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Best Probiotic for SIBO and Histamine Intolerance + Brands

If you are looking for the best probiotic for SIBO and histamine intolerance, there are specific types of probiotics you should try to find. In other words, you probably shouldn’t just grab any old probiotic off the shelf.   

While more and more research is showing that probiotics are beneficial for SIBO, you will want to be careful about the strains you choose.

Especially watch out for the types of probiotics you take if you also have histamine intolerance or allergies as well. 

This is because some probiotics can increase histamine in your gut, and you definitely don’t want that if you have histamine intolerance.

Brooke Foth, RDN is coauthor of this post.

Contains affiliate links.  Visit the disclosure page for more information. 

Overview of best probiotic strains for SIBO and histamine intolerance

Research shows that several strains of probiotics help both SIBO and histamine conditions.

These strains include:

  • Bacillus coagulans
  • Bacillus subtilis
  • Bacillus clausii
  • Saccharomyces boulardii
  • Bifidobacterium infantis
  • Bifidobacterium longum
  • Bifidobacterium breve
  • Lactobacillus rhamnosus
  • Lactobacillus plantarum 

Finding probiotic supplements that contain a broad spectrum of these strains is ideal.  We will help you break that down next. 

Best probiotic for SIBO and histamine intolerance-brands

It is challenging to sort through all the brands of probiotics to determine if they have the right probiotic strains for both SIBO and histamine intolerance.  

To help you with that, here are some top-rated brands that have probiotic strains shown in research to help with both conditions.

Most of our recommended brands contain a 30-day supply with the exception of Florastor, which is a 25-day supply. 

Top Picks

Low Histamine Probiotics by Vita Monk: contains 8 different strains 45 billion units of histamine-blocking probiotic that balance histamine and also reduce SIBO.  This is our favorite pick for overall gut health, SIBO, and histamine intolerance because it contains Saccharomyces boulardii, Bifidobacterium longum, Bifidobacterium bifidum, Bifidobacterium infantis, Lactobacillus rhamnosus, Bifidobacterium breve, Bifidobacterium lactis, and Lactobacillus plantarum.

Primal Earth Probiotic: by Amy Myers MD contains 3 soil-based probiotic strains including Bacillus subtilis, Bacillus coagulans, and Bacillus clausii. This probiotic has over 600 5-star reviews that are positive for supporting overall health and gut balance.  Great for people who want the best soil-based probiotic for SIBO that also supports histamine intolerance. Contains a 30-day supply per bottle. 

Best Value

Florastor: is a popular brand that has over 2000 positive reviews and contains the researched strain of Saccharomyces boulardii lyo CNCM I-745.  This strain helps with many digestive conditions and is also supportive of healing from histamine issues. If you are on a budget, this is the best value for your money.  Contains 50 capsules per bottle. 

Probiotic with gut healing mushrooms and herbs

Ancient Nutrition SBO – Probiotic blend has 25 billion CFUs including Saccharomyces boulardii, Bacillus coagulans, Bacillus clausii, and Bacillus subtilis.  Also contains Adaptogenic mushrooms including turkey tail, Reshi, Shiitake and Maitake, which help support a healthy microbiome.  This is an overall great supplement for the gut because it also contains the gut-healing herbs fermented licorice root and marshmallow root. 

Honorable mention

Seeking Health Probiota Histamine X-has 10 billion CFUs of probiotics that help calm down histamine and also help SIBO,  including Bifidobacterium infantis, Bifidobacterium bifidum, Bifidobacterium longum, Lactobacillus salivarius, Lactobacillus plantarum, Bifidobacterium lactis, and Bifidobacterium breve.  This brand is also a great value as well.

How we selected these brands

Only the best probiotic for SIBO and histamine intolerance strains make this list of brands.  The other criteria for our selection include:

  • GMP certified-third party inspected
  • Highly rated-greater than 4.5-star reviews by over 100 reviewers
  • Contains strains that are good for both SIBO and histamine intolerance
  • Free of histamine-producing or methane-producing bacteria

Strains of probiotics to avoid

Some forms of lactic acid bacteria and bifidobacterium cause the body to make more histamine or can increase SIBO symptoms.  These strains include [R]:

  • Lactobacillus casei 
  • Lactobacillus bulgaricus 
  • Bifidobacterium lactis –increases methane
  • Lactobacillus reuteri 

While you may feel fine taking these probiotic strains, they also may temporarily ramp up some of your histamine symptoms or SIBO symptoms. 

What is SIBO?

SIBO, or small intestinal bacterial overgrowth, is a condition caused when bacteria starts to grow in the small intestine where it normally shouldn’t grow.  

These bacteria begin to digest food particles and the symptoms can be quite uncomfortable. This is known as gut dysbiosis. 

Many people who suffer from irritable bowel syndrome have SIBO too.  It is also quite common to have histamine intolerance at the same time.

Your doctor can determine if you have SIBO by performing a hydrogen and methane breath test. 

Related: How to Reduce SIBO Die Off Symptoms + Prevention


Symptoms of SIBO

If you have SIBO, you can feel quite uncomfortable.  Some common symptoms of this condition include: 

  • Excessive gas (from hydrogen and methane gas) 
  • Bloating 
  • Nausea 
  • Abdominal pain 
  • Intestinal inflammation 
  • Fatigue-due to reduced nutrient absorption

As you can see, these are very similar symptoms to IBS because the two conditions are closely related. 

These also share similarities with symptoms of histamine intolerance too.  

What causes SIBO?

SIBO is generally related to other hidden or not-so-hidden causes. 

These can include [R]:

  • Reduced gastric acid secretion can be caused from aging or medications like proton pump inhibitors. 
  • Impaired intestinal motility caused from IBS, celiac disease, opiates, structural abnormalities 
  • Long term use of antibiotics 

Related: Do you have low stomach acid? Signs and simple remedies

Why use probiotics for SIBO?

Even though it seems conflicting to add probiotics when dealing with SIBO, certain strains of bacteria are beneficial for this condition according to many research studies.

Think of it like this: the good probiotic bacteria can help fight the bad bacteria and also help your immune system work.  

For example, a review of 18 clinical trials concluded that probiotics can be useful in  treating SIBO [R]. 

In summary, these probiotics help to:

  • Reduce bacterial overgrowth 
  • Improve mucosal barrier function  
  • Regulate immune system 
  • Prevent diarrhea
  • Reduce constipation symptoms

Related: The Best Probiotics for Bloating and IBS

Best probiotic strains to help SIBO

Probiotic strains that may help with SIBO symptoms include:

  • Saccharomyces boulardii is actually yeast and has anti-inflammatory effects in the gut while inactivating pathogenic toxins and stimulating gut cell growth [R, R]. 
  • Bacillus coagulans, help the bacteria in the gut colonize, promotes immune stimulation, and can help with oxalate digestion decreasing the risk of kidney issues. 
  • Bacillus subtilis – produces over 12 natural antibiotics to keep your gut free of harmful bacteria. Ferments vitamin K in the gut and supports gut repair by increasing IgA and butyrate [R].
  • Bacillus clausii – helps synthesize IgA an inflammatory and gut repairing immunoglobulin. 
  • Bifidobacterium lactis– reduces SIBO symptoms when combined with other probiotics
  • Lactobacillus acidophilus– used in research to reduce SIBO symptoms
  • Lactobacillus plantarumcombined with the above 2 strains, helps with SIBO [R]
  • Lactobacillus gasseriaids in constipation [R]
  • Bifidobacterium longum-decreases bloating and constipation [R]

Keep in mind, only the strains listed at the top of this post are good for both SIBO and histamine intolerance. 

How about a low FODMAP diet?

While people commonly follow a low FODMAP diet for SIBO, the fact is, no research shows that it helps long-term.  For clarification, a low FODMAP diet limits fermentable carbohydrates in the diet.

Surprisingly, a low FODMAP diet may do more harm than good because it can result in an altered microbiome over time. 

Granted, you may experience some short-term relief from following a low fermentable carbohydrate diet if you are miserable.  

Everyone is different and your diet should be tailored to work for you. 

Related: Do You Need Low FODMAP Tea for IBS?

What are soil based probiotics? 

Soil-based probiotics are bacteria naturally found in the Earth. They have a seed-like structure, which makes them stronger than other probiotic options. 

A fascinating fact about soil-based probiotics is that stay in their spore form state until their environment is safe. They don’t grow in the small intestine, which makes them perfect for SIBO. 

Rather, they go to the large intestine and colon where they belong. 

Soil-based probiotic strains:  

  • Bacillus coagulans
  • Bacillus subtilis 
  • Bacillus clausii   

Research shows that Bacillus coagulans, given for 6 months, reduces symptoms of gas, bloating, and diarrhea in people with SIBO [R].

Soil-based probiotics for SIBO are thought to be especially helpful because they are in spore form and only activate in the large intestine where they are best served.

These beneficial probiotics also may help with allergies and histamine conditions according to research in children [R].

Infographic depicting the reasons why adding the best probiotic for SIBO and histamine intolerance help with symptoms of SIBO and histamine intolerance with graphics of intestines, probiotics, by The Healthy RD

What is histamine?

Histamine is naturally released by the mast cells (specialized white blood cells) in the immune system when the body is exposed to an allergen. 

This compound is also a brain neurotransmitter and an important part of stomach acid to break down food. 

We need histamine, but unfortunately, too much of it can make us feel miserable. 

What causes histamine intolerance?

  • Gut dysbiosis: some gut bacteria break down bacteria while others produce histamine. An imbalance of bacteria can lead to an overload of histamine 
  • Enzyme Diamine oxidase deficiency (DAO): is an enzyme that breaks down histamine in foods 
  • Medications that block the DAO functions or prevent production 
  • Histamine-N-methyltransferase (HNMT) deficiency: the enzyme HNMT breaks down histamine after DAO by adding a methyl group in the brain. 
  • Mast cell activation disorder: occurs when the chemicals that break down histamine are improperly activated and released 

Some people can’t break down histamine in foods too.

If you don’t break down histamine properly in your gut, your body can feel miserable. Histamine overload is inflammatory and can cause headaches, redness and hives, and vasodilation. 

Histamine is broken down by an enzyme known as Diamine Oxidase (DAO). If you lack DAO, you may experience histamine symptoms. 

If your gut is inflamed, your ability to break down histamine is reduced. Luckily, probiotics help the body make its own DAO.

Low DAO enzyme levels are also caused by many kinds of medications according to Medical News Today. It can also be caused by intestinal disorders and genetic defects [R]. 

Luckily, probiotics can help no matter what the cause is for low DAO enzymes.  

High histamine foods

Many foods contain the amino acid histidine and when broken down is converted to histamine. 

Histamine foods include yogurt, tomatoes, tempeh, miso, cured meats, chocolate, cheese, red wine, and other alcohols. 

Histamine liberators

Some foods don’t actually contain histamine, but are thought to be histamine liberating foods, which cause a release of histamine from your mast cells.  

These foods are legumes, nuts, citrus, strawberries, pineapple, bananas, seafood, and some spices. 

Heal the gut for histamine intolerance

Histamine intolerance is likely rooted in the gut which means if we nourish our microbiome with fermented foods and probiotics we can likely fix this issue. 

Studies have shown that probiotics may improve histamine intolerance. 

Bacteria are involved in the production and breakdown of histamine. 

Choose your probiotic wisley as some strains can actually produce histamine.

These include:

  • Lactobacillus casei
  • Lactobacillus reuteri 
  • Lactobacillus bulgaricus 

While a low histamine diet can help manage symptoms, it doesn’t treat the underlying causes of histamine intolerance like some types of probiotics do. 

What probiotic strains aid in histamine intolerance?

Certain bacteria aid in breaking down histamines so let’s talk about the specific strains which lower histamine.  Keep in mind, the research about each of these strains is early. 

  • Bacillus clausii-reduces inflammation and allergic symptoms [R]
  • Bacillus coagulans – reduces allergic responses [R]
  • Bacillus subtilis – breaks down histamine and tyramine [R]
  • Saccharomyces boulardii – a yeast that increases DAO activity [R]
  • Lactobacillus rhamnosus – reduces histamine receptors and reduces inflammation [R]
  • Bifidobacterium infantis – histamine degrading bacteria [R]
  • Bifidobacterium longum – histamine degrading bacteria [R]

Of these strains, the best probiotics for SIBO as well include Bacillus coagulans, Bacillus subtilis, Bacillus clausii, Saccharomyces boulardii, Bifidobacterium infantis, Bifidobacterium longum, and Lactobacillus rhamnosus. 

Make sure to also eat foods full of probiotics too

Fermented foods have long been a traditional staple in all areas of the globe. 

Not only is fermentation a form of preservation,  this also increases digestibility, enhances nutrients, and minerals for absorption. 

Probiotic foods that are fermented contain beneficial food for your gut bacteria and also increase the amount of nutrients absorbed. 

For example, Natto (Japanese dish consisting of fermented soybeans) has three times the amount of vitamin B1 and vitamin B2 and 5 times the amount of vitamin B12 than soybeans alone.   

Fermentation helps break down anti-nutrients

Some foods have compounds called anti-nutrients that reduce your ability to absorb the nutrients you eat.  

A common one is called phytic acid that blocks iron, zinc, and calcium absorption [R]. 

For this reason, most people, especially vegans or vegetarians,  benefit from fermenting seeds, nuts and legumes. 

That’s because fermenting helps to break down phytic acid. 

Fermenting grains, seeds, and beans decreases the phytic acid via the formation of organic acid [R].

These acids promote the phytate breakdown. 

Tip: try fermenting your own seeds in water and apple cider vinegar overnight before eating to enhance absorption and add probiotics. 

Why choose fermented foods?

Probiotic foods that are fermented contain a variety of beneficial bacteria and usually much more so than a probiotic capsule. 

If you are curious what strains and species of bacteria  are present in foods check out this research article in the Integrative Medicine journal.  They include a table with the strain and amount of organisms present of popular brand name brands such as Kite Hill, Activia, and Synergy Kombucha. 

A variety of fermented foods are available on the market full of diverse flavors. 

Here are a few options: 

  • Kimich 
  • Miso
  • Natto
  • Kefir
  • Sauerkraut 
  • Tempeh
  • Kombucha
  • Yogurt 

Histamines are a byproduct of fermentation so if you suspect a histamine intolerance try the probiotic brands for histamine intolerance recommended instead. 

If you are histamine intolerant you might find that fermented food doesn’t work for you at first, and that’s okay. By healing your gut, you should be able to begin to tolerate histamine foods again. 

This is when listening to your body and how you feel after eating becomes very powerful! 

Experiment with a variety of fermented foods to find what works for you.  If you have SIBO too, the same goes.  And start with a small amount, such as a tablespoon of sauerkraut a day. 

Best probiotic for SIBO and histamine intolerance summary

Many types of probiotics can help with both SIBO and histamine intolerance. Just make sure to carefully read your probiotic labels or choose the brands researched above.  For your convenience, those brands include 

Try to also include fermented foods whenever possible to gain the best array of probiotics and to enhance your body’s ability to digest these foods and nutrients. 

Disclaimer – The information contained on this blog, website, and related content is of a general nature and not regulated by the FDA. They are not intended to treat, diagnose, or give specific medical advice. While all content is written by a registered dietitian and strives to provide only accurate, scientific-based information, your specific health needs may or may not apply to the content contained on this website and related content. It is not intended to diagnose or treat any specific medical condition. All content is copyrighted and must be used only with permission and citation to thehealthyrd.com.

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