The Problem With Soil Based Organisms (SBOs) As Probiotics

soil based organisms

Interest in probiotic supplements is soaring these days because of new studies revealing the wonderful benefits of these amazing microorganisms. There are many reasons why literally everyone should take a daily probiotic, and there is a great deal of research supporting the importance of gut health and a balanced gut microbiome. However, one should understand that although soil-based organisms (SBOs) fall under the same category as the probiotics that are resident in the human digestive tract, the truth is, they are simply not the same types of bacteria. SBOs are spores, they come from the ground and are not naturally found in your body. It’s important before blindly adding an SBO supplement to your nutritional regimen, that you familiarize yourself with the controversy that is taking place around these tiny dirt dwellers.

Soil Microbes vs. Gut Microbes

SBOs are beneficial in many ways, but the benefits of SBOs are very different from those of probiotics that live in the human body. Soil organisms enrich the soil for plants, and since humans and livestock eat many of these plants, we want the soil to provide optimal nutrients for crops. Incidental exposure to SBOs can help enhance our immune systems as well. Many of us remember the joy of playing in the dirt and making “mud pies” to feed to unfortunate younger siblings and cousins. While most people cringe at the thought of it now, this grubby childhood rite actually helped build our immunity to many pathogens.

A century ago, soil organisms were normal components in our food, but urbanization and the subsequent rise in processed food production has virtually eliminated soil-based organisms from our diets. These microbes are only transient visitors to the human microbiome, and even though we used to consume more of them, SBOs were never part of the symbiotic relationship that keeps our immune systems strong. SBOs do provide some health benefit when introduced to the microbiome, as these microbes trigger antibodies that act as our main defenders.

Why SBOs may not be safe as supplements

Even though soil probiotics serve as natural inoculation when ingested, this does not make them appropriate strains for probiotic supplements. Now that our gut microbiomes are less familiar with SBOs (due to a decrease in exposure), and most of our gut microbiomes are compromised, they can compete with our resident gut flora rather than complement them. In some instances, SBOs can become pathogenic, and this scenario is more likely when an individual has dysbiosis or a microbial imbalance. One of the primary reasons to supplement with probiotics is to counteract the devastation that environmental toxins, the overuse of antibiotics, and modern dietary choices have wrought on one’s gut flora balance. With that understanding, it may seem logical to supplement with SBOs since we no longer ingest them regularly, but this line of logic is a major cause of disagreement among leading experts.

soil based organismsIt makes sense to replace probiotics that are supposed to live in the digestive tract since an imbalance 
can lead to poor gut health and issues related to  compromised immune function. SBOs are different because they were never supposed to be part of the gut microbiome. Supplementing with soil organisms (introducing foreign microbes) when your intestinal tract is not properly colonized with resident bacteria is like inviting a group of squatters over to a vacant home and crossing your fingers that it will all work out. To make matters worse, SBOs are spore forming and they proliferate rapidly – so rapidly, in fact, that many manufacturing facilities who grow the probiotic strains found in the human gut consider SBOs as a contaminant to their facility. They know that if they don’t take every precaution to keep them out, SBOs could take over and create a nightmare scenario. Because of this, they even refer to them as the “cockroaches of the industry”.

Some studies have suggested that SBOs are similar to the dreaded super germs that resist classic antibiotic treatments. For example, many of the most common strains of SBOs come from the Bacillus genus, including the subtilis and lichenformus species. Bacilli strains are extremely hardy and form spores that can resist stomach acids and antibiotics. This characteristic actually makes SBOs more desirable to marketers because they will survive not only your stomach acids, but also extreme heat and even food processing. The shelf life for SBOs is simply amazing, which also happens to be the biggest challenge manufacturers must overcome for human gut residing microbes. And, since they technically fall under the label of “probiotics”, it’s an incredibly convenient and easy way to add probiotics to everything from supplements to hot teas to nutritional bars without having to figure out a way to keep the organisms alive. Problem solved! No refrigeration required!

It is also this spore-forming trait makes a Bacillus infection incredibly difficult to treat. The spores are so tough that they can hibernate in the intestines throughout a course of strong antibiotic therapy only to resurface after the threat has passed.

According to the U.S Environmental Protection Agency (EPA), many species of Bacillus can cause serious infections and food poisoning, while others are opportunistic pathogens that make great insecticides. Bacillus subtilis, considered a comparatively benign member of this genus, is one of the species used in SBO supplements. Subtilis is also an active ingredient in many industrial detergents and cleaners, and the EPA cautions against allergic reactions and sensitivities to products containing these microbes.

What you don’t know CAN hurt you.

Compared to traditional probiotics, research information regarding the safety of SBOs is limited. Studies show that some SBOs are pathogenic to mammals, and there are species that release peptides capable of interfering with hemoglobin production. Even the least virulent of these organisms are able to integrate foreign genetic material and alter their own cellular makeup. We have no idea what this could mean in the end, but that is a frightening concept, nonetheless.

We spoke with one professional in the probiotics industry and his first comment was: “I think SBOs are fine if added to food but I do not recommend them if they are in a higher quantity supplement form.” Next we asked, “Would you eat food products with added SBOs?” His reply: “Well, no. And my son is immune compromised, so I definitely don’t let him eat those products because the verdict is still out.” Hmmm…

It seems the bottom line is that anyone with a compromised gut might want to think twice before exposing themselves to probiotics containing SBOs, whether in food or supplement form. SBOs may appear on labels as “soil probiotics”, “homeostatic soil organisms” (HSOs), “bacterial soil organisms” (BSOs) or simply “soil organisms” (SOs).

Instead, focus on supplements that contain resident human probiotic strains until you are absolutely confident that your digestive tract is properly colonized and well-equipped to reap the benefits of exposure to these transient soil based strains without putting your health at risk.


Julie Hays is the Communications Director here at Hyperbiotics. Health writer and mama of two little girls, Julie's on a mission to empower others to live lives free of the microbial depletion many of us face today. For more ideas on how you can maximize wellness and benefit from the power of probiotics, be sure to subscribe to our newsletter.

Have an experience with Soil Based Organisms that you’d like to share?
We’d love to hear from you!

Posted in Gut Health, Top Articles