If you’re managing histamine intolerance, choosing the right probiotic can make the difference between symptom relief and a flare-up. While probiotics are widely celebrated for their gut health benefits, not all probiotic strains are suitable for people with histamine intolerance symptoms. Some probiotic bacterial strains actually produce histamine through enzymatic processes, potentially worsening histamine symptoms like headaches, skin irritation, and digestive upset (*).

Histamine is one of several biogenic amines produced or degraded by gut bacteria, and the ability to produce these biogenic amines is strain-dependent.

Understanding which probiotic strains increase histamine levels is crucial if you’re dealing with histamine intolerance, mast cell activation syndrome, or following a low histamine diet. If you’re currently taking a probiotic, pause for a moment and grab your supplement bottle. Take a close look at the label and see if you can identify the specific strains I will be reviewing. Remmber not all probiotics are equal!  Some probiotics increase histamine levels which can actually be making your symptoms worse instead of better.

In today’s article, I’ll walk you through how to spot probiotic strains that increase histamine levels, explain the mechanisms behind histamine production in the gut, and help you understand which probiotics are best avoided.

Histamine Intolerance

Histamine intolerance is a condition that arises when the body is unable to effectively break down histamine, resulting in excess histamine levels and a range of uncomfortable symptoms (*). These histamine intolerance symptoms can include digestive issues like bloating and diarrhea, skin rashes, headaches, nasal congestion, and even respiratory problems. The root cause of histamine intolerance is often an imbalance between histamine production and the body’s ability to metabolize or clear it.

Several factors can trigger or worsen histamine intolerance, such as consuming high histamine foods (like aged cheeses, fermented products, and certain fish), taking medications that interfere with histamine breakdown, or having underlying health conditions that affect gut health. When histamine accumulates, it can overwhelm the body’s natural defenses, leading to symptoms that mimic allergic reactions.

Understanding histamine intolerance is crucial for anyone experiencing these symptoms, as it guides dietary choices and the selection of probiotics for histamine intolerance.

By identifying and managing sources of histamine production, people who struggle with histamine intolerance can take proactive steps to reduce their histamine burden and improve their quality of life.

Read: The Histamine Bucket: Understanding the Root Cause of Histamine Intolerance and MCAS

Probiotic Strains That Increase Histamine Production

Several specific probiotic bacterial strains are known to produce histamine through the action of the enzyme histidine decarboxylase (*). The most commonly identified histamine producing bacteria include:

• Lactobacillus casei
• Lactobacillus bulgaricus
• Lactobacillus delbrueckii
• Streptococcus thermophilus
• Lactobacillus buchneri
• Lactobacillus helveticus
• Lactobacillus hilgardii
• Lactobacillus reuteri

These histamine probiotic strains can also produce other biogenic amines (Serotonin, Dopamine, Norepinephrine and Epinephrine) which may further contribute to intolerance symptoms.

It’s important to understand that histamine production is highly strain-specific rather than species-wide. This means that not all strains within a bacterial species will produce histamine. For example, while some strains of Lactobacillus casei are histamine producers, others within the same species may be histamine neutral or even help with histamine breakdown.

These histamine producing bacteria are commonly found in fermented foods like yogurt, aged cheeses, and sauerkraut, which are considered histamine rich foods due to the activity of these bacteria, as well as in many standard probiotic supplements.

For people with histamine intolerance, consuming products containing these strains—often referred to as high histamine probiotics—can increase the histamine load in the digestive system, potentially triggering uncomfortable symptoms.

How Probiotic Bacteria Produce Histamine

The process of bacterial histamine production involves a specific enzymatic pathway. Bacteria that produce histamine possess the enzyme histidine decarboxylase, which is encoded by the hdc gene cluster.

This enzyme catalyzes the conversion of the amino acid histidine into histamine through a decarboxylation reaction. These processes take place within the complex ecosystem of the human gut microbiota, which plays a crucial role in histamine regulation and overall gut health.

When histamine secreting species are present in the gut or in fermented foods, they utilize available histidine as a substrate. The enzyme histidine decarboxylase removes a carboxyl group from histidine, transforming it into histamine.

This process occurs naturally during bacterial metabolism and can significantly increase histamine levels in both food products and within the human digestive tract.

The key difference between histamine-producing and histamine-degrading bacteria lies in their genetic makeup and enzymatic capabilities. While histamine producing bacteria contain the hdc gene and can synthesize histamine, beneficial gut bacteria like certain strains of Bifidobacterium longum, Bifidobacterium infantis and specific Lactobacillus plantarum, Lactobacillus rhamnosus GG varieties lack this gene cluster and instead may help with histamine metabolism through other pathways.

Read: Check out this aricle on the Best Probiotics To Take When You Have Histamine Intolerance

Bacteria without the HDC (Histidine decarboxylase (HDC) gene simply cannot produce histamine, regardless of how much histidine is available.

Specific Histamine-Producing Probiotic Strains to Avoid

Understanding the specific bacterial strains that increase histamine production is essential for making informed choices about probiotic supplements and fermented foods.

These histamine secreting bacteria can vary significantly even within the same species, making strain-level identification crucial. Overgrowth of histamine-producing strains can contribute to intestinal dysbiosis, further exacerbating histamine intolerance.

While some strains increase histamine, others like probiotic Lactobacillus rhamnosus are valued for supporting gut motility and may be preferable for those with histamine intolerance.

Lactobacillus Species That Increase Histamine

Lactobacillus casei is one of the most well-documented histamine producing bacteria. This probiotic strain is commonly found in fermented dairy products and many commercial probiotic supplements. However, it’s worth noting that Lactobacillus paracasei CASEI 431® has been specifically confirmed not to produce histamine, demonstrating the importance of strain-specific testing.

Lactobacillus bulgaricus is a primary starter culture used in yogurt production and is known for its robust histamine production capabilities. This strain is particularly problematic for people with histamine intolerance because it’s so commonly consumed through dairy products.

Lactobacillus delbrueckii and its subspecies, including L. delbrueckii subsp. bulgaricus, are frequently used in dairy fermentation. These strains can contribute significantly to the histamine content of fermented dairy products and are often found in traditional probiotic formulations.

The probiotic lactobacillus reuteri deserves special attention, as research has shown that certain strains, particularly L. reuteri ATCC 23272, can produce significant amounts of histamine when sufficient histidine is present.

However, some commercial probiotic formulations containing other L. reuteri strains may not show detectable histamine increases, highlighting the critical importance of strain-specific evaluation.

Other Bacterial Strains That Produce Histamine

Streptococcus thermophilus is another major histamine-producing strain commonly used in dairy fermentation alongside L. bulgaricus. This combination of histamine secreting bacteria in yogurt cultures can create particularly high levels of histamine in fermented dairy products.

Enterococcus species have also been identified as potential histamine producers, though their use in commercial probiotics is less common than Lactobacillus species. Some strains within this genus possess the necessary enzymatic machinery for histamine synthesis.

Beyond probiotic bacteria, it’s important to note that pathogenic bacteria such as certain strains of E. coli and Salmonella can also produce histamine.

While these aren’t intentionally consumed as probiotics, they can contribute to histamine production in cases of gut dysbiosis or small intestinal bacterial overgrowth.

Read: Histamine Intolerance Gut Health and SIBO- Another Piece Of The Puzzle

Other lactic acid producing bacteria used in various fermentation processes may also contribute to histamine production, particularly in aged or fermented foods where bacterial activity has been extensive.

Fermented Foods High in Histamine-Producing Bacteria

Many traditional fermented foods contain high concentrations of histamine secreting microbes, making them problematic for people following a low histamine diet or managing histamine intolerance.

In addition to histamine, these foods may also contain significant levels of other biogenic amines, such as tyramine and putrescine, due to bacterial activity during fermentation. Understanding which foods contain these bacteria and biogenic amines can help you make better dietary choices.

Yogurt and kefir are among the most significant sources of histamine-producing bacteria in the typical diet. Commercial yogurt production relies heavily on L. bulgaricus and S. thermophilus, both known histamine producers(*).

These probiotic lactic acid bacteria create the characteristic texture and flavor of yogurt while simultaneously producing histamine and, in some cases, other biogenic amines.

Aged cheeses present another major source of histamine from bacterial fermentation. The longer the aging process, the more time histamine producing bacteria have to convert histidine into histamine and potentially generate other biogenic amines. Hard, aged cheeses like cheddar, gouda, and parmesan typically contain the highest levels.

Sauerkraut and kimchi undergo lacto-fermentation processes that can involve various histamine secreting species. While these foods offer many health benefits, the bacterial cultures used in their production may include strains that increase histamine and other biogenic amines during fermentation.

Wine and beer fermentation can also lead to histamine production, particularly in red wines where bacterial fermentation occurs alongside yeast fermentation. Certain wine bacteria can produce significant amounts of histamine and other biogenic amines, making wine a common trigger for people with histamine intolerance.

Read: Download My Free Ebook On How To Start A Low Histamine Diet

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Why Histamine-Producing Strains Matter for Health

The presence of histamine producing bacteria in the gut can have significant implications for individuals with histamine intolerance, mast cell activation syndrome, or other histamine-related conditions.

Understanding these health impacts is crucial for making informed decisions about probiotic use. For people with histamine intolerance, consuming probiotics containing histamine secreting bacteria can overwhelm the body’s natural histamine breakdown mechanisms.

The primary enzyme responsible for breaking down ingested histamine is diamine oxidase, which is produced in the intestinal lining. When bacterial histamine production exceeds the capacity of this enzyme system, histamine symptoms can develop. Individuals with histamine intolerance tend to have imbalanced gut microflora, which can further impair histamine metabolism and may benefit from targeted probiotic support.

The connection between gut dysbiosis and histamine overproduction creates a complex cycle that can be difficult to break. When the gut microbiome is imbalanced, it may favor the growth of histamine secreting microbes while reducing populations of beneficial gut bacteria that support healthy histamine metabolism.

People with histamine intolerance tend to experience recurring symptoms due to this imbalance, and conditions like irritable bowel syndrome may also be influenced by histamine levels and probiotic interventions.

People with mast cell activation syndrome or other conditions involving human mast cells are particularly sensitive to increases in histamine levels. These individuals may need to be especially careful about avoiding histamine-producing probiotics, as even small increases in histamine can trigger significant immune responses.

Certain probiotic strains can influence histamine release by stabilizing mast cells and downregulating histamine receptors, thereby reducing allergic and inflammatory responses. The ability of some probiotics to stabilize mast cells is an important mechanism for alleviating symptoms.

The relationship or link between leaky gut and histamine intolerance can also be influenced by bacterial histamine production. Research shows that elevated histamine levels may contribute to increased intestinal permeability, potentially worsening the underlying condition(*). Immune regulation is also a key factor, as some probiotics help modulate immune responses and reduce inflammation.

Symptoms that may worsen with histamine-producing probiotics include headaches, skin flushing, digestive upset, nasal congestion, and in severe cases, symptoms resembling severe allergic reactions.

For people with inflammatory bowel disease or ulcerative colitis, the additional histamine burden from bacterial production may contribute to increased intestinal inflammation.

When considering alternatives, it is important to look for histamine degrading probiotic and histamine lowering probiotic options. Specific histamine lowering strains, such as Lactobacillus plantarum, Lactobacillus rhamnosus, and Lactobacillus salivarius, can help manage symptoms by degrading histamine and restoring gut balance (*).

Choosing the right histamine intolerance probiotics that do not exacerbate symptoms is essential for effective management.

Read: Histamine Producing Gut Bacteria-Why Gut Health Matters

Histamine Lowering Probiotics

Not all probiotics are created equal when it comes to histamine intolerance. While some probiotic strains can produce histamine, others have the unique ability to help lower histamine levels in the gut.

These low histamine probiotics are especially valuable for individuals looking to support their immune system and maintain a healthy gut without triggering histamine intolerance symptoms.

Probiotic strains such as Lactobacillus plantarum and Bifidobacterium infantis have been shown to possess histamine lowering properties. These beneficial bacteria can help reduce histamine production by outcompeting histamine producing bacteria and may even support the breakdown of histamine already present in the digestive tract. Additionally, strains like Lactobacillus rhamnosus GG are considered low histamine probiotics and are less likely to contribute to excess histamine.

Incorporating these low histamine probiotics into your routine can help promote a healthy gut microbiome, which is essential for optimal immune system function and overall well-being.

By choosing the right probiotic strains, you can help restore balance in your gut, support histamine breakdown, and alleviate symptoms associated with histamine intolerance.

Read: The Best Probiotic Supplements to Lower Histamine Levels: Histamine-Lowering Probiotics

Diamine Oxidase and Histamine Breakdown

Diamine oxidase (DAO) is a critical enzyme responsible for breaking down histamine in the gut before it can enter the bloodstream and cause symptoms.

For many people with histamine intolerance, reduced DAO activity is a key factor leading to the accumulation of excess histamine and the onset of symptoms.

Certain probiotic strains can play a supportive role in enhancing DAO activity and promoting histamine breakdown. For example, Lactobacillus acidophilus has been studied for its potential to increase DAO levels, helping the body more efficiently process and eliminate histamine. Additionally, the probiotic yeast Saccharomyces boulardii has shown promise in boosting DAO activity, making it a valuable option for those seeking to manage histamine intolerance.

By supporting DAO function with the right probiotic strains, individuals can help reduce the impact of excess histamine and experience relief from symptoms. This approach, combined with dietary management and other lifestyle strategies, can be an effective way to address the root causes of histamine intolerance.

Read: DAO Deficiency- How To Activate The Enzyme That Reduces Histamine Intolerance and MCAS Symptoms

Reading Probiotic Labels to Identify Histamine-Producing Strains

Learning to read probiotic supplement labels effectively is essential for avoiding histamine-producing strains. Most people are unaware that the specific strain designation makes all the difference in whether a probiotic will increase or decrease histamine levels.

When examining probiotic supplements, look for the complete bacterial identification, which should include genus, species, and strain. For example, instead of just seeing “Lactobacillus casei,” a quality label should specify something like “Lactobacillus casei CASEI 431®” or another specific strain designation.

Many commercial probiotic blends contain multiple bacterial strains, some of which may be histamine producers while others are histamine neutral. This creates a complex situation where the net effect on histamine levels may be difficult to predict. When possible, choose single-strain probiotics or carefully vetted multi-strain formulations that specifically exclude histamine-producing varieties.

Selecting a low histamine probiotic supplement is especially important for individuals with histamine intolerance, MCAS, or SIBO, as these supplements are formulated to help reduce histamine levels and minimize adverse reactions.

What to Look For	Red Flags	Safer Options
Specific strain designations	Generic species names only	Bifidobacterium species
Third-party testing results	Undisclosed strain information	Lactobacillus plantarum, Lactobacillus salivarius, Lactobacillus gasseri, Lactobacillus rhamnosus GG
Manufacturer transparency	Proprietary blends	Bifidobacterium longum
Low histamine probiotic labeling

When purchasing fermented foods, ingredient lists can provide valuable information about the bacterial cultures used. Terms like “live active cultures” or “contains L. bulgaricus” should raise red flags for people with histamine intolerance. Opting for a low histamine probiotic can further support safer choices.

Don’t hesitate to contact manufacturers directly for strain-specific information. Reputable companies should be able to provide detailed information about the exact strains used in their products and any testing performed for biogenic amine production.

Order Your Comprehensive Histamine Support Pack Here

Managing Histamine Production from Probiotics

For individuals who need to avoid histamine-producing probiotics, there are several strategies for maintaining gut health while minimizing histamine exposure. The key is finding low histamine probiotics that support digestive health without contributing to histamine burden.

It is important to select histamine intolerance probiotics that are specifically formulated to avoid increasing histamine levels, as some common probiotic strains can actually worsen symptoms by producing histamine.

Choose histamine neutral or histamine-degrading strains such as specific varieties of Bifidobacterium longum, Bifidobacterium infantis, and carefully selected Lactobacillus plantarum strains.

When possible, opt for histamine lowering strains like Lactobacillus plantarum, Lactobacillus rhamnosus, and Lactobacillus salivarius which can help degrade histamine and restore gut microbial balance. These beneficial bacteria can support gut health without increasing histamine levels.

Consider timing when consuming any probiotic supplements. Taking probiotics with meals may help buffer any potential histamine effects, while taking them on an empty stomach might increase absorption and theraputic benefit.

Support your body’s natural diamine oxidase function through proper nutrition and avoiding substances that may inhibit this crucial enzyme. Adequate vitamin B6, vitamin C, and copper are important for maintaining healthy histamine metabolism.

 

Prebiotics and gut-supporting nutrients in addition to implementing histamine-producing probiotics cna be a powerful addition to your protocol. Prebiotic fibers can help nourish beneficial bacteria already present in your gut microbiota while avoiding the introduction of problematic strains.

For some individuals, it may be necessary to avoid histamine-producing probiotics completely, especially during acute phases of histamine intolerance or while following a strict low histamine diet. Working with a Certifed Functional Medicine Practitioner familiar with histamine intolerance can help you develop a personalized approach to gut health that doesn’t exacerbate symptoms.

Consider DAO enzymes. DAO is the enzyme produced in the intestines that help breakdown histamine from the foods we eat.  DAO support overall digestion and may help reduce the histidine substrate available for bacterial histamine production. Some people find that supporting their digestive function helps minimize the impact of any unavoidable histamine exposure.

Monitor your individual response carefully when introducing any new probiotic supplement. Keep a symptom diary to track any changes in histamine symptoms, and discontinue any products that seem to worsen your condition.

The goal is to support a healthy gut microbiome while avoiding the probiotic strains that contribute to histamine overload. With careful selection and attention to strain-specific information, it’s possible to benefit from probiotics without triggering histamine intolerance symptoms.

Remember that managing histamine intolerance often requires a comprehensive approach that includes dietary modifications, lifestyle changes, and sometimes medical intervention. Probiotic selection is just one piece of the puzzle, but it’s an important one that can significantly impact your overall comfort and well-being.

For people with severe histamine intolerance or mast cell disorders, working with a Certified Functional Medicine Pratitioner who understands these conditions is essential. They can help you navigate the complex world of probiotics and develop a treatment plan that supports your gut health while managing histamine-related symptoms effectively.

Read: Learn More About A Functional Medicine approach to Histamine Intolerance and MCAS

Histamine Intolerance and Histamine Producing Probiotics

In summary, histamine intolerance is a multifaceted condition that requires a thoughtful and comprehensive approach to management. Probiotics, especially histamine lowering probiotics, can be a powerful tool in alleviating histamine intolerance symptoms and supporting a healthy immune system.

By understanding the mechanisms of histamine production and breakdown, and by choosing probiotic supplements that foster a healthy gut microbiome, individuals can take meaningful steps toward reducing histamine levels and stabilizing mast cells.

A low histamine diet, combined with targeted probiotic supplements and other supportive therapies, can help manage histamine intolerance, promote a balanced immune response, and maintain a healthy gut.

Read: Download my Free Histamine Ebook

While more research is needed to fully unravel the complex relationship between probiotics, histamine metabolism, and immune function, current evidence suggests that the right probiotic strategy can make a significant difference for those struggling with histamine intolerance symptoms.

Ultimately, working with a knowledgeable healthcare provider and staying informed about the latest research will empower you to make the best choices for your gut health and overall well-being.

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