Probiotics for SIBO

by | Nov 28, 2023 | Blog, SIBO

Disclaimer: The health information on this site is provided for general informational and education purposes only and is not a substitute for professional advice. Accordingly, before taking any actions based upon such information, we encourage you to consult with the appropriate professionals. The use or reliance of any information contained on this site is solely at your own discretion. Revolution Gut Health does not claim to heal, treat or cure any of the conditions mentioned.

The conversation around small intestinal bacterial overgrowth (SIBO) and the role of probiotics is gaining considerable traction.

If you’re researching probiotics for SIBO, you’ve probably come across the same articles explaining what probiotics are and how they may benefit the symptoms of small intestinal bacterial overgrowth.

This guide is different. We don’t want to give you the same information you’ve read before. Instead, we’re offering a complete picture of SIBO, probiotics, and the connection between the two. We will explore the causes, symptoms, and types of SIBO alongside the benefits and limitations of using probiotics as a therapeutic approach, offering a comprehensive understanding of this complex interplay between gut health and microbial interventions.

Plus, we will discuss why some types of probiotics should be off-limits for people struggling with the signs of bacterial overgrowth and which products might be better.

What causes SIBO?

A dysfunctional digestive system causes SIBO. The digestive system may become dysfunctional for many reasons. Most commonly, the gut bacteria changes seen in SIBO happen as a result of stress and hypertoxicity.

Stress impacts gut health by increasing gut permeability (or by producing tiny gaps in the gut’s lining). These gaps allow good bacteria to seep out and bad bacteria and other toxins to invade the gut, leading to SIBO symptoms.

Hypertoxicity happens when the gut is exposed to excessive amounts of environmental toxins. These toxins can kill off gut bacteria, throwing off the careful balance needed for healthy digestion.

Another known cause of SIBO is the overuse of antibiotics. Antibiotics are designed to kill bacteria in the body. When used excessively, they can impact the balance of good and bad bacteria in the gut, too.

It is unlikely that SIBO only has one cause. In most cases, experts can distinguish more than one cause of an individual’s symptoms.

SIBO Risk Factors

Some people may experience elevated stress levels, hypertoxicity, and overuse of antibiotics but not get SIBO. Others are not so lucky. The difference may come down to someone’s predisposition to this digestive disorder.

For example, having one or more risk factors for SIBO may increase the likelihood that a person will develop symptoms. These risk factors include, but are not limited to:

  • Genetics
  • Aging
  • Gender
  • Naturally low stomach acid levels
  • Having a dysmotility diagnosis
  • Being born with a smaller small intestine
  • Pre-existing immune disorders
  • Injuries to the GI tract
  • Eating a diet high in inflammatory foods

SIBO is also linked to other disorders of the GI system. People with diabetes, irritable bowel syndrome (IBS), and irritable bowel disorders (IBDs) like Crohn’s disease are more likely to develop SIBO.

Some studies have found an underlying GI system condition as at least one of the causes behind 80% to 90% of SIBO cases.

Different Types of SIBO

Understanding the symptoms of SIBO requires knowledge of the different types. Experts distinguish between three different types of SIBO: hydrogen-dominant, methane-dominant, and hydrogen sulfide-dominant.

Each type is named for a gas certain species of gut bacteria produce. Bacteria and other gut microbes naturally create gas as a byproduct of carbohydrate digestion.

It’s healthy for the gut to produce small amounts of gas. However, having excessive amounts of one or more of the above gases may indicate SIBO, especially if someone also experiences gut bacterial overgrowth symptoms.

Individuals may receive a diagnosis for only one type of SIBO, but it is also possible to have two or even all kinds at the same time. Learn more about the symptoms of hydrogen, methane, and hydrogen sulfide SIBO below.

Hydrogen SIBO

H2 (hydrogen gas) is one of the most abundant gases the human gut produces. The predominant producers of hydrogen gas are Firmicutes and Bacteroides, which account for 90% of gut bacteria.

When the Firmicute/Bacteroide balance gets thrown off, hydrogen SIBO symptoms may result. Signs of hydrogen-dominant SIBO include severe bloating, stomach discomfort, and diarrhea.

Methane SIBO

Methane SIBO is unique because bacteria do not cause it. Instead, types of archaeans known as methanogens are the primary producers of CH4 (methane gas) in the gut. Methanogens are also the culprits in this type of SIBO.

People with high levels of methane-producing microbes in their gut are more likely to experience dysmotility symptoms, with constipation being the most common.

Hydrogen Sulfide SIBO

The large intestine is home to sulfide-reducing bacteria that produce H2S (hydrogen sulfide gas). Small amounts of hydrogen sulfide are essential for stabilizing the gut lining, among other functions.

However, excessive amounts of sulfide-reducing bacteria have toxic effects. In the gut, high amounts of H2S are associated with SIBO symptoms like diarrhea, stomach pain, and gas.

What are probiotics?

Probiotics are live cultures of bacteria and other microbes that are beneficial for gut health. They are found in certain types of fermented foods as well as over-the-counter probiotic supplements.

The balance of good and bad bacteria is not the only thing determining gut health. A healthy gut will also have a diverse array of bacteria, yeasts, and other microbes.

If gut microbiome diversity declines due to antibiotic use or another cause, SIBO symptoms may result. Probiotics can restore gut microbe diversity and replace low levels of beneficial bacteria for a more balanced microbiome.

The Benefits of Probiotics

The gut microbiome is not just responsible for digesting food. It is also involved in absorbing water to regulate body temperature and eliminate waste products, producing the immune response, and synthesizing essential nutrients.

Taking probiotics can help restore these functions, leading to an array of positive side effects. However, the exact effects of a probiotic depend on the bacterial cultures it contains.

Lactobacillus and Bifidobacterium are the two most common strains found in over-the-counter probiotics. We will talk more about the best probiotics for SIBO in a moment, but first, here are the potential benefits of consuming them.

Balance the Gut

The most obvious benefit of probiotics is balancing the gut microbiome. As mentioned, the gut contains a careful balance of good and bad bacteria essential for healthy digestive function.

When opportunistic bacteria grow out of control, they can cause direct damage to the intestinal lining. Bad bacteria can also destroy beneficial species, which helps mount an immune response against toxins trying to invade the gut.

Throwing a probiotic into the mix will feed the gut with good bacterial strains like Lactobacillus and Bifidobacterium. The result is a more balanced gut and fewer SIBO symptoms.

Stimulate Immune Support

70% to 80% of the immune system’s cells reside in the GI tract. Experts are starting to realize that this is why an unhealthy gut may play a role in a range of physical and even mental health conditions.

Probiotics can help support this aspect of the immune response. The more diverse the gut microbiome is, the better someone’s immune system can fight off pathogens and other foreign invaders.

Additionally, probiotics have a more direct impact on immunity. Studies show that these products regulate the functions of T and B lymphocytes, which are responsible for destroying viruses, bad bacteria, and other toxins.

Promote Regular Bowel Movements

Dysmotility, or the slow transit of digested food through the GI tract, is a common side effect of an imbalanced gut microbiome. It is a precursor to various SIBO symptoms, especially constipation.

Constipation is not the only thing to worry about with dysmotility, though. Irregular bowel movements can also increase the risk of weight gain in people with certain diets, high blood pressure, and even certain cancers.

When digested food stays in the digestive tract longer, unhealthy bacteria may migrate to other areas of the gut, worsening SIBO. Probiotics increase levels of bad-bacteria-fighting microbes to reverse these effects.

Normalize Transit Time

A slow transit time for digested food is not the only thing to worry about when the gut microbiome is imbalanced. Food may also move too quickly through the GI tract, leading to SIBO symptoms like diarrhea.

Eliminating food waste too quickly may compromise digestion. The small intestine will not have enough time to extract water and nutrients from food.

Fast transit time has the potential to cause malnutrition and dehydration, which are detrimental to human health. Luckily, probiotics can optimize transit time, allowing the body to maximize nutrient extraction from our foods.

Support Vaginal Wellness

The collection of bacteria and microbes in the gut is not the only microbiome in the human body. The skin, mouth, saliva, and lungs are also home to collections of good and bad bacteria, fungi, archaea, protists, and viruses.

Female reproductive organs, including the vagina, are also home to microbiomes. When healthy, the vaginal microbiome helps defend against sexually transmitted infections (STIs) and other health issues.

Bacterial vaginosis occurs when levels of Lactobacillus bacteria decline and the vagina’s pH changes. Taking a probiotic containing Lactobacillus can restore this important bacterial strain, reversing the effects of bacterial vaginosis.

Improve Mental Health Conditions

Emerging research has uncovered a link between the gut and the central nervous system. Also known as the gut-brain axis, this connection explains why gut conditions can increase the risk of new mental health conditions or exacerbate symptoms of pre-existing ones.

Dysbiosis (an imbalanced gut microbiome) and gut inflammation are both correlated with common mental health conditions like anxiety and depression. Conversely, a healthy gut is associated with positive mental health symptoms.

Researchers have studied the impact of probiotics on mental health for this reason. In human and animal studies, probiotics containing Bifidobacteria improved symptoms of anxiety and depression.

Optimize Weight

Earlier, we mentioned that dysmotility is a side effect of imbalanced gut bacteria and may cause weight gain. When food stays in the GI tract for too long, the body has more time to extract its nutrients.

Extracting more nutrients is not bad if someone eats a highly nutritious diet. However, the standard American diet features an excess of high-calorie, high-fat, and high-sugar foods.

When these ingredients remain in transit, the small intestine will absorb more of them into the bloodstream. Weight gain occurs if the person doesn’t burn off the excess fat and sugar through physical activity or exercise.

With their ability to promote optimal transit time, probiotics are an ideal supplement to any weight management routine. Additionally, probiotics play a role in metabolism, which also has a direct impact on weight.

probiotic foods

Probiotic Foods

Probiotics are the most convenient way to get beneficial bacteria into your system and fight the symptoms of SIBO, but they are not the only way. Some foods are natural sources of beneficial live bacterial cultures.

Importantly, too much of a probiotic is not always a good thing. Just as having too many pathogenic bacteria can throw off the gut microbiome, too many good bacteria can also cause digestive discomfort and bloating.

To optimize the amount of probiotics ingested through diet and supplementation, individuals should talk to a healthcare professional about the proper dosage for their unique symptoms and lifestyle.


Yogurt is an excellent source of Lactobacillus bacteria. It gets its probiotics from the way yogurt is made. Manufacturers introduce live microbes to pasteurized milk, resulting in fermentation.

Fermentation is a chemical reaction. The reactants (or the chemicals that cause the reaction) are carbohydrates and bacteria. One product (or the substance the reaction produces) is lactic acid, among others, which can combat pathogenic bacterial overgrowth.

The bacteria used to start the fermentation reaction are still present in the final product. However, some types of yogurt contain higher amounts of probiotics. For example, kefir contains three times the probiotics of regular yogurt.

People with SIBO should note that kefir and other probiotic yogurts may worsen their GI symptoms. We’ll discuss the types of probiotics that don’t cause these effects in a moment.

Fermented Foods

Yogurt is not the only fermented food that’s high in probiotics. Other fermented products are also excellent for gut health. The most common fermented items found in the average grocery store include:

  • Kombucha
  • Sauerkraut
  • Fermented pickles
  • Kimchi
  • Miso
  • Tempeh
  • Natto
  • Apple cider vinegar
  • Wine
  • Sourdough bread
  • Cottage cheese
  • Aged raw cheeses

Before loading up on these foods, people should understand the risks. Some probiotics in these items can do more harm than good for SIBO symptoms.

The fermentation process does not just utilize beneficial bacteria strains; it also introduces and produces microbes that are harmful to gut health. Many people choose a supplement instead to avoid this potential effect.

Prebiotic Foods

Prebiotics are particular types of fiber that feed beneficial gut bacteria. People can access prebiotics in supplement form, but many foods are naturally rich in prebiotic fibers, including:

  • Garlic
  • Onions
  • Bananas
  • Apples
  • Leeks
  • Artichokes
  • Asparagus
  • Barley
  • Oats
  • Flaxseeds
  • Bran
  • Cocoa beans
  • Seaweed
  • Chicory root
  • Dandelion greens
  • Konjac root
  • Burdock root
  • Yacon root
  • Jicama root

These goods are excellent sources of prebiotics, as well as other beneficial nutrients that fuel the brain and body. However, as with probiotics, prebiotics can sometimes cause more harm than good.

In addition to feeding beneficial bacteria, prebiotics are food for bad bacteria, too. Feeding pathogenic bacteria may exacerbate SIBO symptoms, making it crucial to correct gut dysbiosis before incorporating the above foods.

Are Probiotics Bad for SIBO?

Yes, some probiotics are bad for SIBO. People suffering from symptoms of this digestive disorder should avoid probiotic foods, certain types of probiotic supplements, and prebiotics until their gut health is restored.

For example, probiotics containing Lactobacillus and Bifidobacterium will feed both good and bad bacteria strains of the gut microbiome. Soil-based bacteria, on the other hand, only promote beneficial gut bacteria.

There are two types of probiotic supplements on the market today: regular and soil-based probiotics. Regular probiotics are not ideal for SIBO. Meanwhile, soil-based probiotics contain the bacteria needed to soothe SIBO symptoms.

Regular Probiotics

Regular probiotics primarily contain Lactobacillus and Bifidobacterium strains. Some may also include a yeast called Saccharomyces boulardii, which can benefit SIBO-related gut problems.

However, even regular probiotics containing this healthful yeast can worsen SIBO. Individuals struggling with symptoms of bacterial overgrowth should address the underlying condition with a SIBO elimination diet and/or antibiotics before trying traditional probiotics.

Another downside to traditional probiotics is that the bacteria they contain often die before they reach the large intestine. Instead, they settle in the small intestine, contributing to SIBO-related bacterial overgrowth.

Soil-Based Probiotics

Soil-based probiotics are also known as SBO probiotics. They differ from traditional options because they do not contain Lactobacillus or Bifidobacterium strains, which can worsen SIBO symptoms.

The microbes SBO probiotics contain are naturally found in dirt. They are more durable and potent than regular probiotics, so people do not need high doses.

Unlike regular probiotics, one advantage of soil-based probiotics’ hardiness is that they do not have to be refrigerated. People taking these products for SIBO can more easily travel with their supplements.

Additionally, the durability of SBO probiotics means the bacteria can survive longer. They do not colonize the small intestine but move on to the large intestine. In the large intestine, soil-based microbes promote beneficial bacterial growth that positively impacts SIBO.

In one study, soil-based probiotics led to a significant reduction in irritable bowel syndrome symptoms. Considering that a large percentage of people with IBS also have SIBO, soil-based probiotics should benefit SIBO, too.

Can Probiotics Cause SIBO?

Yes, probiotics can cause SIBO, especially if someone with pre-existing gut microbiome disturbances uses regular probiotics. For example, people with dysmotility due to bacterial overgrowth might try probiotics, and the probiotics may cause SIBO.

People who have SIBO already may experience worsening gas, bloating, and brain fog. Traditional probiotics are particularly associated with methane-dominant SIBO symptoms, such as constipation, but less so with hydrogen-dominant SIBO, which is associated with diarrhea, bloating, and stomach pain.

Importantly, not all probiotics cause these effects. As mentioned, soil-based probiotics can benefit SIBO, even when regular ones are not. Learn more about the best soil-based probiotics for SIBO next.

Soil-Based Probiotics for SIBO

Soil-based probiotics promise to balance the gut microbiome, support the immune system, and improve digestion without making SIBO symptoms worse. However, as with probiotics, not all SBO probiotics are generally equal.

For example, probiotics containing Bacillus licheniformis and Enterococcus faecium are highly controversial, as they may be unsafe for humans. Meanwhile, Bacillus anthracis (anthrax) is outright deadly.

Best Soil-Based Probiotics for SIBO

Safety concerns aside, some soil-based microbes are better for SIBO symptoms than others. The most well-studied ones are Sacchoromyces boulardii, Bacillus clausii, Bacillus coagulans, and Bacillus subtilis.

    1. Sacchoromyces Boulardii (S. Boulardii)

    S. boulardii is a type of yeast. Its role is to eliminate gut toxins and support regular bowel movements. Researchers have investigated the benefits of this yeast plus dietary changes versus dietary changes alone for SIBO symptoms.

    People suffering from SIBO treated with S. boulardii and dietary changes experienced a significant reduction in diarrhea and hydrogen gas excretion on a breath test. Additionally, the researchers found that this probiotic was very safe.

    2. Bacillus Clausii (B. Clausii)

    B. clausii is part of the Bacillus genus of bacteria. This bacterium plays a role in immunity through its assistance with IgA and bacterin synthesis, both of which are essential parts of the gut’s immune response.

    In studies of people with hydrogen-dominant SIBO, probiotics containing this bacterium were able to reverse symptoms in a way comparable to antibiotics, one of the most common SIBO treatments.

    3. Bacillus Coagulans (B. Coagulans)

    B. coagulans is another member of the Bacillus genus. Like its cousin B. clausii, this bacterial species supports immunity. It is also well-researched for its ability to boost beneficial bacteria in the gut.

    In one study, researchers investigated the benefits of an antibiotic plus a B. coagulans-containing probiotic versus antibiotics alone. After six months, the probiotic group experienced a significant reduction in symptoms like stomach pain, bloating, belching, and diarrhea.

    4. Bacillus Subtilis (B. Subtilis)

    B. subtilis is one of the most widely used species of the Bacillus genus of bacteria. Like other members of its genus, this bacterium supports a healthy immune system. It also produces 12 antibiotic compounds and vitamin K.

    In a recent study of B. subtilis supplements, researchers compared its effects on GI symptoms against a placebo. The probiotic was well-tolerated, safe, and able to improve GI symptoms like bloating, burping, and gas.

    Revolution Gut Health Is Your SIBO Expert

    Probiotics for SIBO are an effective and natural way to address GI complaints like diarrhea and constipation. However, choosing a soil-based probiotic supplement might be best to avoid worsening symptoms.

    At Revolution Gut Health, our expertise is in the name. Our team of healthcare and holistic medicine professionals use a natural approach to supporting gut disorders.

    Book an appointment with our experts and finally start your journey to a healthier gut- and a healthier you!

    Soil-Based Probiotics FAQs

    We get a lot of questions about probiotics for SIBO at Revolution Gut Health. So before you go, check out these most frequently asked questions to find the answers you have been searching for.

    What Are Soil-Based Probiotics?

    Soil-based probiotics are supplements containing live strains of bacteria found in soil. With today’s modern farming processes, humans no longer ingest the same soil compounds as we did historically.

    For this reason, we may be missing out on beneficial microbes our bodies need to thrive. These microbes may include species of the Bacillus genus, which also naturally live in the human gut microbiome.

    Incorporating a soil-based probiotic allows people to replenish lost microbes while also benefiting GI complaints like those characteristic of SIBO.

    What Are the Best Probiotics for SIBO?

    The best probiotics for SIBO are soil-based and contain one or more of the following microbes:

    1. Saccharomyces boulardii
    2. Bacillus clausii
    3. Bacillus coagulans
    4. Bacillus subtilis

    Soil-based probiotics are ideal for SIBO because they do not populate the small intestine. Without growing in the small intestine, these strains will not contribute to bacterial overgrowth, which causes SIBO symptoms.

    Compare these benefits to traditional probiotics. Regular probiotics contain strains that do not live long enough to pass into the large intestine and do contribute to bacterial overgrowth in the small intestine.

    Which Types of Probiotics Are Found in Soil?

    The types of probiotics found in soil are known as soil-based probiotics and include more than 100 species. Among these species are the four we have discussed in this post: S. boulardii, B. clausii, B. coagulans, and B. subtilis.

    1. boulardii is a type of yeast found in tropical soil. It is a member of the fungi kingdom and is not a bacterium.

    Members of the Bacillus genus (e.g., B. clausii, B. coagulans, and B. subtilis) are the most abundant soil bacteria. They are commonly found in extreme climates with highly acidic or alkaline soil. Bacillus bacteria are also present in high volumes in deserts.

    Which Probiotic Is Best for SIBO?

    The probiotic that is best SIBO contains soil-based cultures that do not populate the small intestine or increase levels of pathogenic bacteria. Regular probiotics are not ideal for SIBO, as they may worsen GI symptoms.

    More specifically, soil-based probiotics containing certain Bacillus species of bacteria and the yeast Saccharomyces boulardii are ideal for improving SIBO symptoms.

    These species are hardy enough to survive the small intestine, making their home in the large intestine. They will not worsen SIBO symptoms. Instead, research shows these probiotics are highly beneficial for alleviating them.

    Can Probiotics Make SIBO Worse?

    Yes, probiotics can make SIBO worse if you choose the wrong kind. Most probiotics contain Lactobacillus and Bifidobacterium bacteria. These bacteria are the most common ones found in the GI tract.

    Someone with SIBO will already have many Lactobacillus and Bifidobacterium in their small intestine. After all, SIBO comes about due to an overgrowth of bacteria in the small intestine.

    Soil-based probiotics are different. They contain microbes that will pass through the small intestine into the large intestine, providing benefits for an imbalanced gut microbiome without exacerbating symptoms.

    What Are the Best Probiotics for Methane SIBO?

    The best probiotics for methane SIBO are soil-based probiotics that target constipation. Constipation is the hallmark symptom of methane-dominant SIBO, caused by an overgrowth of archaea called methanogens.

    Methane SIBO can be particularly tricky to improve. Since archaea, not bacteria, cause it, the symptoms are often resistant to antibiotics. Antibiotics are usually the first line of defense against gut bacteria overgrowth.

    For this reason, B. clausii may be the best bacterial strain for methane SIBO. In studies, probiotics containing B. clausii performed as well as an antibiotic for reducing symptoms of SIBO.

    What Is the Best Probiotic for SIBO Hydrogen?

    The best probiotic for SIBO hydrogen is a soil-based prebiotic that contains Saccharomyces boulardii, Bacillus clausii, Bacillus coagulans, and Bacillus subtilis.

    In studies, all four of these probiotics have been beneficial for hydrogen-dominant SIBO, particularly, or the symptoms of hydrogen SIBO, in general. These symptoms include bloating, stomach pain, and diarrhea.

    Finding a prompt and effective treatment is significant for this type of SIBO. Without treatment, individuals may experience more severe complications like malnutrition and dehydration.

    What Is the Best Probiotic for SIBO and Histamine Intolerance?

    The best probiotic for SIBO and histamine intolerance is Saccharomyces boulardii, a soil-based and low-histamine probiotic. Many strains of bacteria are safe for people with histamine intolerance, but none are soil-based and may potentially exacerbate SIBO symptoms.

    People who are intolerant to histamine should also steer clear of probiotic foods. Fermented items may also contain high amounts of histamines.

    To date, there isn’t much research on the subject of probiotics and histamine intolerance. Individuals worried about having an allergic reaction should consult with their doctors to be on the safe side.

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