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Healthy Living
May 26, 2023

4 Benefits of Soil-Based Probiotics

Soil-based probiotics are used in fermentation and to improve human intestinal microbiota. How can they support our health?
Medically Reviewed
Written by
Merve Ceylan
Medically Reviewed by
Dr. Danielle Desroche

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The human gut contains the body’s richest composition of microbial organisms. Probiotics aim to change the intestinal microbiota. They are living organisms, mostly bacteria, that benefit health if ingested in adequate amounts. Probiotics are naturally found in fermented foods and are also available in the form of dietary supplements. (Source)

The normal gut microbiota can be disturbed in many ways, such as by diseases, medical treatments, and lifestyle changes. Probiotics have been used to restore healthy intestinal microbiota, but their efficacy is still being investigated. Soil-based probiotics have started gaining popularity in probiotic research because they may have better stability and survivability in the gastrointestinal environment than other probiotics. In this article, we’ll discuss the applications and potential benefits of soil-based probiotics and what you should consider before trying them.

What Are Probiotics?

Probiotics are organisms that help change gut microbiota for the host’s benefit. Commonly used probiotics include genera of Lactobacillus, Bifidobacterium, Saccharomyces, Streptococcus and Bacillus.

Probiotics may benefit health by:

  • producing organic acids such as acetic, butyric, and lactic acid, which help improve mucosal immune system of the gut
  • producing antimicrobials
  • preventing or minimizing pathogen colonization
  • improving intestinal barrier function

(Source, Source)

Soil-based probiotics for human use consist of mostly Bacillus probiotic strains and others such as Enterococcus faecium, Enterococcus faecalis, and Clostridium butyricum. They are found in soil, fermented foods, air, and the human gut microbiota. (Source, Source)

Soil-based probiotics have been used in treating animals, food fermentation, and even the production of vitamins and other nutraceuticals. Although research has been increasing in the last decade, more research needs to be done to understand the probiotic potential and safety of human health.

a leafy plant in the soil

What Are Soil-based Probiotics?

Soil-based probiotics are living organisms that are found naturally in soil. Your diet likely includes soil-based probiotics from vegetables and other foods that grow low to the ground. Non-soil based probiotics are found in various environments such as air, water, and the intestinal tracts of animals, including humans. (Source)

Probiotics are living organisms, and to be effective they must be able to survive processing, storage, and harsh conditions in the stomach. Soil-based probiotics form spores, or tough outer coatings, that are resistant to extreme conditions. Research suggests the stability of soil-based probiotics is high in heat, moisture, and stomach conditions. One study in mice showed B. cereus bacteria persisted in the mouse gastrointestinal tract for up to 18 days, showing they were able to survive and reproduce. Spore-forming bacteria won’t need refrigeration and have a longer shelf life. (Source, Source, Source)

an extended hand holding four pills

Commercial Types of Soil-based Probiotics

Bacillus Species  

Bacillus species are associated with the fermentation of soy, maize, and rice. Natto, soibum, and ugba are examples of Bacillus-fermented foods consumed in Japan, India, and Nigeria, respectively. Commercial Bacillus probiotics are B. clausii, B. coagulans, B. licheniformis, B. polyfermenticus, and B. subtilis. Let’s look at the research behind potential probiotics effects of each Bacillus species.

Bacillus Clausii

B. clausii is one of the widely used Bacillus strains due to its anti-inflammatory and antibacterial effects. A pilot study published in Therapeutics and Clinical Risk Management assessed the efficacy of B. clausii spores given as an oral solution to children with recurrent respiratory infections. The children receiving the B. clausii spores had fewer respiratory infections than an untreated control group, and when they did become ill they recovered more quickly. There were no adverse effects noted. (Source)

Bacillus Coagulans

B. coagulans is a probiotic naturally found in your body. It produces lactic acid, which has beneficial effects on gut health. On the market, B. coagulans is sometimes misclassified as lactobacillus, which is also a lactic acid producer. However, B. coagulans forms spores while lactobacillus doesn't. (Source)

According to the Natural Medicines Comprehensive Database,  B. coagulans might be beneficial for constipation and irritable bowel syndrome. (Source, Source)

Effects of B. coagulans on irritable bowel syndrome (IBS) symptoms were investigated in a randomized, double-blind, and placebo-controlled clinical trial. The B. coagulans LBSC strain was given to 20 male and female adults with IBS who had symptoms such as abdominal discomfort, cramping, bloating, and change in bowel habits for more than 3 months. Eighty days of treatment with B. coagulans significantly improved abdominal pain, nausea, diarrhea, and constipation, with no adverse events reported. (Source)

Other B. coagulans strains researched in human studies include MTCC 5856, which was shown to improve diarrhea, bloating, vomiting, stool frequency, and abdominal pain related to IBS, and SNZ 1969, which minimized symptoms of bacterial vaginosis. (Source, Source)

The most common dosage of B. coagulans is 1–2 billion colony-forming units (CFUs) orally for 1 to 3 months. However, you should always consult your health care provider for guidance on usage and proper dosage. It’s important to note that so far research hasn’t established the safety of B. coagulans probiotics for use in pregnancy and breast-feeding. (Source)

Bacillus Subtilis

Research suggests B. subtilis may help reduce serum cholesterol levels and mitigate endothelial dysfunction, a condition that causes constriction of arteries in the heart. (Source, Source)

Bacillus Licheniformis

B. licheniformis is used in biotechnology to produce enzymes, antibiotics, and biochemicals. Unlike most bacillus species, B. licheniformis is a facultative anaerobe, meaning it can grow in both the presence and the absence of oxygen. (Source)

An animal study published in Nutrients evaluated B. licheniformis effects on rat gut microbiota balance. Psychological stress was induced in rats for 4 weeks, and they were exposed to excessive antibiotics for 1 week. After, they were given B. licheniformis as a treatment for 1 month. Results showed that B. licheniformis significantly reduced serum TNF-alpha, a pro-inflammatory cytokine. B. licheniformis also changed the gut microbiota. Beneficial genera of bacteria, such as Ruminococcaceae and Lachnospiraceae, increased. In contrast, harmful genera of bacteria, such as Pasteurella, decreased. (Source)

Bacillus Polyfermenticus

Anticarcinogenic effects of B. polyfermenticus SCD were researched on the Caco-2 cell line isolated from a human colon adenocarcinoma, cancer generated from glands. Caco-2 cells treated with B. polyfermenticus SCD showed a decrease in cell growth. In the same study, colon lesions were induced in male rats using chemicals. After 10 weeks of B. polyfermenticus SCD treatment, lesions decreased by 40% compared to a control group. (Source)

Enterococcus Faecium and Enterococcus Faecalis

The Enterococcus genus includes more than 50 species. It is found in the soil and in the gastrointestinal tracts of humans and a wide range of animals. It does not form spores, but Enterococcus species are resistant to a wide range of temperatures and pH. The use of Enterococcal bacteria as probiotics is somewhat controversial, as some strains cause intestinal infections and may have the ability to pass antibiotic resistance on to other pathogens. However, E. faecium SF68 and E. faecalis Symbioflor have been marketed as probiotics and used in the treatment of diarrhea for many years without apparent problems. (Source, Source, Source)

Clostridium Butyricum

Clostridium butyricum is found in soil, vegetables, animals, and the human gut. After birth, babies' guts are progressively colonized by bacteria, including C. butyricum. The bacteria is commonly used in Asia as a probiotic. However, not all strains are safe. Some C. butyricum strains have been associated with botulism and enterocolitis in infants. (Source)

The effects of commercialized probiotic C. butyricum strain CBM588 were researched for the intestinal microbiota changes in relation to Helicobacter pylori eradication. In the randomized controlled clinical trial, CBM588 was given to patients with a gastroduodenal ulcer who were undergoing H. pylori eradication therapy. The therapy involves use of antibiotics, which often cause diarrhea as a side effect. Patients were divided into 3 groups and received no, regular, or high doses of probiotics. None of the patients in the high-dose group experienced diarrhea or soft stools. (Source)

a person holding a basket of strawberries in a field

4 Potential Benefits of Soil-based Probiotics: Controversy and Evidence

1. Anti-inflammatory and Immunostimulatory

The immune system prevents and limits infection. In a healthy person, the immune system can understand which cells are foreign and which are not. In the case of autoimmune diseases, the immune system attacks the body's own cells, causing cell damage in cells, tissues, and organs. Many autoimmune diseases cause inflammation. (Source)

Some Bacillus species promise anti-inflammatory features. In a systematic review, 44 studies were examined for the anti-inflammatory and immunostimulatory effects of Bacillus species. The majority of these studies were done in rats and mice. This review concluded that a probiotic combination with B. subtilis showed an increase in IL-10 (an anti-inflammatory and immunomodulatory cytokine) and a decrease in TNF-alpha (a pro-inflammatory cytokine). B. licheniformis was also reported to decrease pro-inflammatory cytokine IL-8. (Source)

an open extended hand against a brown dirt background

2. Antimicrobial

Probiotics are researched for their potential treatment effects on infections in the hope of limiting antibiotic use, especially in livestock raised for food. In humans, commercial Bacillus probiotics are given in addition to antibiotic therapy to support repopulation of beneficial microbes in the gut.

The ability of Bacillus species to inhibit human pathogens was evaluated in a study published in BMC Complementary Medicine and Therapies. Researchers found that Bacillus rugosus strain Khuz-2 (MH211601) can inhibit the growth of Candida albicans, a common pathogen. (Source)

3. Antioxidant

Antioxidants are compounds found in foods that can help prevent or minimize cell damage and inflammation. Antioxidants work by eliminating radical oxygen species that occur as a natural byproduct of metabolism and from environmental factors such as pollution and toxins. B. lincheniformis, combined with B. subtilis, has been shown to increase important antioxidant enzymes glutathione s-transferase and glutathione reductase. (Source, Source)

a large dark green head of cabbage

4. Vitamin production

Research has shown that some bacillus species are used in vitamin production. B. megaterium is used to synthesize vitamin B12. (Source)

Safety and Precautions: Things You Should Consider Before Taking Soil-Based Probiotics

Pathogen Species in the Genus Bacillus

Two Bacillus species are known to cause disease.

Bacillus Anthracis

Bacillus anthracis causes anthrax, which is a severe infectious disease. B. anthracis is naturally found in soil and affects animals. People can get anthrax if they come into contact with infected animals or animal products. When spores get activated, they multiply and produce toxins that cause the disease. (Source)

Bacillus Cereus

Bacillus cereus is found in many fresh and processed foods and in the environment as well. Foods not properly cooked and/or stored are common causes of B. cereus infection. Toxins produced by B. cereus include the emetic toxin cereulide, which causes nausea, vomiting, and abdominal cramps, and enterotoxin, which affects the gut mucosa and causes diarrhea. (Source)

Be Aware

Probiotics are classified as food, not medicine; therefore, they are not tested and controlled as medicines. Consequently, you can't be sure the probiotic you choose will contain the bacteria stated on the label or enough bacteria to affect the gut microbiota. The survivability of probiotics in the gastrointestinal tract is also an issue. If probiotics can not live through the acidic environment of the stomach, they can not multiply and change the microbiota of the gut. (Source)

a small pile of dirt in the palm of a hand

The Bottom Line on Soil-Based Probiotics

More research is needed to identify specific probiotics and their effects on the body. A probiotic that helps with one problem won’t necessarily help with others.

There are pharmaceutical-grade probiotics that have been tested in clinical trials. They are likely to be more effective than the supplements or yogurts sold in shops.

In the case of soil-based probiotics, although there is promising research on certain Bacillus species, more clinical trials are needed to determine their effectiveness and safety. If you’re struggling with autoimmune symptoms and looking to improve your gut health with probiotics and supplements — WellTheory’s Care Team can support you.

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4 Benefits of Soil-Based Probiotics

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