Dr. Michael Ruscio, DC is a clinician, Naturopathic Practitioner, clinical researcher, author, and adjunct professor at the University of Bridgeport. His work has been published in peer-reviewed medical journals and he speaks at conferences around the globe.
Soil-Based Probiotics Are Safe and Effective If You Take This One Precaution
Soil-based probiotics have been lauded as powerful gut restorers and tiny vitamin factories. They’ve also been vilified as dangerous and risky immune threats. Such differences of opinion aren’t very helpful to you when choosing dietary supplements.
Let’s clear up the confusion with a look at scientific research.
What Are Soil-Based Probiotics?
The age-old saying, “God made dirt, and dirt don’t hurt” may actually be true.
Soil-based probiotics are good bacteria in the soil that have evolved in contact with humans. Until very recently, humans were exposed to soil and soil-based organisms daily by eating, farming, and hunting.
Soil-based probiotics such as Bacillus subtilis are a part of our normal microbiome. They form spores that can survive harsh conditions, like stomach acid, irradiation, and high temperatures. This category of bacteria is also sometimes called spore-forming bacteria.
Which Soil-Based Probiotics Have Health Benefits?
The most studied soil-based probiotics are species in the genus Bacillus.
Like other types of probiotic bacteria, soil-based probiotics help maintain digestive health and regulate the immune system . Unlike other types of probiotics, they appear to colonize the digestive tract .
Clinical studies into Bacillus probiotic strains show benefits that are similar to better-studied probiotic species like Lactobacillus and Bifidobacterium.
Bacillus coagulans is the most studied soil-based probiotic. In nine clinical trials, B. coagulans was shown to have a positive effect on diarrhea [3, 4, 5, 6], bloating and abdominal pain [3, 5, 6, 7, 8, 9], SIBO , and constipation [10, 11].
Bacillus subtilis has shown some benefit in clinical trials for constipation  on its own. It has also been studied in combination with the soil-based probiotic Enterococcus faecium and has been shown to be helpful for irritable bowel syndrome (IBS) , constipation [14, 15, 16], and H. pylori treatment [13, 17]. Research data also suggests that laxatives or motility agents combined with Bacillus subtilis are more effective than the motility agents alone or a placebo [12, 15, 16].
Bacillus clausii has been shown in clinical trials to reduce side effects from H. pylori treatment , including nausea, diarrhea, and pain. It has also been shown to decrease acute diarrhea  and to help in the treatment of SIBO .
Bacillus licheniformis reduced the risk of gastrointestinal side effects from radiotherapy treatment , such as nausea, diarrhea, and vomiting. It also improved diarrhea symptoms in another clinical trial .
Soil-based probiotics have also been shown in studies to:
Increase secretory IgA, which plays an important role in immune function 
Despite these documented benefits of soil-based probiotics, a few studies show no benefit from soil-based probiotics.
In two studies, children with acute diarrhea showed no meaningful benefit with illness duration, stool consistency, or stool frequency from soil-based probiotics [31, 32]. Another study showed that Bacillus subtilis R0179 populated the digestive tract but didn’t improve gut symptoms .
Are Soil-Based Probiotics Safe?
In some circles, soil-based probiotics have a reputation for doing harm. Some claim spore-based probiotics may become invasive in the human gut. Others claim these species may cause a severe immune response in patients with a compromised immune system. So, are soil-based probiotics unsafe, or are they safe and helpful?
Soil-based probiotics are safe, as long as the product contains known soil bacteria species from a reputable supplier.
Safe Soil-Based Bacteria
As noted in the studies above, these soil-based probiotics have been shown to be safe and effective in a number of human clinical trials:
There have also been specific studies into the safety of these two Bacillus strains for human use:
Bacillus subtilis CU1 was found to be generally safe and non-toxic in a clinical trial , as well as in vitro studies [35, 36].
Bacillus clausii UBBC07 was found to be generally safe and non-toxic for human use in a clinical trial .
Controversial Soil-Based Bacteria
Some species of soil-based bacteria have been associated with adverse human effects, including Bacillus licheniformis and Enterococcus faecium. The EPA was asked to review the safety of Bacillus licheniformis in 1997.
In the summary of their review, the EPA concluded that Bacillus licheniformis is not pathogenic or toxic to humans . In fact, the study noted that Bacillus licheniformis is commonly found in water and soil and is known to naturally enter the human digestive tract.
Enterococcus faecium FS68 strain was also found to be safe and beneficial for human use .
Unsafe Soil-Based Bacteria
There are some dangerous species of soil-based bacteria.
The most famous example is Bacillus anthracis, also known as Anthrax. Anthrax isn’t just bad bacteria — it can kill you if you aren’t treated immediately with antibiotics . Another species of Bacillus, B. cereus, is known to cause a severe form of food poisoning .
Are Soil-Based Probiotics Safe? A Reality Check
No one avoids eating carrots because they’re in the same plant family as poison hemlock. And yet, internet advice continues to caution people to stay away from soil-based probiotics because some Bacillus bacteria are unsafe.
Research clearly shows that specific bacillus species are beneficial and safe.
And while it’s very unlikely that your soil-based probiotic supplement would be contaminated with Anthrax, it is important to pay attention to labelling and safety when buying ANY probiotic supplements.
Probiotic Labeling and Safety
In the United States, probiotics aren’t well regulated by the Food and Drug Administration (FDA) [42, 43], and dietary supplement label claims are often not accurate [44, 45, 46]. Inaccurate labels or contamination in manufacturing may increase the risk of ingesting undesirable bacterial species . One study of five brands of soil-based probiotics showed that only one brand matched its label claims .
The best way to safely use soil-based probiotic supplements is to choose high-quality products from reputable suppliers and manufacturers.
Use the following guidelines to help you choose quality products:
The product has a clearly stated list of species.
The product has a clearly stated number of colony-forming units (CFUs) in the billions.
The product has a manufacturing date or expiration date.
The product is labeled free of common allergens and other substances you may wish to avoid (e.g. gluten-free, non-GMO, vegan).
The product has Good Manufacturing Practices (GMP) certification.
The product is lab-verified for probiotic species and potency by third-party analysis (independent lab testing).
My soil-based probiotic supplement contains Bacillus coagulans and Bacillus subtilis probiotic strains and meets quality standards for probiotic supplements.
Using Soil-Based Probiotics
Soil-based probiotics are one of three categories of probiotics that work together synergistically like the legs on a three-legged stool. I advocate using Probiotic Triple Therapy because research suggests that single species formulas are less effective than multiple species formulas [30, 49, 50].
My experience in the clinic reflects this, as I have found that people get the best benefits of probiotics by using three categories together.
For soil-based probiotics, try one quality product, like our Soil-Based Probiotic, and see how you feel. Start with a dose of 100 billion CFU (colony forming units) per day and slowly work up to a higher dose.
If your symptoms improve, there is no need to further increase your dose. If you have any type of reaction when taking soil-based probiotics, you should stop.
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