Is Bacillus Subtilis Dangerous? Primal Defense, a Review

Is Bacillus Subtilis Dangerous? Primal Defense, a Review

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.

  1. John, the information that you present on Bacillus Subtilis is absolutely correct and well researched. Your book and coaching have been helpful in helping me deal through things.

    Taking bacillus subtilis as a “probiotic” is not worth the risk. I experienced this for myself, when for over the past year I have been dealing with the harmful effects of bacillus subtilis. When I took these pills in an attempt to support my immune system, I experienced an upset stomach, vomiting, and then shingles. After rounds and rounds of antibiotics, it became more manageable and it turned out I had candida at the same time which allowed the bacillus subtilis to escape the intestinal track and travel to other parts of my body. This is hard to get rid of, as the bacillus subtilis continue to populate. NAC pills help with the symptoms. The effects of bacillus subtilis vary from person to person. If I can warn anyone, it is not worth the risk to see how it will react in you. There are too many other ways and options to build healthy bacteria in the body, Thank you.

    • Hey,

      is it the same for every bacillus subtilis strains? How about DSM 21097?


  2. John – While I do believe that your research and information dissemination is well intentioned, I do not believe you are presenting both sides of the story equally.

    There is a ton of research on SBOs along with a links/citations to number double-blind clinical human studies which show the safety of several strains of SBOs.

    I would love to see you write a blog post addressing the evidence posted by Lucy Mailing at regarding the safety of several strains of SBOs.

    For your audience: For anyone interesting in reading about the information Mr. Brisson does not mention please take a look at:

  3. Yes, natto isn’t eaten daily on average, but that’s because natto is only consumed in part of Japan. Where natto is common, it is eaten nearly every day for breakfast.

    There’s also an interesting study from Thailand: those who were colonized with B. subtilis were always negative for MRSA. I can understand your trepidation with some of the bacteria in the Bacillus genus, but I’m not particularly worried about subtilis or coagulans.

  4. I am interested in whatever would help MRSA. My husband was in a hospital. MRSA traveled from a bed sore to his spine (osteomyelitis) to his spine. The wound , two years later is still colonized with MRSA and pseudomonas aeruginosa. I think I have MRSA as well. Twice I have had minor irritation in my left nostril and developed painful pustules. This last one traveled to my left side throat and putules in my left eye. I had a red line traveling down my face. I did two courses of oral antibiotics. I still have fevers and feel awful. still ahve throat sore and eye, very swollen painful glands. I am his caretaker and I need my health and his wound to heal. Keeping the colonization in check does not allow for skin healing of my husbands wound.

  5. Hello John
    This article was sent to me after visiting several naturopathic doctors for a chronic viral type infection that I can’t seem to get rid of. I read both your part 1 & 2 of this article and was wondering if you could tell me in brief what kind of symptoms a overgrowth/toxicity of bacillus subtilus would cause? I’m interested to see if any of mine could be linked!! Thank you!

  6. I was told that bacillus subtilis 3 will help fight H. Pylori. Not true? What do you recommend using for H. pylori? Thanks.

  7. John,

    Thank you for your posts. I have a serious problem with my health. All the doctors keep saying that I am healthy which I know is wrong. Approximately I get an infection each 6th mounth which leaves some disability. I know that I am colonized internaly with at least staphylococcus aureus and enterococcus faecalis at places these bacteria should not be. I searching for anything that will give me hope. This article ( is currently my best hope and since I read it I start using sporebiotic with bacillus subtilis each day. What do you think I should do?

    • I would ask your healthcare professional about looking into the use of the natural antimicrobial Allicin which works well against Staph to my knowledge. There are many things you can do to bolster your immune system, make sure you are getting enough natural sunlight to produce endogenous vitamin D depending on where you live, you might only be able to do it in the Spring and/or Summer. Making sure you have good sleep hygiene to produce melatonin and ingest healthy sources of Omega 3 fatty acids to help increase mitochondrial function and reduce inflammation. Good luck!

  8. Ok so this. All of this. I took a spore probiotics all last winter after trying to fix my gut problems that came about from food poisoning and then the reintroduction and became sick with high fevers and swollen nodes that only went away with antibiotic. This happened three times. Through moving and inability to get amazon packages easily I stopped taking them all summer. Fast forward to Monday this week, I found a cheap spore probiotics with B coagulans, subtilis, and clausii. Took two doses Monday and wouldn’t you know Tuesday I woke up with a fever and swollen lymph nodes in my neck again. This post has really made me feel a lot better and not crazy that these probiotics could be the cause of my illness. Thank you for writing. Going out to get the probiotic you suggested. Thank you thank you! I’m not immunocompromised though I’ve been on many many antibiotics in my short life at 26. I learned the tools to never need antibiotics for sinus infections anymore. Here’s to empowering me to making myself stronger once again.

  9. Hi, what’s you comment on this article ?

    • The study was done in worms and reaches vast conclusions.

      “Could probiotic B. subtilis extend human life expectancy? Ranking at the top of human welfare, Japan exhibits the highest world longevity (84 years and 81 years, for female and male, respectively), and home to more than 65,000 centennial persons. Together with a longer longevity, a good quality of life and strong health are desired in elderly people. Japan also exhibits the highest healthy life expectancy (78 years for both sexes at the time of birth). What is the secret of the healthy Japanese longevity? Aging depends on genetic and environmental factors, including dietary habits. In the regular diet of the Japanese population exists the millenarian food called natto (“vegetable cheese”), a natural food that consists of soybean fermented by cells of B. subtilis. Because B. subtilis is the active ingredient of this popular and ancient food, it is tempting to pay attention to this probiotic bacterium, which might naturally contribute to the long and healthy longevity of Japanese people. Taking into consideration that probiotic Bacilli can be incorporated in a daily and safe dose (i.e., 1.0-2.0 x 109 spores/day) in many types of human foods and beverages; the centenarian Metchnikoff hypothesis; and our results, it might be worth investigating whether the regular consumption of probiotic B. subtilis in human food might decrease the rate of aging and detect and stamp out disease because of downregulation of insulin/IGF-1 signaling and enhancement of innate immunity, respectively, at the earliest possible moment. Future studies will address the validity of this provocative hypothesis, elucidate the detailed biochemical mechanism responsible for Bacillus-induced ILS/DR-dependent long longevity and its contribution to the current war against the second cause of natural death: aging (Figure 1).”

      First off the Japanese do not consume natto as often as the study indicates. What about other cultures like the Mediterranean that live as long of lives, they do not eat natto. Would ingestion of more plant matter, eating less refined sugar, frequent seafood ingestion, sunlight exposure, proper sleep hygiene, be better reasons they live healthier lives?

      • I am interested in taking a probiotic for managing my health. A male, age 85 but I need help in selecting a very good product, not requiring cold storage. Please suggest one or a couple that I can buy. Thank you very much.

  10. I’m glad that I found this website. I was a little wary when I bought this probiotic, after reading that the bacteria were somewhat indestructible.
    Can you possibly recommend a probiotic simply for maintaining good health? (I’m actually hoping to shrink down pancreatic cysts.)

  11. Hi,

    Just wanted to add my bacillus subtilus experience to the discussion. So I bought some hummus at Whole Foods. Wasn’t sure which I would like, so I bought 3 different containers. One was WF brand, one was Peppi’s (a local brand) and one was Cava. Started eating the hummus at 1PM, was violently vomiting by about 2:45. And I do mean violently and repeatedly. It was a really terrible experience. I called WF the next day. They did not pull anything off of the shelves, because it was just one complaint. I really did not want this to happen to anyone else. I was lucky to be at home. If I had been out, I would have been puking all over myself. I ended up taking the containers to the Health Dept. They tested them and found something unexpected. Yep. Bacillus subtilus. B.S. can cause food poisoning, though it does so more rarely than other substances and it’s symptoms include rapid onset and acute and projectile vomiting. My experience with this substance was very bad. I will never eat commercial hummus again. It was in two of the containers, the WF and the Peppi’s, but it was prob. only in one and I cross contaminated the other with a pretzel or spoon. The Health Dept. went to WF and is conducting more tests to find out how this happened. I say beware of b. subtilus!

  12. John I liked the article and thought it gave a different look at using a spore former as a probiotic. I believe you made a error though when you said that BS was used to make Natto, I think its B. Coaglans.

  13. This is paranoid. Opportunistic infection w well studied commensal bacteria is rare. The odds of you not having any potentially harmful bacteria in your gut is slim to none.
    The bacteria work in a balance. Subtilis is expensive to use bc it’s a temporary colonizer. You’d seriously need to keep taking large amounts. While I don’t discount supplements evidence shows dietary modifications such as eating fermented foods including yogurts and fermented vegetables alter gut bacteria more. Some scientists think supplementation is a waste bc we seem to
    Maintain what we are born with. At least if you do the dietary changes you are eating healthier anyway

  14. And that’s the problem writ large for me – the idea of ‘safe intervention’ in the absense of diagnosis or careful thought. However this applies as much or more to the unquestioned problem of using antibiotics without first identifying their target. That’s the elephant in the room. So i take your point – i really do! But the scenario you build involves overlooking the antibiotic trigger or simply accepting it as unavoidable, or maybe simply not discussing it as the elephant in the room. Yet you point out that many with native gut c diff could be triggered in the same way. yes it’s one more risk. But how does one play off the benefits of l plantanum against b subt.within their biome without trying them? The answer is the can’t. Everyone has to weigh the pros and cons with huge amounts of self education and trial and error. And at the end of the day the mechanism of the probiotic alone can’t be determined with any evidence to be a strong reason for paranoia.

    Personally the elephants in the room are the blunt instrumentation of antibiotics vs the shots in the dark that are most probiotics.

    Everyone will make their own decisions but personally i think b ingantis and moderated intake of fermented foods is the best course of action. Whole and traditional foods at least have empirical merit if not scientific necessarily. It certainly seems it’s hard enough to police / vet the perils of food sources without this level of speculation, unless of course it is to merely observe that mindless supplementation is potentially dangerous. But there are many who are desperate for help and frankly there are very few better options. And when the medical fraternity reaches for antibiotics almost constantly and without success for their patients long term, the idea of probiotic danger has to be measured against the supposed danger of probiotics.

    • More simply it seems the problem is this: supposition
      is not science… nor even empirical or traditional knowledge. sb subt.might be not worth the risk… for some. But for that matter neither are antibiotics in many similar scenarios. If your life is thought to depend on antibiotics I’d say you’re in bigger trouble than theorising that b subt might pose some hitherto unobserved risk.

      And even so, as you rightly point out c diff might be a problem anyway in this scenario. So is there an extra theoretical risk from b subt. Maybe. Doesn’t seem like a strong pretext for the severity of the warning unless people out there are popping probiotics purely for leisure.

  15. What every article on the web on this topic fails is that none gives informations on how remove or kill these soil bacteria from the body.
    I’ve took all those kind of Soil bacteria like Prescript-Assist, Lateroflora, Threelac…
    and i ended with arthritis. Lots of joint pain.

  16. Thanks for the article! I really need your help!!! I would gladly pay you, or order multiple books to bring me to a solution!

    I have had a weird problem for over 20 years and I only recently was able to determine the cause. Whenever I eat food containing phytic acid my body get’s all twisted up. Muscles all over my body get tense. After about 6-12 hours, when the Phytic Acid is leaving my body I slowly have what I think are called myofacial releases, where the tension gradually releases. It is very uncomfortable. You can literally hear muscles/tendons in my face, head, neck, back, hips. actually cracking.

    Other evidence that Phytic Acid is the culprit is that consuming lemon juice or apple cider vinegar seems to quicken the process. From what I have read, these help to breakdown or block the negative effects of Phytic Acid. The best evidence is that when I eliminate phytic acid from my diet, I do not get these symptoms.

    I am now seeking a permanent solution via probiotics, restoring whatever it is that I am missing in my gut. Working backwards I have figured out that phytase is the enzyme that breaks down phytic acid. I just purchased a probiotic with Bacillus Subtilis, which I see you don’t recommend.

    First, I see you say Bacillus Subtilis from Natto is safe, will I still get the bacteria if I order the dried version? How should I make this so I get the benefit of the bacteria?

    What other bacteria/probiotic should I take that will safely produce the phytase I seem to be missing?

    If you provide me with a thorough answer I will order your book. If your available for consult let me know as well.


  17. I jus want to say to the Author, I like the way you handle your comments and defending your position in a respectful way. You don´t see this a lot online. Therefore, it was a pleasure for me to go through all the comments, seeing a range of stories and opinions. Good work!

  18. Dear author,

    Considering the widely consumed dish natto, and similar dishes throughout Asia (7,000+ tons annually of natto alone), I request your article include objective information about B. subtilus use in foods for centuries. B. subtilus is now used for supplement production of d-ribose as well, with great benefit for athletes, and the symptoms of CFS, fibromyalgia, and other chronic illness diseases. Your opinion here may be scaring people far too much, preventing them from trying something that could be a big part of their road to recovery. Thank you.

    • I mentioned that eating Natto would be for some people as long as they do not have histamine issues. B subtillis in Natto would be different than what is in a supplement in CFU.

  19. I wasn’t ever interested in probiotics until recently (and I had no idea of HSOs until now), but I’m half Japanese and eat what I think is a large amount of natto because it’s cheap and an easy dinner. Now I am a little concerned. Should I be taking a probiotic of different bacteria to keep the b.subtilis in check?

    • Eatting natto occasionally is fine, I see no issue, it is different than supplemental B. subtilis.

      • stop scaring people. this Probiotic has literally saved my gut. I want actualo evidence of people dying or it becoming opportunistic.. not comparing it to things that have been known to do what you say. you need more proof before you start making claims like this

  20. Wow! Thanks for this article. I am just recovering from SIBO (have just finished 2 weeks of Rifaxamin and Metronidazole), and I need to repopulate with probiotics. I am very weary of them, because the SIBO came on after taking a very strong probitioc/prebiotic supplement from Renew Life. I am extremely reluctant to take them, but everyone says that keeping good bacteria in your gut is so important to prevent problems. So I have been researching the best options. Everyone keeps saying soil based, soil based, soil based for SIBO – and after going through SIBO I am very concerned and cautious about taking something that could cause the SIBO to come back or create another problem. Thank you so much for this article, and sharing your research.

    • You might look into Mutaflor. There is some evidence that the difference between normal folks and those with gut issues are the concentration of e. coli in the gut. The strain of e coli in Mutaflor has been genetically sequenced and examined for any virulence genes and has a 100 year track record of safety. It also has no antibiotic resistance genes, and creates no spores. Therefore, it would be easy to remove if it were to cause problems.

      This fellow has a good article which explains how the lack of e coli in those with IBS may be a reason for their symptoms. He also goes on to explain that lactobacillus may be contraindicated in some people with SIBO or IBS. So you are not without justification to be distrustful of some probiotics.

  21. What a post of debate on Bacillus Subtillis! I’d say – based on much reading from practitioners & researchers, listening to educated, knowledgeable researchers and first hand reviews from many long term users, and being ill with gut issues for 25 years, I’d go with evidence Bruce Topping from Garden of Life – (which Dr. David Perlmutter is now very involved with)!
    Do you realize you are communicating to people who have been through much misery – some for many years – and are so sick and tired of being sick, tired, restricted and in lots of pain with no real help?? So with so many being helped with spores like Bacillus Subtillis and others that are in Primal Defense & MegaSpore Biotics (which I started taking) and the great reviews from so many, why the scare tactics to sell a book??? Give us a break. We don’t want another book or protocol to follow, robbing us of more years of life! We just want help and to feel better!

  22. I have taken Prescript-Assist for three days, one capsule each day.
    After reading your informative articles I decided to stop taking it.
    Can it become opportunistic after three days? I’m a bit worried.

    What are your thoughts on the following probiotic?


  23. What do you say about Prescript-Assist. Its like father of SBO based probiotic. I’ve heard wonderful reviews from people using PA. Some have even cured their digestive issue using it. I need genuine reviews from people who have taken Prescript-Assist. I even checked Amazon’s website and none the people in the reviews section mentioned about backfire from it apart from minor bloating and gas.

  24. Mr Brison, tell me what you think about this

    Lactase 100000 IU 90,00mg
    Lactobacilli Reuteri 100 billion CFU/gr l,00mg 100 δισ. ufc
    Spores of Lactobacilli Sporogenes 15 bn CFU/gr 33,50mg 500 δισ. ufc
    Spores of Lactobacili Subtilis 25 bn CFU/gr 83,28mg 2,5 δισ. ufc
    Prebiotic Maltodextrin 1.000mg

    • Not a fan, HSO’s and maltodextrin which can cause issues.

      • what about VSL3? what probiotics would be best to take for someone with Hashimoto and former IBS sufferer who is undergoing antibiotic 1 week treatment (nitrofurantoin) for UTI? thanks!

  25. Here is a scholarly article on Bacillus subtilis. At least here there is scientific proof, and not just speculation, that Bacillus subtilis is not as bad as you made it to be.

  26. Hello
    I have read this post with great interest. Recently I had a faecal microbial analysis done and to my surprise I have a massive overgrowth of Bacillus subtilis. It’s distribution is 94.33%. I also have zero, yes zero Lactobacillus or Bifidobacterium. After reading this post and the comments I’ve realised it is from the Digestive Enzymes I’ve been taking. The reason I was taking them is because I have had my gallbladder removed and have problems with fat malabsorption. I also contracted a parasite (from getting Bali belly a few years ago) and have undergone 4 lots of different antiobiotic treatment. So I have nuked my gut and unknowingly caused a massive overgrowth of this bug. My doctor has got me taking Orthoplex Intestaclear, plus trying to repopulate my gut with E.coli and probiotics. However, my doctor didn’t have any knowledge about this bug and given your detailed knowledge I would be most appreciative of any suggestions you have? Thank you so much.

  27. To break down biofilms formed by bacillus subtilis which biofilm disruptor must be used?

  28. For gut flora altered by bacillus subtilis, what can be done?

    • It depends on the dosage and how long one took the probiotic. For most it would not colonize and they can recover. For some people it can cause differing gut issues. It depends on the problems one is now having on what should be done.

  29. Just wondering how this protein or enzyme Nato Kinase been absorpt from human intestine? If this bacteria in our gut how does it benefit toward our human body health?

  30. Bacillus subtilis is a killer. I took a digestive enzyme with bacillus subtilis and my digestive system is screwed up and my tension headache worse.

    • How do i restore my gut flora after taking a digestive enzyme with bacillus subtilis which i am afraid may have wrecked my gut flora and digestive system.

      • It depends on how long you took the supplement, if it was for less than a month you should be fine and it probably didn’t colonize. I do not recommend nuking your gut with antimicrobial agents unless it is causing you issues.

  31. I just wanted to say, this was one of the dumbest, most self important, least academic, pseudoscientific “health” blog I’ve come across in a while. Considering how low the bar is set these days, that is really something! Thanks for giving me something to laugh at: you’re stupidity and intellectual shortcomings.

    Have an idiotic day!

    • Thank you for your comment. It contributes greatly to the conversation.

      For your information, there is a mistake in your comment. I believe you meant to say your instead of you are.

      Have a great day!

      • I have serious SIBO, which ruins my life on almost a daily basis. I have dr. tried a reginmen of Xifaxin, which made it worse. Now on Lotronex, which helps but too expensive. What probiotic would you recommend? Am sensitive to high levels — gives me terrible gas.

  32. My daughter passed January 30,this year.she was one and a half months into her seventh year of only child and in the morning she woke up laughing and happy about our dog.I went to work,her dad got her to noon she came home because of throwing up once.when I get home she seemed weak and confused but thought it was just part of being sick.she was very heathy runs to the clinic except for the common girl died in bed next to me that night.the autopsy gave us no closer to what happened.they told us it was a viral infection in her bowel.e coli was mentioned put not confirmed, bacillus and others were mentioned but still not confirmed. My girl ended up septic and was gone hopefully in her sleep but I dought it because her eyes were open a bit.I’m begging for someone to give me answers. Please

    • I apologize in the loss of your child and I understand your search for answers for your loss. My heart goes out to you.

      Sometimes answers are sadly not always there. With Abel we knew he was sick and it was a matter of time till he passed away be we did not expect it would be so soon.

      To this day, we do not have a full picture of what happened. Through the autopsy, it appeared that he had a pulmonary embolism from being on a ventilator for so long.

      Losing a child is one of the hardest things anyone can ever endure I believe. It must be harder for you and your family because, unlike Abel, your daughter appeared to be healthy.

      I can only speculate on what happened and nothing more. The viral infection caused some gram-negative overgrowth sub-clinically (this is one of the proposed causes of SIBO,) a lot of cytolethal distending toxin was produced, it overstimulated her immune system, and she either passed away from her overstimulated immune system (cytokine storm) or bacterial toxemia.

      In addition, when people pass away in their sleep, their eye muscles slightly relax and their eyes can appear open as if they were awake. Saw it with Abel and my father.

      But again I am not a doctor, and this is purely speculation. E. coli and Bacillus are normally found in the gut. I am sorry for your loss.

  33. I believe you are correct about probiotics especially b subtilis being unsafe. Cancer is caused by two different types of bacillus viruses plus now things like papilloma virus.

    How do I know this? I was immune compromised and taking primal defense. I had a ear and jaw bone infection not to mention the gut. The jaw bone infection got worse. I had surgery and cavitations. They cultured the bacteria at Dental DNA in Colorado. I had 27 different species in jaw. Most are supposed to be in the gut. I had a bio comp research company send me rife machine frequencies to help clear these. The highest bacteria aalmost off the chart at a dangerous level is eikenella corrodens. It is a bacillus infection!!!! Based on frequencies my body is now telling me to kill those but also b subtilis the spore form of b anthracas. Also almost all bacillus species except lichenformis.

    So yes u are correct. The word needs to get out. I believe children are meant to get dirt in there bodies and build these things up naturally but not adults! Now my body is not telling me to taking any probiotics not even yogurt. I can’t stomach antibiotics. My do Dr believes in rife macines. I’m not about to get pumped with vancomycin well see what happens.
    I am a full believer in Jesus and the bible one night I was having pain. I was told in minds ear to read psalm 45 He said the verse with cassia aloes and myrrh. I looked up the things. There are government studies on all of them due to antibiotic resistance just google it. They are powerful they agree with me but I have to be very careful not to use too much. I have a family and am struggling to regain balance in my body and live a normal life again!

    You can use my comments but change my name!!!!! U can email back I am very smart can answer if u have more questions. Why did I take primal defense, I trusted what I read in j rubins books, like the guy but do not believe what helps one person will help the next. I should have really prayed before taking. Unless there is a chance it was trying to chase the infection out? But I wouldn’t mess with it again.
    So when my immune or body tells.e I’m ready for probiotics what would u recommend. I ws taking pb8 but even that says not for immune compromised.
    Thank you for the website.

    Please pray for my family if you believe what I do.

    • I would not recommend any probiotics. I would advise instead to eat some probiotic foods if you can tolerate it like probiotic sauerkraut or kimchi. If not as long as you have your appendix eating a variety of FODMAP foods as long as your digestion is fine and stay away from gluten.

      Be careful with Cassia since it can have elevated coumarin. Ceylon cinammon is better and has antimicrobial properties, so does the myrrh. Aloe can cause loose stools because of aloin. Georges Always Active dows not have any of the laxative effects associated with it.

      It is possible that the probiotic you were taken was mislabeled and instead of B. subtilis it was Eikenella corrodens. Nonetheless, both can cause issues for some people.

  34. Shocking to see so much bull in one blog post. Unlike Bruce, I do not work for any probiotic company. He is completely correct about the safety of probiotic strains of Bacillus subtilis. Saccharomyces boulardii is a bigger risk, and even that pretty much harmless. Like E. coli, most strains of Bacillus subtilis are beyond harmless and in fact often quite beneficial. I found it amusing you don’t give Bacillus subtilis the same level of objectivity you give E. coli. You should tell the countless eastern Japanese that eat natto for breakfast every single day what a risk they’re taking.
    I’d also like to know where got your number of only 10,000,000 cfu per large serving of natto. Most the the sources I’ve found say its around 5,000,000,000 PER GRAM. That’s five trillion per gram, not ten million per large serving.

        9.7+/-0.1 Log cfu/g
        10^9.7=5011872336 cfu/g
        These experiments in culturing natto resulted in natto with 3.7*10^9 to 4.1*10^9 cfu/g. That’s 3,700,000,000 to 4,100,000,000 cfu/g slightly lower, but still many orders of magnitude higher than

        I don’t have access to Koch and Sonenshein’s books, (which from your link, seem to have nothing but praise for Bacillus subtilis,) but I would be interested in looking at the primary source as opposed to a poorly scanned secondary and possibly tertiary source of an FDA document.

        What you’re doing here is just fear mongering to sell your book.

        • Ok let us say that it is 3 billion CFU per gram of natto. Some of the endospores of the bacteria would be inactivated due to stomach acid (the same as if you took a supplement.) Most B. subtilis that we come into contact anyway are either eliminated by stomach acid or pass right through us without germination.

          B. subtilis is widely distributed throughout the environment, particularly in soil, air, and decomposing plant residue. It has shown a capacity to grow over a wide range of temperatures including that of the human body (Claus and Berkeley, 1986). However, B. subtilis does not appear to have any specialized attachment mechanisms typically found in organisms capable of colonizing humans (Edberg, 1991). Given its ubiquity in nature and the environmental conditions under which it is capable of surviving, B. subtilis could be expected to temporarily inhabit the skin and gastrointestinal tract of humans, but it is doubtful that this organism would colonize other sites in the human body (Edberg, 1991).”

          The problem with the bacteria is not the CFU amount consumed, the issue stems from the Bacillus subtilis itself in its possibility to cause intestinal issues if your immune system is weakened.

          • The issue of infection from a compromised immune system can be said of just about any bacteria. Also, that government webpage you’ve quoted fails to make a distinction between different Bacillus subtilis strains. If that did that with E. coli I could make E. coli nissle look like the worst bacteria ever. Shoot, there might be a horrible toxic strain of Bacillus subtilis out there somewhere. That’s not going to stop me from scarfing down natto constantly.

            I say again, you are fear mongering for the sake of selling books and getting amazon commissions.

          • You are correct even Lactobacilus acidophilus can cause opportunistic infections if given the chance, but are a lot easier to eliminate then most endospore producing bacteria. Eat as much natto as you would like, all I am doing is trying to provide the other side to a HSO that everyone claims is perfectly safe.

  35. I work as an educator for Garden of Life. B. subtilis and “Primal Defense” have gained a cult following and are recommended by many experts and researchers. This is because this particular strain is OFTEN able to modify bowel ecology in favorable ways when other lacto/bifido strains have been tried repeatedly and symptoms persist. To say that plantarum has all the same features is absurd. It’s like saying a hammer can do all the same things as a jackhammer can do because they’re both made of metal and both can be used as a mallet.

    B. subtilis produces MANY compounds which are not produced by common lactic acid bacteria. Many byproducts of subtilis metabolism are actually alkaline products, by the way. Soil bacteria should be considered more of an anti-infective than a classical “probiotic” and as such it should be used with care.

    Technically Primal Defense is the best selling probiotic of the last decade and remains in the top 25 probiotic formulations of the industry. As this blog noted many experts and researchers (such as Chris Kresser and Natasha McBride) will attest that the strain B. subtilis is uniquely effective. This doesn’t mean it is always the best therapeutic agent for all people in all scenarios.

    Over the years there have been dozens of smear campaigns against B. subtilis and Primal Defense mostly coming from competitive probiotic vendors trying to influence sales.

    One of my co-workers in the field sent me a link to this blog. I saw the title and I yawned and figured right away before even reading this blog post that it would be more of the same old points:

    1) Spore-forming” microorganisms are supposedly horribly frightening. Of course the fear mongers never mention that spore forming microbes are all around us every second of every day and that human exposure to them is constant.

    2) I figured this blog would discuss the case study from Italy about the 73 year old who was found to have B. subtilis in the bloodstream. The fear mongers have gotten A LOT of mileage out of this one. One would think that if B. subtilis were so deleterious to human health then you wouldn’t have to go back nearly 20 years to find a single anecdote of harm. And even then you can only find it in people who are on death’s door. Garden of Life sells over a million bottles annually and we’re just one single supplier among many that distribute this strain all over the world! Where’s all the evidence of harm? (This blogger had to dig through papers from the 80’s just to find any additional sentinel events -and those were not deaths. )

    3) And of course usually the fear mongers will try to convince people that B. subtilis is like anthrax’s cousin. Of course lay people who have never studied biology will think that the two species are close relatives and that surely it’s a pathogenic strain just by association.

    I found it funny that the author recommends colloidal silver as part of an anti-microbial protocol. A red flag that someone is failing to use critical thinking and is instead letting their confirmation bias guide them.

    Silver is a great anti-septic such as in a catheter or as a gel applied to keloid scars — but it is NOT an antibiotic and worthless for intestinal infections. There is absolutely no evidence that colloidal silver has ever been successful for any internal infection. not even in an animal model. Go look around PubMed or Medify and you will see. Colloidal silver makes our whole industry look stupid.

    Hope this helps.

    • Dear Bruce,

      I am glad you were honest that you stated your bias in the beginning. You work for GOL therefore you have every right to defend PD.

      HSO’s exist everywhere you are correct. Some are more benign that others. Brevibacterium linens, for example, lives on our feet and produces odor. We do not however want this bacteria in our lungs or colon where it does not belong.

      Bacillus subtilis is not part of the native gut flora for most people. Consumption of natto is one way to introduce the bacterium to the colon. No perfect bacteria or flora exists for anyone. It is a lot easier to eliminate rogue Lactobacillus acidophilus then most HSO’s.

      You are correct that I did use alarmist tactics, comparing Bacillus subtilis to Bacillus anthracis. The same could be said about the difference between E. coli nissle and E. coli 0157:H7. The main difference between the two species is that E. coli nissle is a lot less harmful compared to Bacillus subtilis if your immune system ever goes south.

      I did use a 1980 study you are correct. I also used a study from 2012:, why did you pick and choose?

      I raise another question for discussion. Why did GOL drop Bacillus licheniformis from its PD culture? Did GOL drop it because it is associated with so many infections?

      Silver does not enter the bloodstream you are also correct and is a poor systemic antimicrobial agent. But why would it not work in the gut? If it works through direct contact on the skin and even in embedded medical devices IE g-tubes and endotracheal tubes, why would it not work through direct contact in the gut? You swallow the silver, and it passes through your digestive tract. Granted minute parts of it become embedded in the digestive organs, and it does take time for it to be eliminated.

      I also raise this for discussion:

      I look forward to your rebuttal.


      • you started by saying that HSO’s exist everywhere. And that’s true. Especially for subtilis. It is ubiquitous in natural environments. It is measurable on virtually every surface that has come into contact with soil. (…so food, and all that.)

        Then you claimed it is NOT part of native gut flora for most people.

        Which doesn’t make intuitive sense to me

        I believe you were the one who cited Hong’s paper from 2009.
        Here is the full paper:

        here is the conclusion from the paper YOU cited:

        “This study reinforces a growing view that B. subtilis and probably other species have adapted to life within the GIT and should be considered gut commensals rather than solely soil microorganisms”

        ….so do you have any evidence to back up your claim that this ubiquitous strain is NOT a commensal strain?

        I would need evidence to back up your claim that B. subtilis is not native flora.

        Now let us move on to the question of safety.

        I was unimpressed with the paper you cited from over 30 years ago that implicated B. subtilis. This is partly because the tools back then that were employed were not near as good at identifying the exact species within a complex genus like bacillus. (they didn’t have PCR analysis). Back in those days people made observations about what they THOUGHT was B. subtilis but actually turned out later to be a different species. So the sentinel events in the 80’s that were cited may not have even been related to the B. subtilis strain that is in PD!

        And as far as the one other paper you cited from 2012 – it is even weaker evidence of B. subtilis being a bad guy.

        Here is a quote from the 2012 paper: “Species of the genus Bacillus are a common laboratory contaminant, therefore, isolation of these organisms from blood cultures does not always indicate infection. In fact, except for Bacillus anthracis and Bacillus cereus, most species of the genus Bacillus are not considered human pathogens, especially in immunocompetent individuals.”

        and of course the entire paper is really just a single case-report… and the guy didn’t die. ….and THIS is your big smoking gun that shows B. subtilis to be “not worth the risk”?

        Well if that’s how you feel let’s discuss other LAB strains that have extremely rare adverse events:

        The most studied strain in the world is L. rhamnosus.

        If you go to L. rhamnosus wikipedia page you will see the following text:

        “L. rhamnosus has been discovered to be pathogenic in rare circumstances, primarily involving those with a weakened immune system or infants.[1]”

        —-or how about the 2010 review of seventy-two different papers and here is the quote:

        “There were 20 case reports of adverse events in 32 patients, all of which were infections due to Lactobacillus rhamnosus GG or Saccharomyces boulardii; the risk factors included central venous catheters and disorders associated with increased bacterial translocation. There were 52 articles reporting 53 trials in which 4131 patients received probiotics. Most trials showed either no effect or a positive effect on outcomes related to safety (eg, mortality and infections).”

        So would YOU say that due to these rare events reported in the literature that Lactobacillus and Sachharomyces are “NOT WORTH THE RISK”?

        —as to your question of why PD formulation was changed to remove lichenformis I must say that I did not work for the company back then but I think it was for a variety of reasons some of which were about dealing with perceived fear and also logistics/cost/availability.

        I do think B. subtilis is a better supplement than B. lichenformis —but I haven’t poured through the literature on lichenformis. I will tell you that I’ve met literally hundreds of people over the last five years that implore our team to resume manufacturing the original formula because of their anecdotal responses to the original formula.

        Now let’s move on to colloidal silver. The reason it won’t work in the lumen of your intestine is because the concentrations are ridiculously low once it is ingested.

        Sure, silver kills pathogens in a petri dish at high concentration.
        ….the question is can you really get that kind of accumulation in the lumen of your intestine, or in the bloodstream or lymph? or intracellular?

        once you swallow a solution of 10ppm or even 1000 ppm it is going into a much bigger volume of digestive fluids and so therefore becomes very dilute. of course you could just swallow more silver but since it is a metal that is not involved in our biology this is dangerous.

        Bottom line: you will never have enough bio-accumulation of silver at the binding sites of infection for it to actually work. and that is why there isn’t a SINGLE study showing effectiveness. Not even an animal trial.

        Yes it can work in catheters or in bullet wounds because the concentrations are thousands of times higher than what could ever safely be ingested.

        the nature paper you cited is really all academic theory and all of it is demonstrated in test tubes. there is this quote from the article:

        “Collins says that he and his colleagues saw good results in mice using non-toxic amounts of silver. ”

        so I have no idea what “good results” means – probably just that the silver did not cause agryia in the mice. I must presume that If there WERE really impressive results from his mice study with silver/antibiotic compound then he would have published a paper on that!

        I’m so tired of test tube studies being used to bamboozle people in this industry. There are literally thousands of compounds which can degrade a cancer cell or a microbe in a test tube or petri dish. Vitamin C, Neem Oil, Raw Milk, IP-6, CLA, colloidal silver, etc etc etc. This does NOT mean they will ever be effective cancer drugs or potent antibiotics.

        here is a good review of the silver bullshit:

        So… I will wrap this up by saying that B. subtilis is in fact a commensal strain based on the evidence – and it possesses amazing therapeutic potential – and also that colloidal silver is utter bullshit without a shred of evidence that it will ever be useful as an antibiotic (but is a great antiseptic at mega-concentrations).

        Hope you have a good day!

        • If a “Native” gut flora exists it would depend on a few things:

          1. What part of the world you live in or visit
          2. The food you eat
          3. Your genetics
          4. If you were breastfed or born vaginally

          Everyone on this planet has a different gut flora. Different bacteria in different populations working either together or against one another makeup one’s flora. Some bacteria seem to be more beneficial, and some tend to cause more harm than good. Any bacteria can cause any infection at any point in time.

          Some people have picked up Bacillus subtillis from their environment. The Japanese and Nigerians acquired it from foods fermented with the bacterium. Other people might have acquired it from ingestion of soil as well. The amount that these native populations consume would be far lower than any probiotic supplement. The same could be said about most people with it as native flora. There were less then 100 people in the studies combined. In addition, the amount of spores and strains cultured in the ileum were very low (you would see that normally unless a person has SIBO.) Universal Ubiome results do not show it in most guts that were tested. There is a possibility that it is not tested for by Ubiome.

          It is a lot easier to eliminate an opportunistic Lactobacilli infection then it is a Bacillus infection. Bacillus can propagate by using endospores that give it a greater chance of survival against antimicrobials. So, therefore, the statement “So would YOU say that due to these rare events reported in the literature that Lactobacillus and Saccharomyces are “NOT WORTH THE RISK”?” is a poor argument.

          Silver is not absorbed well systemically of course or in correlation with antibiotics that work on a systemic basis. I have mentioned this already. Silver might improve the usefulness of Rifaximin however because it stays primarily in the gut and is used to deal with gut dysbiosis. Remember, the only way for argyria to occur is that ingested silver would have to be absorbed systemically and be excreted from the skin to turn it the color gray / blue.

          Most people would ingest enough Silver in a standard dose for it to work in the digestive tract until it is eliminated in the feces. Some amounts of silver would be accumulated in the digestive organs though, and the body would eventually eliminate it over time.

  36. What I’ve seen of B. subtilis is that it is a very good ‘ancestral’ species, a true SBO, that we should seek out. It’s in AOR Pro-3, but somewhat mislabeled as Bacillus mesentericus. (Former species designations that are now considered to be members of the species B. subtilis include B. aterrimus, B. mesentericus, B. niger, B. panis, B. vulgarus, B. nigrificans, and B. natto (Gibson, 1944 and Smith et al., 1946 as cited by Gordon, 1973). )

    From what I read, it’s non-pathogenic and very good.

  37. All of the probiotics that I recommend are in my book, Fix Your Gut, along with individual strains recommendations and purposes.

  38. I’m a bit worried now since I see that my expensive “Prescript-Assist Broad Spectrum Probiotic” contains “Bacillus Subtillis.” So what probiotics do you recommend?

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