Bacillus subtilis, a soil based organism contained in certain probiotics, has recently been under attack for potentially causing septicemia. Truth be told, this probiotic is not for the novice, must be taken with knowledge of what you are doing and imperatively must coincide with a proper gut healing protocol that seals any potential intestinal damage due to pathogen overgrowth.

When taken properly, this exact bacterial organism is considered one of the most powerful gut healers. B. subtilis grows in the soil right at the level of the roots in grass or garden zones. 

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In 1994 the EPA saw such extreme dangers with B. subtilis they set forth regulation for facilities using the bacteria saying, “Standards for minimizing emission specify that liquid and solid waste containing the microorganisms be treated to give a validated decrease in viable microbial populations so that at least 99.9999 percent of the organisms resulting from the fermentation will be killed.”

Like most issues regarding food today, the probelm arrises with the “other” form of A-amylase as there are two. One is found naturally in food and in soil, the other is man made. The Food And Agricultural Organization says A-amylase, “Is a genetically engineered enzyme that is thermo-stable and active at a relatively low pH and low calcium concentration.”

That is why B. subtilis is avidly used in the production of enzymes, including commercial products, like ethanol, as well as naturally being found in food. A-amylase is also the main enzyme found in humans and mammals. In addition to saliva A-amylase is released from the pancreas, an organ which releases digestive enzymes into the intestinal tract to digest food. It is found in some seeds and mushrooms. A-amylase is found in saliva where it breaks down starchy food. People who do not digest starch foods have a malfunctioning breakdown occuring somewhere in their body causing a deficiency in A-amylase. Collectively these Soil Based Organism enzymes, certain chemicals and antibiotics containing A-amylase are considered a Class 1 Containment Agent by the NIH as well as by the European Federal of Biotechnology guidelines.



The EPA goes on to say, “To date, EPA has reviewed three premanufacture notices (PMNs) for strains of B. subtilis. One of the strains was modified for enhanced production of the enzyme A-amylase to be used primarily in production of ethanol. Another strain was modified for enhanced production of a lipase enzyme for use in heavy duty detergents.” L-lipase is another enzyme both on foods, in the body and man made.

The Journal Of Clinical Microbiology says, “Data on the general importance of infections due to B. subtilis are incomplete, since it is a general practice of most microbiological laboratories to discard these strains or to report them as contaminants. Also, in the cause-of-death statistics of the World Health Organization no data on B. subtilis infections are present. B. subtilis spores are available in Italy as a pharmaceutical preparation for oral use. Each dose contains a mixture of 109 spores of four distinct antibiotic-resistant derivatives of ATCC 9799 (Enterogermina; distributed by Sanofi Winthrop, Milan, Italy) per vial. The pathogenic potential of B. subtilis is generally described as low or absent.”



The NIH reported (presumably) the one case in question, a 73-year-old man with recurrent septicemia resulting from chronic lymphocytic leukemia. The man showed numerous markers for Intestinal Permeability (Leaky Gut in layman’s terms). 

The man had been taking B. subtilis , reportedly, for over a month before he encountered symptoms of high fever, mental confusion and diarrhea that caused admission to the hospital. Blood tests, in triplicate, showed B. subtilis in his bloodstream. They administered antibiotics, the symptoms disappeared, but he remained hospitalized. B. subtilis was not re-administered. Sixteen days later symptoms returned, tests again detected B. subtilis in his bloodstream, more antibiotics were given. Six days later the patient died. The NIH said, “Lymphoid cells were detected in the cerebrospinal fluid (cerebrospinal fluid was not cultured), and the patient died probably due to central nervous system involvement.”

Research Gate, a professional network for scientists and researchers, reports, “Central nervous system involvement is a rare complication of chronic lymphocytic leukemia.” Meaning, in some cases, lymphocytic leukemia presents with central nervous system involvement with or without B. subtilis administered orally.

dr natasha


Dr. Natasha McBride, specialist on Intestinal Permeability, advocates sealing the Intestinal Permeability first before taking probiotics like Soil Based Organisms. This prevents foreign matter from the leaky intestinal tract, including undigested food particles, putrid rotting food particles and pathogens from leaking directly through the intestinal wall into the blood stream. Most importantly when you begin introducing probiotic strains which build up the good bacteria in the gut, the bad bacteria will die, releasing toxic gasses and waste. Sealing the gut first will mitigate these toxins from passing through into the bloodstream. She advocates a specific method of introducing probiotic strains in an effort to complete the healing in proper order including lactobacillus and bifidus, the starting point. (Click here for  her specific order, click here for lactobacillus and bifidus strains from home brewed probiotics).

 John Brisson, author of Fix Your Gut, has been very vocal speaking out against B. subtilis saying, “Everyone believes I have a vendetta against HSO’s (the soil based organism B. subtilis). Maybe I do, maybe I do not. Honestly I am just tired of everyone saying that HSO’s or that probiotics in general have no side effects whatsoever and that they are perfectly safe.” I will not link his book because I feel it would be negligent to lead people astray from proper healing.

Recently Brisson posted an article “Bacillus Subtilis: Any Benefit of the Bacteria Is Not Worth The Risk” where he attempts to defame B. subtilis but then contradicts himself saying, “There are a few known clinical case studies that mention opportunistic Bacillus infections occurring in patients with compromised immune systems. One of the case reports theorizes that the main reason for such few reports of infection is that Bacillus subtilis are recognized by most medical professionals as a safe bacteria.”

All gut healing includes die off of toxins which can be interpreted as ill side effects when in fact it is a sign telling the body what it happening, showing the person what to do next. Click here to learn more. 

Acupuncturist and columnist for the Huffington Post, Chris Kresser says in an interview with Steve Wright from SCD Lifestyle, “Soil based organisms are a different approach than the lactic acid forming types of probiotics. I’ve found they’re better tolerated in people with SIBO.  As a fairly unrelated side note, they tend to work better for constipation than a lot of other probiotics. Oftentimes, probiotics can make constipation worse, so soil-based organisms and Prescript-Assist, I think, is a really good choice for people with SIBO.”

As stated, B. subtilis grows in the soil right at the level of the roots in grass or garden zones. Digging in the soil and not rinsing vegetables from your homegrown non-pesticide using garden, could prove beneficial. Many people sensitive to the beneficial bacteria B. subtilis find it necessary to cut back on dosage during the months they do garden work to keep die off in check as they are getting B. subtilis naturally from working in the dirt.

Prescript Assist is quite possibly one of the most commonly taken soil based organism probiotics, contains 29 strains of microflora from soil-based organisms and is shelf stable, not needing refrigeration. It is considered a prebiotic and probiotic with the manufacturer saying probiotic bacteria are encompassed in a seed-like barrier which ensures the probiotic bacteria makes it thru the stomach and into the intestines with over 95% effectivity. This same protective barrier allows for a two year shelf life. The manufacturer recommends taking this product with meals. Click here to order prescript assist.

NOTE on Prescript Assist. Some concerns have been questioned about PA since it is a prebiotic. I posted the question to GAPSdiet.com and this was the answer, “Prescript-Assist came on the market after the Gut and Psychology Syndrome book was published.  Information surrounding the use of prebiotics has been very mixed and inconclusive, so it has generally been recommended to initially avoid them in serious digestive conditions in case they are feeding bad bacteria.  However, many Certified GAPS Practitioners and holistic health professionals are using Prescript-Assist with their patients, as all of the strains are soil-based and they have reported great results with their patients.

Click here for a list of the best rated probiotics which contain no fillers or binders that could feed pathogens in the gut.

Garden Of Life (click here to view product) also contains from however I DO NOT recommend taking this probiotic as it contains rice maltodextrin, a man-made GMO rice/corn product which feeds pathogens in the gut negating the positive effects in this otherwise beneficial product.

*If you learned something from this post share it so others can do the same. To support the efforts of this blog shop the affiliate links above like this one. You pay the same shopping through Amazon while the author receives a small referral fee from Amazon. This offsets the costs of this site.

*Nourishing Plot is written by Becky Plotner, ND, traditional naturopath, GAPS who sees clients in Rossville, Georgia. Since her son was delivered from the effects of autism (Asperger’s syndrome), ADHD, bipolar disorder/manic depression, hypoglycemia and dyslexia through food she continued her education specializing in Leaky Gut and parasitology through Duke University, finishing with distinction. This is not a news article published by a paper trying to make money. This blog is put out by a mom who sees first hand the effects of nourishing food vs food-ish items. No company pays her for writing these blogs, she considers this a form of missionary work. It is her desire to scream it from the rooftops so that others don’t suffer from the damaging effect of today’s “food”.




27 Responses to Soil Based Organism Probiotics Under Attack

  1. Lauren says:

    I got sick after taking a probiotic that includes b subtilis 3 years ago. i have still yet to recover, and have spent thousands of dollars trying to. biggest mistake of my life, i might end up doing fmt finally to reverse the devestating damage it as done to my digestive system.

  2. Melanie says:

    I am but worried. After dealing with SIBO, I got Primal defense and I felt great for the last four months but now reading this, I am terrified. I will stop now but am I doomed? I’m 33 years old

    • Becky Plotner says:

      I’m not sure I understand why you stopped if it made you feel good. If you’re concerned with the added ingredients you can switch to the one listed that is clean – Prescript Assist.

    • Jason Klinger says:

      think you guys are overreacting

  3. Carol says:

    I have been taking GOL Primal Defense Ultra. The label says it contains organic rice hull. There is no listing of “maltodextrin.” I believe it is helping to improve my health. The changes are slow and subtle but I detect progress. What do you base your claims on?

    • Carol says:

      The picture of the label from the link here is inaccurate. I don’t know if it is old or if the formula has changed but it is not like the label on mine.

      • Becky Plotner says:

        Thanks for the update. What’s the difference?

        • H says:

          Genestra HMF Intemsive Powder. Probiotic Formula. I noticed it has maltodextrin in it.
          He has been feeling a bit sick from it. Should I stop it and try the one you recommended above?
          He is 8 years old and struggles with ADHD.

          • Becky Plotner says:

            Thank you for the heads up. The one linked in the other post does not show maltodextrin. I have updated the listing there for caution. Maltodextrin causes many folks intestinal upset.

    • Becky Plotner says:

      Organic rice hull is not approved due to the starch, the inability to digest for GAPS guts. If your damage isn’t deep, a GAPS gut, then it’s a fine product for you. So glad it’s working for you!

      • Hillee says:

        Should people do coffee enemas along with probiotics to prevent illness? In researching to cleanse and detox for breast cancer survival, I have often read that with a detox, it is also important to do enemas to eliminate toxins as they die off. Does a probiotic cause toxins to die off? Too many questions? Sorry and thank you for what you do!

    • David Morse says:

      GOL specifically says they don’t use GMOs. The link is to a 15 CFU product but they also make an 85 CFU strength.

  4. […] nourishingplot.com/2015/02/06/soil-based-organism-probiotics-under-attack […]

  5. nathan says:

    I personally have a compromised immune system.I decided to try prescript assist.I thought for sure it would help.I got a major infection from its use.I do not want to steer people away from it.I would however be very cautious and take it very slow if your immune compromised and you decide to try it!

    • Becky Plotner says:

      Yes, Nathan, you are correct. This is a very strong probiotic which can and will cause a lot of die off with deeper damage in the microbiome. The deeper the damage, the lower and slower you go for sure.

    • Jason Klinger says:

      not an infection it was a die off. you should stick with it and eventually you will improve

  6. Kate L says:

    I had die off reaction from Prescript assist I was taking 1/3 capsule and it was lets say ok, itchy and irritated, with 1/5 I woke up sweating in the middle of the night and racing heart, lets say it was a die off but it was unpleasant, I am sensitive in terms of supplements, and I am cautious of what and how I take but this was really bad, also itching during the day

    • Becky Plotner says:

      That’s fantastic that you have found where you are weak and need rebuilding. Some people are so weak in certain strains that they have to start with one spec or put one spec in a glass of water and take one teaspoon of that.

  7. Sanya says:

    Thank you so much for this article. I am on my 3rd day of Prescript – Assist and I have such a sever reaction. I have psoriasis that after 20 years turned into arthritis. I was doing better, and then I introduced SBOs and all hell broke loose today, when my stiffness is all of a sudden back, had a low fever and couldn’t get out of bed. It lasted one day, fever is gone, but stiffness is still intense. I can’t decide if it’s a die-off, or is it too early to introduce the SBOs to an unsealed leaky gut. I so much don’t know what to do. I know it’s a trial and error, but I am just worried not to cause any permanent damage. I would love to get your opinion on this if it’s possible. Thank you kindly for all of your effort and sharing, it is much appreciated.

    • Becky Plotner says:

      First, I would check the ingredients on their bottle. Unfortunately, they have just transferred ownership and changed the ingredient list which now includes pea protein- an ingredient which feeds the pathogens in a damaged microbiome. The one linked above, at this time, is still the old bottle, without the pea protein. If it’s a bottle without pea protein, too much probiotic can cause great die off. For people in that situation, they need to take less, sometimes just what fits on the tip of a toothpick. Opening the capsule and just taking a small pit reduces the die off, some have to start with one speck in a teaspoon of water and take one drop of that, or a cup of water, or two cups.

      • Crystal says:

        Have you ever had people develop neuro muscular symptoms from SBOs? I took them for a month and have twitching, tremors, feel achy at times, feel like I’m getting a fever but don’t have one. My immune system was compromised by Lyme and co infections. The onset of neuro symptoms correlates perfectly with taking SBOs I just didn’t connect the two until a month in

  8. bob says:

    This product (prescript-assist) was recently tested by a certified U.S. lab and found to contain high levels of lead and aluminum. It is not fit for human consumption.

  9. Jessy says:

    Nathan, any chance you have recovered? I believe the same thing happened to me and I am still I’ll. TIA

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