Is Bacillus Subtilis Dangerous? Primal Defense, a Review – Updated 2025

Bacillus Subtilis: Any Potential Benefit of the “Probiotic” Bacteria in Primal Defense Is Not Worth The Risk

I will not recommend probiotic-containing strains from the Bacillus genus, including Bacillus subtilis, to my clients. I will not recommend the world-renowned probiotic Garden of Life probiotic Primal Defense. Primal Defense is highly recommended for digestive ailments by most experts in the natural health blogosphere.1 I believe that the risk of supplementing with Primal Defense is too significant, compared to any benefit towards your health that you possibly obtain from it. Lactobacillus plantarum would give you most of the same benefits. These benefits include being acid-stable (plantarum survives stomach acid)2 being immunostimulatory,3  produces anti-inflammatory byproducts,4 colonizes our colon, and is also a bactericide (a substance that eliminates bacteria), producing strain. 5 Lactobacillus plantarum would also be a much easier bacterium to reduce its colonies if it did become opportunistic, compared to most HSO’s.

The most common “probiotic” bacteria in the Bacillus genus are Bacillus subtilis, which is in Primal Defense. Bacillus subtilis is ubiquitous in nature and is found mainly in the soil. Bacillus subtilis is Gram-positive and is heavily commercially researched. The bacteria were studied in space during the 1960s, where their endospores have been theorized to survive six years in space, without oxygen or nutrients, and exposed to extreme ultraviolet radiation if coated with space dust.6 Subtilis might be a more benign species from the Bacillus genus. Still, bacteria in the genus cause infections and health conditions, including Bacillus cereus, Bacillus thuringiensis, Bacillus licheniformis, and Bacillus anthracis. Now granted, there are significant differences in the opportunistic and virulence capabilities of anthracis versus its gentler cousins. However, both bacteria share common characteristics: endospore production and interactions with your gut-associated lymphatic tissue and mucosal barrier.7

Endospores (not a true spore) are dormant Gram-positive bacteria generally from the Firmicutes phylum. The endospores are tough encapsulations that protect spore-forming bacteria from your immune system, antibiotics, antibacterials, and microbiome. Spore-forming bacteria can lie dormant in endospore form until their environment becomes favorable for faster reproduction and survival. Spore-forming bacteria form endospores when there is a lack of nutrients and can survive for a very long time till they get the nutrients they need to survive (the amino acids l-alanine, l-valine, l-asparagine, and fructose are some of those nutrients). They will germinate and multiply. Bacterial endospores may germinate within the small intestine over time if you are not producing enough bile and there are enough nutrients available, and for some, worsen small intestine bacterial overgrowth symptoms. Bacillus subtilis is resistant to stomach acid, but cannot germinate in the presence of bile. It can, however, germinate from repeated ingestion in the colon if you consume dietary nitrates or enough of the above nutrients for fermentation. Endospores will likely germinate in the colon from repeated exposure (if enough colony-forming units are ingested) or supplementation. The bacteria may also share a commensal relationship with probiotic bacteria for a while and continue replicating when nutrients are available. Bacterial endospores resist ultraviolet radiation, desiccation, many antibiotics, boiling, extreme freezing, and most chemical disinfectants. For example, bacteria in the Bacillus genus are spore-forming, and it becomes difficult to eliminate them if they become opportunistic and return to their spore form.

Most proponents say that the endospore aspect of Bacillus is a good quality in a “probiotic,” which is why many people recommend Primal Defense. Their reasoning behind this recommendation is that since Bacillus subtilis is encapsulated in an endospore, the bacteria can survive stomach acid when ingested, survive bile released into the small intestine, and propagate easily with reported exposure eventually in the colon. Most strains of Bacillus are known to be immunostimulatory and produce bacteriocins to help eliminate other bacteria and reduce competition, which can be bad if it starts reducing probiotic strains. Bacillus exposure early in life may help develop your gut immune system and gut-associated lymphoid tissue. However, studies were performed on rabbits, and the bacteria Bacteroides fragilis were also studied and found to accomplish the same goal: gut flora. Pathogenic strains of Bacillus, like B. anthracis, can infect the gut-associated lymphoid tissue. From the mentioned study: “We wonder whether germination and sporulation of B. anthracis spores in the GIT can also play some role in dissemination. Our inference from this work is that B. subtilis is probably representative of many spore formers that can use the GIT for growth and proliferation. Although it cannot yet be considered a gut commensal, it is certainly autochthonous. This seems reasonable for an organism that is going to be ingested and raises the interesting question of whether the spore evolved to enable survival in the environment or to enable survival in the GIT.” Finally, if you believe that taking a Bacillus subtilis containing probiotic, like Primal Defense is causing you issues or you are worried after reading my blogs that they colonized it might be a good idea to ask your medical professional about stopping the probiotic for two weeks and take a GI Effects stool test to see if Bacillus grows in their culture. If Bacillus grows in the culture, it likely has colonized your digestive tract. If you think it is causing you issues, I recommend contacting me for coaching to hopefully find relief.8 9 10 11

In the rare case that subtilis becomes opportunistic, it would not be easy to eliminate using standard antimicrobials. Antimicrobials that are used in removing Bacillus infections include both potent conventional antibiotics (tetracycline, vancomycin, and gentamicin) and natural antibacterial agents; both have issues in treating a Bacillus subtilis opportunistic infection successfully on their own.12 The enzyme lysozyme can be used to help break down the bacterial endospores (breaks down the lipid layer of the endospore) and biofilms that are formed, so that antimicrobial agents can relieve the opportunistic Bacillus infections. Bacillus subtilis is hardy, so I am reluctant to recommend supplementing with the bacteria. If Bacillus subtilis becomes opportunistic, reducing its colony-forming units and relieving the dysbiosis can be challenging.13

A few known clinical case studies mention opportunistic Bacillus infections in people with compromised immune systems.14 15 16 17 One case report theorizes that the main reason for such few reports of infection is that most medical professionals recognize Bacillus subtilis as a probiotic. Therefore, the bacteria are not tested as the cause of disease or death in most potentially infected patients. One study also mentions that Bacillus subtilis may cause liver toxicity in some people.18 Although rare, there are reported incidences of B. subtilis causing infections in healthy people.19 Most strains of Bacillus subtilis can produce biofilm, and some also have virulence potential.20 Bacillus subtilis can also inherit virulence genes from incorporating weakened or dead bacteria in a process known as horizontal gene transfer. Proponents will say it is safe to supplement with Bacillus subtilis because, unless your immune system is compromised or the bacteria become, it is a beneficial “probiotic.” The fatal flaw with this line of thinking is that no one can predict when their immune system may become compromised.

A scenario in which one’s immune system could become compromised is as follows: You get into a severe car accident, and because of an injury to your intestinal tract, your immune system becomes compromised. You are then given antibiotics to stop the sepsis. From taking the antibiotics, you decimate your natural probiotic gut flora. Bacillus subtilis survives because it is in a protective endospore, and it becomes opportunistic, inheriting virulence and antibiotic-resistant genes from your deceased microbiota to increase its chances of survival. Most conventional antibiotic treatments are ineffective due to the endospores, and you become very ill from the opportunistic Bacillus subtilis infection. Do you believe that this scenario can happen? Just replace Bacillus subtilis with another endospore bacterium, Clostridium.21 Clostridioides difficile, native flora for at least 10% of the population, can become opportunistic during hospitalization and heavy antibiotic use, which may be very difficult to treat!

Finally, multiple studies have found that Bacillus subtilis may produce histamine. I have coached many clients who developed or worsened histamine intolerance and mast cell activation disorder from taking probiotics containing Bacillus subtilis. If you experience multiple symptoms that develop or worsen, including itching, hives, asthma, postnasal drip, diarrhea, abdominal pain, bloating, GERD, insomnia, anxiety, racing thoughts, brain fog, and, rarely, anaphylaxis while taking a probiotic that contains Bacillus subtilis, contact me for coaching. I will hopefully be able to help you find relief.

What About Ingested Bacillus subtilis From Eating Natto?

There is some evidence that Bacillus subtilis might be normal gut flora for a small percentage. Bacillus subtilis, as normal gut flora, has been theorized because the soil is known only to be a reservoir for the bacteria and needs a host to function. Therefore, for the bacteria to propagate, they must be able to colonize higher lifeforms. Some human intestinal biopsy samples have shown that subtilis does populate the gut in a small percentage of people. Still, not all of the biopsies in the study showed subtilis as a keystone or core species.22 For most people, ingested Bacillus subtilis passes through and does not germinate. However, the Japanese use Bacillus subtilis to produce a fermented soybean product known as natto. The colony-forming units of Bacillus subtilis in natto and most supplements are in the billions.23 Organic natto is an excellent source of vitamin K2 for vegans. On average, the Japanese do not consume natto daily, but most people supplement with probiotics, like Primal Defense. Some subtilis they ingest during supplementation may cause opportunistic dysbiosis in the future. The problem with the bacteria is not the colony-forming unit amount consumed; the issue stems from the Bacillus subtilis in its ability to cause intestinal problems if your immune system is weakened.

I hope I have convinced you to think before supplementing with Primal Defense or any supplement that contains Bacillus subtilis. Try to supplement with other safer non-spore-forming probiotics. Remember, any probiotic can become opportunistic. If you take a probiotic supplement, ensure it is a species with easily reduced colonies.

 

  1. http://www.bulletproofexec.com/the-red-meat-scapegoat-the-new-york-times-carnitine-heart-disease-and-science/
  2. http://www.ncbi.nlm.nih.gov/pubmed/15702859
  3. http://www.ncbi.nlm.nih.gov/pubmed/19120072
  4. http://www.ncbi.nlm.nih.gov/pubmed/15985548
  5. http://link.springer.com/article/10.1007%2Fs12602-013-9136-0
  6. http://web.mst.edu/~microbio/BIO221_2009/B_subtilis.html
  7. http://www.ncbi.nlm.nih.gov/pubmed/10974126
  8. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC127533/
  9. https://www.ncbi.nlm.nih.gov/pubmed/9891797
  10. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3993344/
  11. https://www.ncbi.nlm.nih.gov/pubmed/3106749
  12. http://jcm.asm.org/content/36/1/325.full?ijkey=1903da10e5f13b43cfe75e8ae3b2de7e0ee01a92&keytype2=tf_ipsecsha
  13. http://jcm.asm.org/content/36/1/325.full?ijkey=1903da10e5f13b43cfe75e8ae3b2de7e0ee01a92&keytype2=tf_ipsecsha
  14. http://jcm.asm.org/content/36/1/325.full?ijkey=1903da10e5f13b43cfe75e8ae3b2de7e0ee01a92&keytype2=tf_ipsecsha
  15. http://www.ncbi.nlm.nih.gov/pubmed/3145864
  16. http://informahealthcare.com/doi/abs/10.1080/089106000435491
  17. http://www.ncbi.nlm.nih.gov/pubmed/22918867
  18. https://goo.gl/gd2Mj5
  19. http://www.journalofhospitalinfection.com/article/S0195-6701(16)30449-2/fulltext
  20. https://www.researchgate.net/publication/299538914_Identification_and_Pathogenic_Potential_of_Clinical_Bacillus_and_Paenibacillus_Isolates
  21. http://www.avianbiotech.com/diseases/clostridium.htm
  22. http://www.sporegen.com/pdfpapers/Gut%20microbe/Hong2009.pdf
  23. http://maxwellsci.com/print/ajfst/v7-704-708.pdf