Best Soil Based Probiotics + Proven Benefits for IBS and SIBO

Image of assorted vegetables in soil like carrots, peppers, onions, tomatoes, cucumbers on a light green background with wording The Best Soil Based Probiotics by The Healthy RD

Finding the best soil based probiotics is definitely worth your time. This is because soil-based probiotics are emerging as some of the best probiotics for overall health according to research.  

If you have GI issues such as IBS, they may be your next best friend.

Clinical trials have confirmed their benefits for IBS, gut health, and more. 

Additionally, they are often the best-tolerated types of probiotics.

In this post, learn the benefits of soil-based probiotics and the best soil-based probiotic brands.

Criteria for the best soil based probiotics

Soil-based probiotics, also known as soil-based organism probiotics (SBO), are found in the soil.

But they aren’t just about keeping dirt healthy. Many health conditions can benefit from them as well.  Choosing a high-quality and reputable brand will help you get what you pay for.

Here are the criteria used to determine the best soil-based probiotics on the market today:

  • Contains strains that are highly resistant to stomach acid
  • Have a long shelf life 
  • Resistant to heat and light
  • The source is a trusted, third-party certified company
  • Has excellent brand reputation
  • Ingredients include soil-based probiotics that are native to the human gut
  • Has research to support its effectiveness
  • Includes at least 2 Bacillus strains of probiotics
  • Have doses of around 2-4 billion colony forming units (CFU) or more

Related post: The Best Probiotics for Acid Reflux in 2021 (

Best soil based probiotics brands overview

Many brands contain some strains of soil-based probiotics, but for many people, it is best to stick to purely soil-based probiotics. 

In all honesty, I’ve tried many probiotics, but soil-based are my favorite.

This is because they are gentle and more effective than most for my gut and for my brain.

Many reviewers also agree that they make a difference when other probiotics do not.

Research also is growing strong for its fascinating benefits.

My colleagues use and love them too.

Related post: The Best Probiotics for Anxiety and OCD

Best soil based probiotics brands list

Please note that I provide links to Fullscript, which provides pharmaceutical-grade supplements, and to my other trusted affiliates.

Here are the best soil-based probiotic brands based on the above criteria: 

MegaSpore Biotic

  • Mega Spore Biotic is a brand that has been clinically studied to reduce symptoms of irritable bowel syndrome [R]. You can use code HEALTHYRD and save 10% too. This is the best brand of spore probiotics for irritable bowel syndrome as it has been studied clinically for this condition.  Impressively, it also increases Akkermansia muciniphila in the gut, which helps manage diabetes and metabolism [R]. It contains the probiotic Bacillus coagulans, Bacillus clausii, Bacillus licheniformis, Bacillus subtilis, and Bacillus indicus.  It is GMP-certified. Also available on Amazon

Amy Myers Primal Earth Probiotic

  • Amy Myers Primal Earth Probiotic promotes a normal bowel pattern and is among the best soil-based probiotics for SIBO and IBS. It is a very highly rated and trusted brand. Contains multiple sources of soil-based probiotics and is GMP-certified. Contains bacillus coagulans, bacillus subtilis, and bacillus clausii. Also available on Amazon.

Gastro Defense Stomach Armor

  • GastroDefense® Stomach Armor acts as a prebiotic, contains healing colostrum-LD, and contains 5.3 billion CFUs including Bacillus lactis and Bacillus coagulans.  It also contains gut-healing zinc carnosine, Acidophilus, Lactobacillus rhamnosus, Bifidobacterium bifidum, and peppermint. Low in lactose but does contain dairy. 

Klaire Labs Biospora

  • Klaire Labs Biospora contains spore-forming probiotics that are gentle and effective for gut function and healthy immune response. Contains Bacillus coagulans and B. subtilis. Klaire Labs is a pharmaceutical-grade company that is GMP-certified and highly rated. It is also free of all common allergens. Also available on Amazon.

Ortho Spore IG

  • Ortho Spore IG  is another professional-grade SBO probiotic that contains, Serum-Derived Bovine Immunoglobulin Concentrate (ImmunoLin®), Immunoglobulin G (IgG) Bacillus coagulans SNZ1969, Bacillus clausii B106, and Bacillus subtilis HS43 with 4 billion CFUs. It is GMP-certified.

Designs for Health Spore Based Probiotics

  • Designs for Health Spore / Soil Based Probiotics stand out because it contains 5 different bacillus strains. These are bacillus coagulans (Lactospore®), Bacillus subtilis (De111V®) Bacillus coagulans (Lacris-15), and Bacillus clausii (CSI-08) for a total of over 10 billion CFUs. It is GMP certified. Also available on Amazon.

Ancient Nutrition SBO Probiotics

  • Ancient Nutrition SBO Probiotics is a natural probiotic formulated by Dr. Axe.  Dr. Axe’s soil-based probiotics contain a good combination of fermented organic ingredients, Saccharomyces boulardii, Bacillus subtilis, Bacillus coagulans, and Bacillus clausii. This probiotic contains 50 billion CFU which is a higher amount than the other brands because it contains S. boulardii, a beneficial fungal probiotic. It is also third-party verified. Also available on Amazon.

What are soil-based probiotics?

Soil-based probiotics, as the name implies, are tiny microbes. They live in the rich dirt of garden beds, forest floors, and other earthy, natural environments.

Also, they are spore-forming organisms which makes them uniquely beneficial to you as you will soon learn.

Not found just in soil exclusively, these probiotics are also found in the human gut. 

The most popular and well-research soil-based probiotics are the Bacillus strains. 

Additionally, they are generally recognized as safe, according to the FDA.

Historically, soil-based probiotics would hitchhike into the digestive tract of the foods we eat.

Benefits of the best soil-based probiotics overview

Soil-based probiotics, also known as dirt probiotics, help plants. They do so by mining minerals in the soil and delivering these nutrients to plant roots.

In this way, soil probiotics help plants grow and increase the mineral content of foods.

Researchers have also recently discovered that many of these soil-based probiotics help the human gut.

They complete a vast number of tasks that help the human body.

In particular, soil-based organisms may help:

Our digestive tract holds the key to so many aspects of our health, so finding out how to best improve digestion is key for ALL of us.

Probiotics, the tiny, beneficial microorganisms in our body, are always a cornerstone of digestive health.

Best types of soil-based probiotics

Soil-based probiotics are different than your typical probiotics.

The soil-based probiotic strains are clinically proven to help replenish the natural gut microbiome, help with indigestion, and reduce stomach discomfort and bloating. 

Soil-based Bacillus probiotics that are the most researched include:

  • Coagulans
  • Subtilis
  • Clausii
  • Licheniformis
  • Indicus

All of these Bacillus species increase the amount of Lactobacillus and Bifidobacteria in the gut. This is good because Lactobacillus and Bifidobacteria are the most popular probiotics found in many supplements.

Soil-based families of bacteria improve digestion, improve immunity, and lower inflammation.

Interestingly, soil-based probiotics such as Bacillus subtilis and Bacillus clausii also work together with other types of probiotics in your gut. 

Bacillus coagulans

Bacillus coagulans strain helps the body because it increases your gut microbiome amount and diversity. 

This probiotic also increases bowel movement frequency in healthy adults with occasional constipation. It also helps to decrease abdominal discomfort. 

Fascinatingly, Bacillus coagulans may also help people lose weight after bariatric surgery. 

Pilot research also shows that a type of Bacillus called B. coagulans MTCC 5856 (LactoSpore®) is especially good. It is helpful for improving symptoms of major depression in people who have irritable bowel syndrome. 

Another study shows that this strain reduces headaches and anxiety in people with IBS. 

Bacillus clausii

Bacillus clausii is commonly used as a probiotic to help balance the microbiome. It also helps people with SIBO. This is because it helps reduce hydrogen levels during a hydrogen breath test. 

In a pilot study, Bacillus clausii plus antibiotics were able to reduce SIBO symptoms. Working much better than the placebo, this SBO probiotic worked in 93% of people compared to 67 percent in the placebo plus antibiotic group. 

Using Bacillus clausii may even reduce the chances of gut infections like rotavirus

Bacillus subtilis

Bacillus subtilis helps to relieve GI distress in many patients.  This strain helps to increase the number and diversity of bacteria that live in the gut. 

Early research even suggests that a Bacillus subtilis supplement may help people stay in remission if they have inflammatory bowel diseases.  

It also helps to dampen inflammation and strengthen the gut lining. 

Using Bacillus subtilis as part of a multi-strain probiotic also reduced symptoms of depression in a double-blind, placebo-controlled trial. 

Bacillus licheniformis

Bacillus licheniformis may help increase overall immunity and also strengthens the gut wall. 

A combination of Bacillus strains, including B. Licheniformis, reduces symptoms of irritable bowel symptoms too. 

Bacillus indicus

Bacillus indicus is less commonly found in probiotic supplements but is part of a probiotic combination that has been clinically studied to reduce IBS symptoms.  

The only researched probiotic that contains B. indicus is the brand Megaspore probiotic.  

Inclusion of bacillus indicus in probiotic strains appears to increase healthy bacteria, both in amount and diversity. 

How do SBO probiotics work?

The Bacillus species help the body to break down food. Resistant dietary starches are broken down by them which makes them easier to digest. Once these starches are broken down they become prebiotics. And by becoming prebiotics, they help to feed the healthy bacteria in your gut.

Breakdown of starch from soil-based probiotics results in postbiotics too. These postbiotics are compounds that help to fuel gut-friendly bacteria.

Also, friendly bacteria are made by soil probiotics and include F. prausnitzii and Akkermansia muciniphila.­­

Friendly bacteria like these help to prevent leaky gut and boost metabolism.

So using soil-based probiotics plus prebiotics helps increase healthy bacteria in the gut.

Do you need a soil-based probiotic supplement?

Soil-based probiotic supplements can be a good way to restore gut health.

After all, it’s not always possible for people to dig in the dirt. Additionally, soil isn’t always high quality anymore.

Research shows that adding soil-based probiotics is especially helpful for people with gut issues or leaky gut. They are also beneficial for conditions like IBS and SIBO

The most exciting part is that soil-based bacillus species are spore formers. Spore formers are usually more easy to tolerate than other types of probiotics.

Spore formers also have:

  • High resistance to stomach acid
  • A long shelf life
  • Resistance to heat, light, and other factors
  • The ability to be stored at room temperature

Therefore they are able to survive digestion. They also arrive safely in the large intestine where they are reactivated and begin to work their magic.

What happened to our gut probiotics?

Humans of the modern age are much more sanitary than they used to be.

Handwashing, pesticides, antimicrobial cleaners, and triple-washed vegetables have created a separation between us and soil-based microbes.

While greatly reducing the risk of infection, sanitation reduces our exposure to good bacteria, too. 

Some experts even notice that the decrease in beneficial bacteria increases some kinds of infection.

Researchers also speculate that this hyper-sanitation is bad for other health issues. A rise in autoimmune and gut-related disorders are some of the unintended consequences of sanitation.

How soil-based probiotics promote and restore gut health

The human gut microbiome operates as an ecosystem. Soil-based probiotics give our bodies a beneficial interaction between two things.

Here is an example of how soil-based probiotics give us balance.

Healthy bacteria formed from SBO organisms can increase the acidity of the gut.

This acidity creates an environment where harmful bacteria cannot thrive.  It also promotes the production of anti-inflammatory molecules such as butyrate. Butyrate, a type of postbiotic, helps to fuel the gut lining too. 

Helps reduce IBS symptoms

Using soil-based probiotics is also likely helpful for the challenging-to-treat diarrhea symptoms that can accompany irritable bowel syndrome. Providing Bacillus coagulans is helpful for people with this condition. 

For example, soil-based probiotic supplementation B. coagulans MTCC 5856 reduces diarrhea symptoms in people with IBS in a recent study [R]. 

In fact, this probiotic helped IBS more than a low FODMAP diet or a medication used for IBS called rifaximin.

Soil-based probiotics also reduce abdominal pain as shown in people with IBS.

Bacillus reduced feelings of illness and nausea, indigestion, and flatulence as well as colitis symptoms in another study.  The study used Prescript-Assist, which is a spore-based probiotic.  

Unfortunately, the formula for this probiotic brand has since changed. So it doesn’t make the list of best soil-based probiotics at this time. 

Best soil-based probiotics for SIBO

As reviewed above, SBO probiotics are likely among the best probiotics for SIBO. This is because they are in spore form and become activated lower in the intestinal tract.  

B. clausii is one example of a spore-based probiotic that can help SIBO. It does so by helping to reduce hydrogen levels during a hydrogen breath test.

Around half of the people who have IBS also have SIBO and may or may not know it.  Luckily, soil-based probiotics help reduce both IBS and SIBO symptoms

Bacillus strains found in SBO probiotics also help to increase IgA levels. This in turn helps to enhance immune function. Increasing immunity reduces bacterial overgrowth in people who have dysbiosis, SIBO, or other gut conditions. 

Soil-based probiotics for leaky gut

Leaky gut is a common term used for a gut that is inflamed and has increased permeability.

One recent study found that daily supplementation with a 5-strain bacillus spore probiotic for 30 days led to a significant reduction in leaky gut symptoms.  

With leaky gut symptoms, there is often inflammation in the whole body.

Inflammation throughout the body is often caused by substances called endotoxins. These substances are formed when harmful bacteria like Gram-negative bacteria cause systemic inflammation.  By the way, the gut is the main natural storage of these inflammatory endotoxins in the body.

These endotoxins are released when harmful bacteria die. From the gut lining, they cross the gut barrier and end up throughout your body.  This is known as leaky gut and endotoxemia.

Luckily for us, soil-based probiotics reduce these toxic effects and reduce leaky gut as well.

Bonus: these soil probiotics reduce blood triglycerides and inflammatory biomarkers.

In a recent randomized placebo-controlled clinical trial, spore-based probiotic supplements reduced toxins in the body. 

The soil-based probiotics in this study reduced endotoxin levels by 42 percent. They also reduced triglycerides by 24%. 

On the other hand, the placebo group had a 36% increase in endotoxin.

Impressively, soil-based organisms also help to develop a strong innate immune response. This is because they increase gut immune compounds

Soil-based probiotic respiratory benefits

Not surprisingly, the benefits of soil bacteria may extend to the lungs as well.

Another double-blind, placebo-controlled study assessed the effects of Bacillus subtilis supplementation in 100 elderly people.

The goal was to see how this treatment changed respiratory and gastrointestinal illness. 

Using B. subtilis activated the immune system and significantly reduced the rate of respiratory infection.

Do soil-based probiotics help acne?

Soil-based probiotics may also be useful in the treatment of acne. This is because acne patients have altered intestinal bacteria.

Doctors as far back as the 1930s recognized the potential benefits of probiotics for the skin.

To support these theories, the diets of hunter-gatherer societies to this day have little to no acne

Meanwhile, acne rates in Westernized cultures continue to rise.

Gut bacteria influence body fat profiles.  They may improve skin fat production. Additionally, healthy gut bacteria may improve the skin bacteria.

Best soil-based probiotics from nature

Beneficial bacteria exist in natural places.

Here are ways to increase soil-based probiotics in your gut naturally:

  • Spending time outside
  • Gardening
  • Purchasing foods from local, organic farms

Spending time doing these activities helps to increase your chances of picking up these hitchhikers on the food you eat. But, make sure the soil is free of chemical use and contains lots of natural compost and humic material.

There are also some fermented foods that contain the same bacillus species.

For example, natto is a natural source of Bacillus subtilis.

Probiotic supplementation is therefore not necessary for all healthy adults.

However, adding soil-based probiotic supplements provides a consistent source of beneficial bacteria.

Are soil-based probiotics safe?

Soil probiotics have no known side effects. This is because they are natural and beneficial bacteria,

Other types of probiotics are sometimes related to mild digestive issues. This can include gas, bloating, and changes in bowel movements.  

However, these are usually short-term side effects and improve after a week or so.

You should always check with your doctor before taking any new supplement, however.

Best soil-based probiotics summary

Soil-based probiotics are emerging as beneficial for many aspects of health.  This includes benefits for reducing symptoms of irritable bowel syndrome, SIBO, and more. 

When finding the best soil-based probiotics on the market, you have several good options as listed above. 

My current favorite is MegaSpore. However, all of the supplement brands listed here are of high quality.

If you are feeling weary about taking them as supplements, you can turn to nature instead. For example, you can spend more time outdoors and eat local, organic foods to acquire these naturally.

The information on this website is for informational purposes only and should not be used as medical advice.  Always consult with your healthcare provider, preferably a healthcare provider with extensive training in food and nutrition, before changing your health regimen.

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