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.

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*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”.




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