacterium longum
  • Lactobacillus plantarum

These strains can help restore microbial balance and improve histamine tolerance over time.

 

3. Improve Gut Motility and Digestion

• Increase fiber intake from vegetables and flaxseeds to help clear histamine and estrogen.
• Support digestive enzymes and bile flow with bitters, ginger, and dandelion root.
• Hydrate properly to ensure smooth digestion and detoxification.

 

The Bottom Line

If you are struggling with histamine intolerance, focusing only on food eliminations will not solve the problem. Your gut plays a critical role in how your body processes and eliminates histamine, and if your microbiome is imbalanced, histamine intolerance will persist.

By improving gut health, increasing DAO activity, and choosing the right probiotics, you can build long-term resilience against histamine-related symptoms.

For a full step-by-step plan on managing histamine intolerance through gut health, download the Estrogen + Histamine Guide here.

 

References:

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