My Stance on Homeostatic Soil Organism (HSO) “Probiotic” Supplements

One of the most significant pieces of misinformation exchanged in the natural health blogosphere is the notion that HSO organisms are 100% safe. HSO stands for homeostatic soil organism or microorganisms that are found natively in the soil and they are used in many different “probiotic” supplements. Some but not all HSO’s are spore-forming bacteria others are yeast. Some HSO’s are also native to the human gut microbiome, but most, however, especially the ones that are used in supplements are not. Many HSO’s have been implicated as the cause of infections and can cause many health issues, even those that are taken in “probiotic” supplements. Ingestion of homeostatic soil organisms may occur when one has eaten soil,¹ consumed food fermented with HSO’s,² taken homeostatic soil organism “probiotics,” or eaten improperly washed produce. It has been theorized that these homeostatic soil organisms have always colonized the human microbiome because ancient humans did not properly clean and sanitize their fruits and vegetables. Ancient man frequently consumed dirt on their food! The consumption of large quantities of soil by ancient man has been widely debunked.

Humans have not always known that dysbiosis from microorganisms is the exact cause of most disease. Our ancestry did, however, learn from our humble beginnings that eating certain foods would make us ill. Human beings developed hygiene practices since the dawn of time; we began by defecating away from where we lived (mainly because it smelled horrible, let us be real here, haha.) Ancient man groomed themselves and even produced soap after fire was invented. Humans eventually buried our dead at first as a spiritual practice and later we buried our dead in coffins encased in concrete for hygienic purposes. But did our ancestors clean/cook their plant matter before consuming? Research has shown that even our ancestors prepped starchy foods like tubers and roasted them over a fire before consuming. Why might you ask? Because cooked starches taste better when eaten then cold starches, even our ancestors knew that. However, ancient man were excellent hunters and carnivores, but they did not always have a sophisticated, varied diet.

Endospores (not a true spore) are dormant Gram-positive bacteria 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. 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 UV 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.” Their reasoning behind this recommendation is that since Bacillus 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 forms 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. Finally, if you believe that a Bacillus containing probiotic you are taking 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 to try to relieve the dysbiosis.^{3 4}

Ingested HSO’s that are spore-formers most of the time pass through the digestive system without germination and colonization. There are some native HSO’s that are found in the gut microbiome, for example, Clostridium, but many of them do not regularly colonize unless consumed for a period of time. In addition, most spore-forming bacteria seem to not be able to germinate in the very low pH environments in the stomach and the small intestine if bile (most spore-forming bacteria fail to germinate or perish when exposed to bile salts, except Clostridium difficile which germinate when exposed to bile) is being released properly. For most people, any improvement from taking an HSO probiotic would be an immune reaction to the spores relieving dysbiosis of other organisms and not from the HSOs becoming flora through colonization.^{5 6}

Though I have issues with the use of some HSO’s as probiotics, I mostly avoid the stance that none of them have any value and that they should be avoided entirely (except for Bacillus thuringiensis in Prescript Assist). I do also, recognize that some people’s health has improved with their use. My issues with HSO’s are that most people in the health blogosphere do not state that they can cause issues as well, they only report the positives and that they are 100% safe. The statement that homeostatic soil organisms are 100% safe is not only incorrect but downright harmful. In the comment section throughout the following HSO series, you can read how the supplements that contain them have helped some people and caused serious issues for others.

Homeostatic Soil Organism (HSO) “Probiotic” Supplements I Do Not Recommend

AOR3 probiotic

Dr. Ohhira’s

Ganeden’s B. coagulans

Just Thrive

MegaSporeBiotic

Prescript Assist

Primal Defense

Hemostatic Soil Organism (HSO) “Probiotics” I Do Recommend

S. boulardii

Digestive Author Jini Thompson on HSO’s, Primal Defense, and Natren

Jini Thompson gives her opinion of homeostatic soil organisms, Primal Defense, and Natren in her following blog post:

“On page 108 of the IBD remission diet, I suggest that readers may want to try a product called Primal Defense after they’ve been completely healed for 3-5 months. I learned of this product from numerous readers who wrote in to let me know how well it’s worked for them. Since I couldn’t try the product myself (I’ve been pregnant or breastfeeding for four years and counting), I questioned numerous respected naturopaths, microbiology professors, and gastroenterologists for their opinion on the product and all said it looked fine.

However, since meeting the founder and president of Natren, Inc. (top quality probiotic manufacturer), Natasha Trenev, I must change my opinion of bacterial soil organisms. Natasha is a world-renowned expert on microorganisms and maintains one of the largest research libraries on that topic in the world. She has sent me an entire CD-ROM of articles, research, and clinical data, and other scientific studies (most done outside of North America) outlining why it is not safe to consume bacterial soil organisms (like those contained in Primal Defense and numerous other products).

To summarize the research briefly, soil organisms (SO) are spore formers, so they make good competitors for yeast, fungus, and other pathogens. This is why so many people taking soil organisms will initially experience very favorable results. However these spores are extremely difficult to kill, surviving sterilants, disinfectants, acceleration forces, heat, pressure, radiation and many antibiotics. Strong antibiotics — like Vancomycin — can suppress certain spores. Spores are so persistent in the intestines that another round of germination may occur after the the drug is stopped. Soil organisms can also adapt loose genetic material and incorporate it into their cellular structure — the ramifications of which are yet unknown. Various soil organisms can also produce harmful peptides, affecting hemoglobin in the blood. It’s important to keep in mind that virtually all antibiotic drugs were initially developed from soil organisms and as antibiotics become more potent, they cause more damage to the host, not just in the immediate gut environment, but systematically as well.

In the EU (European Union) the use of soil organisms in animal feed is being stringently controlled and questioned at this time. There are simply too many questions and unknowns to sanction the use of soil organisms for human consumption and one certainly cannot qualify them as safe at this time.

I’m very sorry for any confusion this may have caused you. To be honest, this is the very first time I’ve recommended a product that I’ve not tried and tested exclusively myself — I admit I was swayed by so many good recommendations from readers. Rest assured that I will not do so again!”

My sincerest apologies,

Jini Patel Thompson

July 2003⁷

Jini never softened her stance on HSO probiotics or prebiotics, I was mistaken to make that assumption from her blog article. Jini is cautious of Garden of Life’s previous use of Bacillus licheniformis (so am I) which Garden of Life was using in its Primal Defense supplement before 2011. Currently, the only HSO strain used in the supplement is Bacillus subtillis.

I completely agree with her views on Natren, how to select a probiotic supplement that is hopefully right for you, natto, and probiotics and probiotics manufacturers and to quote Jini directly from her updated blog article (which I recommend you read) “The bottom line is that you cannot rely on probiotic manufacturers to have your best interests at heart. Manufacturers are often genuinely ignorant, and marketing concerns like price and accessibility (shelf-stable) often take precedence over health benefits.” I could not have said it better myself. Research before you take any supplement.

Chris Kresser No Longer Recommends Prescript Assist

Even Chris Kresser changed his stance on Prescript Assist when they changed the formula from it being one of the safest probiotic supplements in existence to the supplement might be dangerous because of a lack of studies on the new formulation.

“I’ve recommended Prescript-Assist as one of my top choices for probiotics for many years. I like that it contains soil-based organisms that mimic the natural flora found in ancestral diets. I’ve also found it to be effective, well-tolerated by most people (including those that don’t tolerate other probiotics), and easy to use and travel with (since it doesn’t require refrigeration). I know that hundreds of my patients, and thousands of my readers and listeners, have benefited from it—and the same is true for my family and me.

This is why I’m disappointed to let you know that I will no longer be selling Prescript-Assist on my website, as it is coming off the market in its current form.

The CEO of Enviromedica, which has long distributed Prescript-Assist, informed me that the company has discontinued distribution of this product. He was distraught, as he knows that I’ve been a huge advocate of Prescript-Assist and that many of you have come to rely on it.

Enviromedica made this decision because the manufacturer of Prescript-Assist made a substantial change in ingredients. The result is that the product is now vastly different from the original formula, which had been tested and clinically verified. The new product no longer meets Enviromedica’s quality standards.

They made clear that discontinuing the product was not something they wanted to do, but once the ingredients and manufacturing practices changed, the decision was made for them. And I respect them for making it.”

HSO’s are not without fault, and the ignorance in the natural health community about the issues they can cause is why I wrote the following blog series. Educate yourself, talk with your medical professional, and make an informed decision if they are right for you.