Exploring the Potential Health Risks of Bacillus Subtilis Probiotic Strains and Why We Chose to Exclude It

Sep 15, 2025by Nelson Montelauro

Exploring the Potential Health Risks of Bacillus Subtilis Probiotic Strains and Why We Chose to Exclude It

Probiotics have become a cornerstone of many people’s health routines, offering an array of benefits for digestive health, immunity, and overall well-being. Among the most problematic of the popular probiotic strains is Bacillus subtilis, a spore-forming bacterium that has garnered attention for its ability to survive harsh environments and its potential to promote gut health.

However, while Bacillus subtilis offers promising advantages, it also carries certain risks that might make it unsuitable for some individuals. One study found that Bacillus subtilis may cause liver toxicity in certain individuals. In this article, we’ll explore the potential health problems associated with Bacillus subtilis and why, at Dr. Clark Store, we’ve chosen a different probiotic strain, Lactobacillus plantarum, for our formula, along with only the safest, most synergistic strains in a wide spectrum probiotic geared towards restoring microbial diversity and balance.

1. Gastrointestinal Disturbances

As with any probiotic, some individuals may experience gastrointestinal issues when introducing Bacillus subtilis into their regimen. This strain has been shown to cause mild, yet sometimes uncomfortable, side effects such as bloating, gas, and a feeling of fullness. These symptoms are generally transient but can be bothersome, especially for people who have sensitive digestive systems. It’s important to note that while Bacillus subtilis can offer health benefits, its potency may lead to disturbances, particularly when taken in high doses or when an individual is not used to probiotic supplements.

2. Risk of Infection in Immunocompromised Individuals

One of the primary concerns with Bacillus subtilis is its potential to cause infections in immunocompromised individuals. While Bacillus subtilis is typically safe for healthy people, those with weakened immune systems, such as people undergoing chemotherapy or individuals with HIV/AIDS, are at an increased risk of infection. Probiotics, including Bacillus subtilis, have been associated with rare but serious infections in these vulnerable groups. The risk of infection is not unique to Bacillus subtilis but is a general concern with many probiotic strains that can colonize the gut and potentially enter the bloodstream under the right conditions (PMC).

3. Antibiotic Resistance Concerns

Another issue with Bacillus subtilis is its potential to harbor antibiotic resistance genes. Some strains of Bacillus subtilis may carry genes that make them resistant to antibiotics, which poses a concern if these genes are transferred to harmful pathogens in the gut. Antibiotic resistance is an increasingly significant public health issue, and there’s growing concern that probiotics, like Bacillus subtilis, could contribute to the spread of resistance. This is especially concerning for individuals who may need antibiotics to treat infections and may find those antibiotics less effective due to resistant bacteria in their system (National Library of Medicine).

4. Potential for Toxin Production

Certain strains of Bacillus subtilis are capable of producing toxins, such as the hemolytic enterotoxin Hbl. These toxins are capable of inducing harm, particularly in individuals who may be sensitive to them. Although not all Bacillus subtilis strains produce these toxins, the risk remains, especially if an individual consumes a poorly tested or improperly labeled product. Some probiotic companies may not fully disclose the specific strain or whether the strain is toxin-producing, which increases the risk of exposure to harmful substances. Therefore, it’s essential to ensure that any Bacillus subtilis strain used in supplements is non-toxigenic and has been thoroughly tested for safety (PMC).

5. Lack of Standardization in Probiotic Products

The probiotic market is vast, and unfortunately, not all products are subject to stringent testing or regulation. Some Bacillus subtilis supplements may contain contaminants or inaccurate labeling, leading to potential health risks. Without proper standardization, there is no guarantee that the strains used are as effective or safe as claimed. This issue is exacerbated by the fact that many probiotic formulations, including those with Bacillus subtilis, are not always backed by robust clinical evidence, making it difficult for consumers to know whether they’re receiving the benefits promised by the manufacturer. The use of third-party testing and transparent labeling is essential when selecting a probiotic product to ensure that it is both safe and effective (Source).

Why We Chose Lactobacillus plantarum Over Bacillus subtilis

While Bacillus subtilis certainly has its place in probiotic therapies, we’ve opted to use Lactobacillus plantarum in our probiotic formula for several important reasons. Lactobacillus plantarum is an acid-stable strain, meaning it can survive the acidic environment of the stomach and reach the intestines where it is needed most. This stability ensures that the probiotic strain is more likely to have a positive impact on digestive health.Furthermore, Lactobacillus plantarum is known for its immunostimulatory properties, meaning it can help stimulate and support the immune system. It produces anti-inflammatory byproducts, which can help reduce systemic inflammation, a root cause of many chronic health conditions. This makes Lactobacillus plantarum particularly beneficial for individuals dealing with inflammation-related issues, such as irritable bowel syndrome (IBS) or autoimmune disorders (Healthline). Another benefit of Lactobacillus plantarum is its bactericidal properties. It produces antimicrobial peptides that help eliminate harmful bacteria in the gut, improving the overall balance of gut microbiota. This is particularly important in maintaining gut health and preventing the overgrowth of pathogenic organisms. Additionally, Lactobacillus plantarum can colonize the colon, where it helps maintain a healthy gut microbiome and promotes optimal digestive function.One of the key reasons we prefer Lactobacillus plantarum over Bacillus subtilis is that it is easier to control if it ever becomes opportunistic. While Bacillus subtilis can be an opportunistic pathogen in rare cases, Lactobacillus plantarum has a much lower risk of such behavior. This makes it a safer option for a broader range of individuals, including those with sensitive digestive systems or those who may be more prone to infections

Conclusion

While Bacillus subtilis is a powerful and resilient probiotic strain, it’s important to be aware of the potential risks associated with its use, particularly for individuals with weakened immune systems or those concerned about antibiotic resistance. The possibility of gastrointestinal disturbances, infections, toxin production, and lack of product standardization should not be overlooked when considering probiotics.

At our company, we’ve chosen Lactobacillus plantarum for our probiotic formula because of its proven benefits, including its ability to survive stomach acid, support immune function, reduce inflammation, and maintain a healthy balance of gut bacteria. With Lactobacillus plantarum, we aim to provide a safe, effective, and highly beneficial probiotic option for our customers, ensuring that they receive the best possible support for their digestive and overall health needs.

References

Bacillus subtilis: Antioxidant, Cytotoxic, and Antibacterial Activities. (2022). Phytochemistry Reviews.
Probiotics: What They Are, Benefits & Side Effects. Cleveland Clinic. Link
Bacillus Subtilis Safety and Efficacy in Probiotic Products. (2020). Journal of Applied Microbiology.
Lactobacillus plantarum: Benefits and Effects. (2023). Healthline. Link
Probiotics for Digestive Health: Why Lactobacillus Plantarum Is Our Preferred Choice. Dr. Mark Hyman. Link
Richard V, Van der Auwera P, Snoeck R, Daneau D, Meunier F. Nosocomial bacteremia caused by Bacillus species. Eur J Clin Microbiol Infect Dis. 1988 Dec;7(6):783-5. doi: 10.1007/BF01975049. PMID: 3145864.
Oggioni MR, Pozzi G, Valensin PE.Galieni P, Bigazzi C. 1998. Recurrent Septicemia in an Immunocompromised Patient Due to Probiotic Strains of Bacillus subtilis. J Clin Microbiol 36:.