The Best Soil-Based Probiotics

Last Updated on April 26, 2024 by Lindsay Delk, RDN

Did you know that the microbes in your gut weigh 1 to 2 kg (2.2 to 4.4 pounds) in total?! That is about the same weight as your brain! And, appropriately, these gut microbes are sometimes called your second brain. Having a healthy gut can go a long way toward overall good health and mental wellness. These best soil-based probiotics are one way to make your gut healthy.

This post was written by Lindsay Delk, RDN. It is for informational purposes and is not intended to replace medical advice or instructions given by your healthcare provider. 

This post may contain affiliate links. If you purchase through these links, I will earn a small commission at no extra cost to you.

Hands holding to soil to represent soil-based probiotics

What Are Soil-Based Probiotics (SBO Probiotics)?

Probiotics are live microorganisms that provide a health benefit to the human body. Soil-based probiotics are probiotics that are naturally found in soil. They are sometimes called soil probiotics or soil-based organisms probiotics (SBO probiotics). Soil-based probiotics can improve your health by directly introducing healthy soil bacteria into your large intestine.

Your gut microbiota is the total community of bacteria in your gut, both good and bad bacteria. If this community has more bad bacteria than good bacteria, it can cause many problems. 

Probiotics are the good, beneficial bacteria. So, putting probiotics into your gut helps balance your microbiota so that the harmful bacteria don’t outnumber the healthy bacteria and cause symptoms.

Are spore-based probiotics the same as soil-based probiotics?

The most common soil-based probiotics are Bacillus bacteria. They are also spore-forming probiotic organisms, so soil-based probiotics are often called spore-based probiotics. 

The ability to form spores is what makes SBO supplements shelf-stable and able to survive the travel through the digestive tract.

Are Soil-Based Probiotics Better Than Regular Probiotics?

Regular probiotic products have plenty of research showing their ability to support a healthy gastrointestinal tract. But what are soil-based probiotics, and how are they different from traditional probiotics? What are the benefits of soil-based probiotics, and are SBO probiotics better?

The benefits of soil-based probiotics are the same as regular probiotics, but they have a few advantages:

>Durable & survivable

A major difference between SBO probiotics and regular probiotics is that SBOs can tolerate your stomach acid much better, which helps them make it to the lower GI tract where you want them to be. If the good bacteria in your probiotic supplement are killed by the acid in your stomach before they even reach the gut, then they obviously aren’t as helpful. 

The reason that soil-based probiotics are able to tolerate the travel through the digestive system goes back to the spores that they form. These spores form a hard shell that make them very stable and resistant to acid and other extreme conditions. 

Once they reach the intestines, the spores can then change into the form that colonizes the gut. SBO probiotics are also able to colonize the gut  better than regular probiotics, which means they can stay in the gut longer. 


SBO probiotics don’t need to be refrigerated, making them more convenient for storage and for travel.

Infographic on the effects of probiotics and prebiotics on the gut microbiota
Infographic from

What Are the Benefits of Soil-Based Probiotics?

All probiotics offer these positive effects, not just soil-based organism probiotics:

  • Diversifies your gut microbiota, which in turn…
  • Supports gut health/GI health, which in turn…
  • Supports digestive health
  • Improves depression symptoms by helping to regulate the neurotransmitters in your brain
  • Supports your immune system
  • Reduces diarrhea
  • Improves abdominal pain, bloating, and possibly constipation
  • Improves irritable bowel syndrome (IBS) severity
  • May reduce “leaky gut” by helping maintain the integrity of the gut lining
  • Lowers inflammation
  • Has antimicrobial properties
  • Reduces the negative effects of antibiotics
  • Decreases muscle soreness after exercise

Soil-Based Probiotics for SIBO (Small Intestinal Bacterial Overgrowth)

SIBO happens when there is too much bacteria in your small intestine. You may experience gas, diarrhea, and/or bloating. 

Some health professionals recommend taking soil-based probiotics for SIBO. Soil probiotics may not exacerbate symptoms of SIBO like regular probiotics can. Soil-based probiotics may increase the effectiveness of your antibiotic treatment for SIBO. Bacillus clausii seems to be the most effective probiotic for SIBO.

Are Soil-Based Probiotics Safe?

Some have questioned the safety of SBOs. But just like with many plants and bacteria, there are good soil-based organisms and bad ones. Some species or strains of SBOs are not safe for human consumption but that does not mean that there aren’t others that are very safe. 

Many safety studies have shown no major negative effects from the SBOs found in probiotic supplements. There are 2 SBOs that are not safe (Bacillus anthracis and Bacillus cereus), but these are not used in probiotic supplements.

Probiotics aren’t well regulated by the Food and Drug Administration (FDA), so make sure you choose a product from a reputable manufacturer that has the good manufacturing practices (GMP) certification.

If you are immunocompromised, SBOs may not be safe for you. Be certain to check with your doctor before taking SBOs to make sure they can’t overcolonize in your gut.

SBO Probiotics Side Effects

SBO probiotics side effects can be the same as the side effects of regular probiotics. Side effects of SBO probiotics might include a mild upset stomach, diarrhea, bloating, and/or gas. 

The side effects of SBO probiotics usually pass after a few days. If not, you may need to try a different strain or talk to your doctor.

Soil-based organism probiotics might cause more serious problems for immunocompromised individuals, so always check with your doctor before taking SBO probiotics.

The Importance of the Strain

When using probiotics, it’s important to understand each type of bacteria in the product you are considering.

Bacteria are classified in the following levels from the most general to the most specific:

  • Kingdom
  • Phylum
  • Class
  • Order
  • Family 
  • Genus
  • Species
  • Strain

The strain is the series of letters and/or numbers after the species name. So, using Bacillus coagulans MTCC 5856 as an example: Bacillus is the genus, coagulans is the species, and MTCC 5856 is the strain.

You need to consider the strain because different strains of the same species may have different characteristics and health effects.

Many probiotic supplement labels don’t list the strain. I recommend choosing a product that provides the CFU count, dose, genus, species, and strain on the label.

Drawing of the gut with a microscope showing bacteria characters

The Best Soil-Based Probiotics Strains

Based on the current research, these are the best soil-based probiotics to look for on the supplement label. Look at the graphic below to make sure you are buying a supplement with the best SBO probiotics strains for your needs.

>Bacillus coagulans (B. coagulans) 

B. coagulans is the most well-studied species of soil-based probiotics. All of these strains have been generally recognized as safe (GRAS) by the FDA. Research has found the following benefits for these strains:

>Bacillus subtilis (B. subtilis)

  • CU1
    • Qualified presumption of safety by the European Food Safety Authority
    • Stimulated immune responses

>Bacillus clausii (B. clausii)

  • UBBC-07
    • Generally recognized as safe by the FDA
    • Decreased the duration and frequency of diarrhea in children
Infographic on how to read a probiotic label
Infographic from

Using the Best Soil-Based Probiotics for the Most Benefit

  • Consider the CFU (colony-forming unit) count.

You can find products with 1 billion to several trillion CFUs. More is not necessarily better. 

You should take the lowest dose that still gives you the full benefit. This will be different for each person and each probiotic strain. 

I recommend that you start with a lower CFU count and increase it as needed and as tolerated to find the optimal CFU count for you.

  • There is not one particular strain of probiotic that is the “best.” 

The best SBO probiotics strain really depends on the needs of the individual. Usually, the overall goal is to increase gut microbial diversity, so using a probiotic supplement with more than one strain is beneficial. 

But, you may also choose a specific strain or strain combination that sound research has proven to accomplish a specific health goal.

  • MegaSporeBiotic is the specific SBO probiotic supplement used in many of the studies. We have also used Youtheory spore probiotic supplement and had good results.

Probiotics, the Gut-Brain Axis, and Mental Health

  • The human gut microbiota plays a role in regulating neurotransmitters, such as serotonin, GABA, and dopamine. When there is less diversity in the gut microbiota, you might experience GI and psychological distress, disturbing your mental health.
  • Research also indicates that inflammation in the body can cause symptoms of depression. According to this study, inflammation can be caused by bacteria leaving the gut and getting into other parts of the body (leaky gut). Probiotics could be one therapy to help heal a leaky gut and, therefore, reduce inflammation and the symptoms of depression.
  • This study found that Bacillus coagulans MTCC 5856 was very effective in reducing the symptoms of major depression and IBS symptoms in IBS patients.
  • This recent study found that Bacillus coagulans LBSC eased IBS symptoms and anxiety in IBS patients.
Carrots, bell pepper, onion, and zucchini on a vegetable skewer

Other Ways to Support Gut Health & Mental Health

  • Manage your stress. Stress changes the gut microbiota and increases inflammation.
  • Exercise regularly. Try to get at least 150 minutes of physical activity each week.
  • Get enough sleep. Adequate sleep increases the diversity of the gut microbiota.
  • Only take antibiotics if necessary.

Because a healthy gut is vital for overall health and mental wellness, talk to your doctor about taking these steps and adding the best soil-based probiotics supplement to your daily routine.  And read my article about the pillars of a good mental health diet here.

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