Is Bacillus Subtilis Dangerous? Primal Defense, a Review

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

I will not recommend any probiotic that contains any strains from the Bacillus genus, including Bacillus subtilis, to my clients. I will not even recommend the world-renowned probiotic Garden of Life probiotic Primal Defense. Primal Defense comes highly recommended for digestive ailments by most of the 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 being an anti-inflammatory substance producing probiotic,4 colonize the colon, and also being a bactericide (a substance that eliminates bacteria) producing strain as well. 5 Lactobacillus plantarum would also be a much easier bacteria to eliminate if it did become opportunistic, compared to most HSO’s.

The most common “probiotic” bacteria in the Bacillus genus is Bacillus subtilis which is what 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 was studied in space during the 1960s where its endospores have been theorized to be able to survive six years in space, without oxygen or substance and exposed to extreme ultraviolet radiation if space dust coated.6 Subtilis might be a more benign species from the Bacillus genus, but there are bacteria in the genus that cause health problems including Bacillus cereus, Bacillus thuringiensis, Bacillus licheniformis, and Bacillus anthracis. Now granted; there are major differences in the opportunistic and virulence capabilities of anthracis versus its gentler cousin subtilis. However, both bacteria share common characteristics: endospore production and interactions with the GALT.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 your microbiome. Spore-forming bacteria can lay 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 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 in 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 are likely to germinate in the colon from repeated exposure (if enough colony forming units are ingested) or supplementation. The bacteria may also share in a commensal relationship with probiotic bacteria for a time and continue to replicate when nutrients are available. Bacterial endospores are resistant to ultraviolet radiation, desiccation, many antibiotics, boiling, extreme freezing, and most chemical disinfectants. For example, bacteria in the Bacillus genus are spore-forming, 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 bactericides to help eliminate other bacteria and reduce competition which can be a bad thing if it starts reducing probiotic strains. Bacillus exposure early in life may help develop your gut immune system, gut-associated lymphoid tissue. However, the studies were performed on rabbits and in addition the bacteria Bacteroides fragilis was also studied and found to accomplish the same goal, and it is keystone species of gut flora. Pathogenic strains of Bacillus like B. anthracis use the gut-associated lymphoid tissue for infection. From the same 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 then more than likely it has colonized your digestive tract, and if you think that it is causing you issues I recommend following the endospore protocol in my book Fix Your Gut to try to relieve the dysbiosis.8 9 10 11

In the rare case that subtilis became opportunistic, it would be difficult to eliminate using standard antimicrobials. Antimicrobials that are used in eliminating 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 being hardy is why I am reluctant to recommend the bacteria because if Bacillus subtilis becomes opportunistic, it can be difficult to reduce its colony forming units and relieve the dysbiosis.13

There are a few known clinical case studies that mention opportunistic Bacillus infections occurring in patients with compromised immune systems.14 15 16 17 One of the case reports 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 There are even reported incidences of B. subtilis causing infections in healthy people, though it is rare.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 that it is safe to supplement with Bacillus subtilis because unless your immune system is compromised, or the bacteria become opportunistic, 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 possible scenario when 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 then rendered ineffective due to the endospores, and you become very ill from the opportunistic Bacillus subtilis infection. Do not believe that it is possible that this scenario can happen? Just replace Bacillus subtilis with another endospore bacterium, Clostridium.21 Clostridioides difficile, which is native flora for at least 10% of the population, can become opportunistic during hospitalization and heavy antibiotic use which may also be very difficult to treat!

But What About Bacillus subtilis That Are Ingested 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 it needs a host to function. Therefore, for the bacteria to propagate, it 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, but not all of the biopsies in the study showed subtilis as keystone or core species.22 For most people, ingested Bacillus subtilis passes through and does not germinate. However, the Japanese do 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 on a daily basis, but most people supplement with probiotics, like Primal Defense regularly. 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 itself in its possibility to cause intestinal issues 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. So if you decide to take a probiotic supplement, make sure it is a species that can be easily reduced.