This article was originally published in September 2018 and was updated in June 2021 to include the latest research and products. As many readers recently commented, my previous top choice, RightBiotics Rx, underwent a formula change and no longer contains soil-based strains.
Soil-based probiotics have been touted for their ability to improve digestion, stimulate the immune system, and help maintain a healthy gut microbiota. On the other hand, some people believe that SBOs should be avoided at all costs, due to their spore-forming nature and ability to compete with resident gut microbes. So, should you be taking soil-based probiotics? If so, which formula or brand is best? Read on to find out.
Probiotics are becoming increasingly popular these days, in part due to the surge in research on the importance of the microbiome to our overall health. Anyone can now walk into a grocery store and be faced with an entire section dedicated to probiotics.
But not all probiotics are created equal. Some probiotics can be extremely therapeutic, while others are at best neutral and at worst potentially harmful.
One type of probiotics that has received a great deal of attention in recent years is soil-based organisms (SBOs). Perhaps no other category of probiotics is more controversial. Yet instead of an evidence-based approach that considers the diversity and complexity of SBOs, most voices on the subject have firmly taken up one side or the other.
In an effort to provide some clarity, this guide is a result of 80+ hours of independent research on soil-based organisms and the products commercially available today. I have no affiliations with any probiotic companies and had no preconceived notions about any particular products going into this.
First, I’ll review what soil-based organisms are, the controversy, and the evidence for the most commonly used species.
What are soil-based organisms?
The term soil-based organism (SBO) encompasses over 100 highly diverse species of bacteria (and other life forms) naturally found in soil. Before the introduction of industrialization and modern farming, we had regular, daily contact with these bacteria. In recent years, some SBOs have been isolated and adapted for use as probiotics.
A key characteristic of many SBOs is that they are spore-forming. When conditions are less favorable, SBOs can form a small spore, a dormant form of the bacterium with a hard, protective outer coating. In this form, the bacterium is highly resistant to heat, acid, and most antibiotics.
The controversy and the evidence
There is much debate within health circles about the safety of SBOs. Advocates claim that they are probiotics that normalize bowel function, aid in digestion, beneficially stimulate the immune system, and help re-seed the gut microbiota. They also praise SBOs for their ability to resist stomach acid and the lack of need for refrigeration.
Opponents of SBOs argue that because of their spore-forming nature, they proliferate rapidly, compete with our resident gut microbes, and in some cases, could even become pathogenic. Due to their spore-forming capacity and natural resistance to most antibiotics, an unintended overgrowth would be very difficult to treat.
My take: Many individual SBO strains have been shown to be beneficial, with few reported adverse effects, in randomized, placebo-controlled, human clinical trials. However, other strains have limited or no clinical evidence and may be able to cause infection in people with a compromised immune system. Rather than broadly labeling SBOs as good or bad, I think we need a more nuanced discussion – one that considers the evidence for each particular species, strain, and formula. That’s what I’ll attempt to provide in the next few sections.
First, we’ll look at the research on the species commonly used in soil-based probiotics, and then I will share my analysis of commercially available soil-based probiotic products. If you just want to see my recommendations, feel free to skip down to the “Conclusions” section at the end.
Common soil-based species used in probiotics:
Here are the eight soil-based species used most frequently in probiotics:
Bacillus coagulans (Weizmannia coagulans*)
Bacillus clausii (Alkalihalobacillus clausii*)
Bacillus indicus (Metabacillus indicus*)
You can see that until recently, most soil-based probiotics were from the Bacillus genus, two from the Enterococcus genus, and one from Clostridium. All of these fall within the major phylum Firmicutes.
*In 2020, researchers proposed reclassifying many Bacillus species into new genera to more accurately reflect their genetic divergence.1,2 Only species from the subtilis and cereus clades were recommended to be retained within the genus Bacillus.
For simplicity, and since most probiotic labels do not yet reflect this change, I will continue to use the old naming system throughout the remainder of this article.
The importance of probiotic strain
It’s important to note that microbes are denoted by their genus, species, and strain. The list above provides the genus (e.g. Bacillus) and species (e.g. subtilis), but does not tell you anything about the strain. Strain is denoted by a series of letters/numbers that comes after the species name (e.g. DE111).
Strain is extremely important since two strains of the same species can have very different characteristics.3 Their therapeutic effects are strain-specific. And as we’ll see shortly, some strains are more well-studied for certain conditions than others.
A recent study published in the journal PLOS One highlighted the strain-level differences of commercially available probiotics, underlining “the importance of accurate labeling to empower consumers to find clinical evidence behind each strain’s beneficial effects.”4 Unfortunately, only about half of probiotics on the market list the specific strains they contain on the label.
Clinical research for the top eight soil-based species
I searched PubMed and Google Scholar for every available human clinical trial for the eight species listed above, to determine which strains have the most supporting evidence.
To see my full analysis of the available literature, click here to download my Excel spreadsheet. For just the key findings, read on: