Probiotics for Histamine Intolerance: What You Need to Know

probiotics for histamine intolerance

If you've been trying to find the best probiotics for histamine intolerance - your search is over.

Probiotics are one of the most essential supplements for healing histamine intolerance. But many people don't know that most probiotics actually produce histamine.

Wait, what? That's right. Even those healthy strains of bacteria you've been taking daily may be making your symptoms worse.

To get a healthy gut and promote DAO enzyme production (the enzyme that helps break down histamine) it’s so important to ensure you are taking low histamine probiotics. And, today, I'll explain exactly which strains (and even brands) are the best probiotics for histamine intolerance.

Let's get started.

The Importance of Probiotics for Histamine Intolerance

Our body houses over 100 trillion bacteria which are, in some way, involved in every single bodily function, ranging from immune health to daily mood and energy.

Disorders such as histamine intolerance, are no exception when considering the role of gut bacteria in your symptoms.

In fact, in my previous post about what causes histamine intolerance, I explain how gut bacteria can not only be a contributor to your histamine symptoms but can actually be the main underlying cause of histamine intolerance itself. With the multitude of systems impacted by histamine intolerance and the multi-symptomatic nature of this disorder, there will always be some level of bacterial involvement.

This is exactly why finding the best probiotic for histamine intolerance is always going to be important.

Buying the wrong strain is the most common mistake histamine intolerance sufferers make when selecting probiotics - one that actually makes their symptoms worse.

​How Bacteria Influence Histamine Intolerance

Bacteria are involved both in the production and degradation of histamine.

When we consume foods containing the semi-essential amino acid, histidine, certain types of bacteria within the gut can convert this amino acid into histamine. This conversion increases internal histamine levels - even if the food itself was not considered a histamine-rich food.

In most cases, the conversion of histidine to histamine is non-problematic and even beneficial.

But for those who experience histamine intolerance, there can be a buildup of excess histamine in their body; and an imbalance of the gut bacteria may be responsible for degrading histamine. If the population of these histamine-degrading bacteria falls too low, this also contributes to a chronic increase of internal histamine levels.

As you can see, there are several bacterial paths promoting histamine intolerance.

But why the heck is your gut bacteria so out of whack to begin with?

There are several reasons these bacterial populations can go haywire, including illness, pathogenic invasion, dietary factors, antibiotic use, chronic stress and other environmental and lifestyle influences.

In fact, bacterial production of histamine is the very same reason why histamine intolerant individuals should avoid fermented foods (bone broth, kefir, wine, cheese). While bacteria are busy digesting and fermenting to produce your wines and cheeses, they also turn these into high histamine foods!

In nearly all cases, eating a diet based on low histamine foods and finding the right probiotic for histamine intolerance are essential.

Restoring Gut Bacterial Balance

In an attempt to restore gut bacterial balance, many people naturally turn to probiotics for histamine intolerance. Numerous studies have shown that probiotics may improve gut bacterial populations and improve overall health. So this is generally a great solution.

But histamine intolerance poses an additional conundrum.

Grabbing any random bottle of probiotics off the shelf is one of the biggest mistakes you can make if you’re histamine intolerant. Even if you've heard it's the best probiotic on the market.

Almost all probiotics will contain strains of bacteria that produce histamine and, therefore, they possess the ability to throw off your bacterial balance and worsen symptoms.

I have many, many clients who have experienced this and, as you can imagine, it’s not fun. It’s a waste of time, money, and a lot of unnecessary suffering.

My goal is to reduce that suffering and make this journey easier for you.

​The Best Low Histamine Probiotics

I’ve done a lot of research to find you the absolute best probiotics for histamine intolerance. The list below details exactly which have shown to be beneficial probiotics for histamine intolerance, which ones should be avoided, and which are still in question (or may only benefit certain symptoms).

​Low Histamine Probiotics and Strains to Look For

When it comes to reducing symptoms, these are the probiotics I recommend to my clients with histamine intolerance.

Probiotic Strains to Avoid 

These species may increase your body’s natural histamine production or contain histamine themselves.

  • Lactobacillus casei
  • Lactobacillus Bulgaricus
  • Streptococcus thermophilus
  • Lactobacillus delbrueckii
  • Lactobacillus helveticus

​Additional Strains of Importance

I’ve found these strains that are either still being evaluated or have been effective in treating specific symptoms. 

  • Lactobacillus reuteri – Although many low histamine foods lists put this bacterial strain in a histamine producing category, Lactobacillus reuteri is an interesting case. In addition to raising histamine, it also is helpful in increasing levels of anti-inflammatory cyclic adenosine monophosphate (cAMP).
  • Saccharomyces-Boulardii – This is a low histamine probiotic that also helps regulate digestive issues, like diarrhea.
  • Lactobacillus lactis – This strain is still being debated by scientists and medical professionals.
  • Lactococcus Lactis – This is a strain used to make some high-histamine foods but some studies found it to be histamine-neutral.
  • Lactobacillus acidophilus – This strain has been heavily studied by medical professionals and lower doses (below 1 billion CFU) appear to be histamine neutral while reducing inflammation and improving gut health.

My Favorite Probiotics for Histamine Intolerance

Although it's easy to put together a list of low histamine bacteria, finding an actual brand that carries a probiotic for histamine intolerance in stores can be very difficult. High histamine species from the 'avoid' or 'questionable' lists, such as Lactobacillus acidophilus (in doses above 1B CFU) or Streptococcus thermophilus, tend to be some of the most commonly carried strains by stores and pharmacies.

In my extensive work of using probiotics for histamine intolerance sufferers, I’ve found this to be the best low histamine probiotic, as it contains only strains that have shown to be histamine-friendly. Most of my clients are able to incorporate this probiotic with no issues.

This probiotic, paired with a diet full of low histamine foods, promotes a healthy gut bacteria balance AND helps reduce histamine intolerance symptoms.

Now that you know exactly where to start, you can begin improving your gut bacterial balance with confidence!

Because life's too short to let symptoms control you,

Anita Tee, Nutritional Scientist

To improve gut health with a scientist on your side, get daily tips using:

Anita Tee, Msc

Anita Tee is a nutritional scientist specializing in histamine intolerance and gut health. Anita carries a Master of Science in Personalized Nutrition and a Bachelor of Science in Human Biology, specializing in Genetic & Molecular Biology.

  • Kumar says:

    It took me 4 years to self diagnosis this condition as I was getting consused with food IGG/intolerence. All antibodies tests are negative.
    does Kyo-Dophilus 9 supplemention cure disbiosis and histamine intolerance in your experience with clients.

    San Francisco

    • Anita Tee says:

      Hi Kumar,

      Each client would be different regarding a “cure” – as it would depend what the root cause is. Most people need to take multiple angles however, as far as the probiotic angle goes, Kyo-Dophilus 9 has been great for my histamine intolerance clients, as it balances bacteria without adding any strains that make histamine intolerance worse. I’ve had great success with my clients so far by using Kyo-Dophilus 9 as an addition to their regime.

  • Steph says:


    I’ve found Nature’s Way Primadophilus Original contains only rhamnosus & acidophilus. Seems to be good for histamine situations.
    Also a good probiotic is called Megasporebiotic by Microbiome Labs.

  • Jacqueline says:

    I’ve been so pleased to find the d-lactate free probiotic from Custom Probiotics. I’ve tried SO many probiotics and none of them worked for me. I finally figured out it was a histamine issue. The one mentioned is histamine friendly. It looks very pricey, but if you do the math it’s actually a lot cheaper than all others because it’s a powder. Plus, it has NO additives or fillers!

  • Kaycee says:

    Not my intention to seem rude but to be clear; do you have any financial interest in any of the product you recommend?
    Kind regards

    • Hi Kaycee,

      I am in no way sponsored by companies for any of the supplements I discuss, nor have been nurtured or paid to use or recommend the products I choose. I have individually hand-selected each product I recommend through a combination of my own research and practice with clients (and, myself!).

      Don’t worry at all about asking – I understand that we all want what’s best for our health, without having the funding of a larger company secretly influencing us to buy things.

      But, I can assure you all of the supplements and brands were chosen because I found them to be the most effective in research and the most helpful in practice 😉

  • Leslie Solomon says:

    I had my entire colon removed after diagnosis with severe ulcerative colitis 20+ years ago. It was perforated during a sigmoidoscopy. Since, I’ve had chronic pouchitis and now have histamine intolerance among other problems. VSL#3 made me bleed like a stuck pig and I haven’t done well on the few others I’ve tried, so I’ve been avoiding all probiotics for fear of making imbalances worse. No one seems to know about this, especially gastroenterologists. Since I now only have a small bowel, might you have any suggestions for which strains would be best to try? Thank you.

  • Cheire says:

    Hello, why do I continue to read on many websites, articles, even from holistic practitioners, etc. for a probiotic to be effective it needs to be at least 50 billion CFU’s? I noticed the one you are recommending contains only 3 billion.

    • Anita Tee says:

      Hi Cheire,

      CFUs are actually irrelevant compared to viability – you can have a multi-billion probiotic where the majority of bacteria will die off in the harsh stomach environment before reaching their final destination and making any difference. In fact, one of the best probiotics I use (not safe for histamine intolerance) is a spore-based probiotic that only contains 4 billion CFUs! The spore-based nature allows bacteria to proliferate in the appropriate environment and it works much more effectively than other probiotics with a higher number of CFUs. It’s the same case with any vitamins/minerals – depending on the way they are created and the combination of ingredients, a lower dosage of a certain brand can be more effective than a higher dosage of a different brand. What I’m getting at is it’s all in the formulation so use something you trust 🙂

  • Jessica says:

    I need many more billions (200+billion) while on antibiotics for aggressive tick-borne infections (probably my underlying cause which refuses to be eradicated). I react to dairy, soy, gluten, and CORN (glutamate issue?) so Kyo-9 is out for me. Do you have any recommendations for much higher CFU probiotic? Organic3 GutPro and Custom Probiotics D-Lactate Free look good to me, but they refuse to tell me what strains they use (it’s proprietary). Are strains of that much importance? I’ve also been recommended Primal Probiotics but that’s so low in CFU, it’d cost me $300 a month. I’m in over my head.

    • Anita Tee says:

      Hi Jessica,

      I’ve mentioned before on my website that CFUs are actually irrelevant compared to viability – you can have a multi-billion probiotic where the majority of bacteria will die off in the harsh stomach environment before reaching their final destination and making any difference. In fact, one of the best probiotics I use (not safe for histamine intolerance) is a spore-based probiotic that only contains 4 billion CFUs! The spore-based nature allows bacteria to proliferate in the appropriate environment and it works much more effectively than other probiotics with a higher number of CFUs.

      Kyo-dophilus has had really great reviews from histamine intolerance sufferers and it’s a bit hard to find histamine intolerance probiotics. I have yet to come across one that I trust with a higher number of CFUs that I can rely on, but have had great results with my clients using Kyo-dophilus 9.

      Best of luck Jessica!

    • naomiaznm says:

      Gut Pro lists their varieties, and they are all on the helpful list.

  • Patrice says:


    Thank you for the article. Is there a probiotic blend with all of the histamine reducing benefits without the potato starch as in the kyo? ALSO IS THERE ON IN POWDER FORM FOR TODDLERS?

    • Hi Patrice,

      Glad you enjoyed the article.

      If you can’t tolerate the potato starch you can open the capsule and sprinkle it onto yogurt or cold/warm food. Just ensure it’s not hot food which will threaten the viability of the bacteria.

      If you’re aiming for probiotics for toddlers I would recommend consulting with your paediatrician, naturopathic doctor, or someone who personally knows your toddlers case. The microbiome is heavily forming until the age of two years old and you want to ensure you’re giving the right bacteria to your child.

  • Debbie says:

    What if I have IGE allergy to dairy. I get throat and tongue swelling with lactose!

  • Kay Constable says:

    Is the corn in the capsule or in the ingredients?

  • Bette says:

    Great article and I switched probiotics a few weeks ago and starting to feel better. Confusion though on best time to take probiotics? Morning, with food? At night?
    Thank you!

  • Sara says:

    Hello! I have an 18 month old who reacts to salicylates and amines (indicating the histamine intolerance). I do believe he has some gut issues from birth and from his year of breastfeeding with my having to go on antibiotics several times. He gets severe eczema and is on a very restricted diet. When I would give him probiotics, his eyelids would get eczema. 🙁 I do believe he needs some gut healing, so it might we worth trying your recommendations. Is this a safe does for a toddler?

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