The complete guide to soil-based probiotics

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 subtilis

Bacillus clausii (Alkalihalobacillus clausii*)

Bacillus indicus (Metabacillus indicus*)

Bacillus licheniformis

Enterococcus faecium

Enterococcus faecalis

Clostridium butyricum

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:

Bacillus (Weizmannia) coagulans

Bacillus coagulans is a gram-positive bacterium that produces L-lactic acid and, as a result, was formerly misclassified as Lactobacillus sporogenes. It exhibits many characteristics typical of the Lactobacillaceae family, but unlike most lactic acid bacteria, B. coagulans can form spores.

Six strains of B. coagulans have been well-studied in human clinical trials:

GBI-30, 6086 (“Ganeden BC30”): with at least 10 human placebo-controlled, randomized controlled trials (RCTs), this is one of the most well-studied soil-based strains. GBI-30, 6086 has been shown to improve irritable bowel syndrome (IBS),5–7 immune function,8,9 and may beneficially modulate the gut microbiota.10,11 In vitro studies suggest that it may aid in the digestion of fructose and lactose.12

LBSC (DSM 17654): two placebo-controlled RCTs showed benefits of this strain on IBS patients13 and patients with acute diarrhea and abdominal discomfort.14

MTCC 5856 (“LactoSpore”): two placebo-controlled RCTs showed that this strain significantly reduced bloating, abdominal pain, and depressive symptoms in IBS patients.15,16

SANK 70258 (“Lacris-S”): one placebo-controlled RCT and one open-label study found that this strain improved stool frequency in healthy adults with reduced stool frequency, with no adverse effects.17,18 A recent study using a model system of the human gut found that this strain suppressed pro-inflammatory bacteria in the family Enterobacteriaceae and increased the abundance of butyrate-producing Lachnospiraceae in healthy individuals.19  The GRAS notice for this strain cites two additional RCTs (not available in English databases) that reported no adverse events. The strain has been used as a food ingredient in Japan since 1966.20 In 1973, the formulation and fermentation technology of this strain was offered to Sanzyme Ltd and became SNZ 1969.

SNZ 1969: one placebo-controlled RCT found that this strain significantly improved colonic transit time and reduced bowel discomfort in adults with mild intermittent constipation.21 It has also been shown to be effective for bacterial vaginosis.22 Another RCT using SNZ 1969 in a three-strain formula along with B. clausii and B. subtilis found reduced belching, bloating, pain, and total symptoms in adults with GI discomfort.23

Unique IS-2 (“ProDURA”): four human randomized, placebo-controlled RCTs have found this strain to be efficacious for bacterial vaginosis24 and IBS in both children25,26 and adults.27 This strain has been shown to metabolize fructose in vitro.28

All six of these strains have also been assessed for safety as a food ingredient and received “Generally Recognized as Safe” (GRAS) status by the FDA.

Verdict: These strains of Bacillus coagulans appear to be safe, well-tolerated, and may be especially beneficial for those with bacterial vaginosis or IBS.

Bacillus subtilis

Bacillus subtilis is spore-forming, gram-positive bacterium and recognized as a normal inhabitant of the human gut.29 It has long been considered the “type species” of the Bacillus genus, and is one of the earliest- and best-studied bacteria. Even before the introduction of antibiotics, cultures of B. subtilis were popularly used worldwide as an immune stimulant to aid in the treatment of urinary tract and gastrointestinal disease.30,31

B. subtilis produces an enzyme that can degrade oxalate32 and may also produce small amounts of Vitamin K2. B. subtilis is found naturally in natto, a traditional Japanese food made from fermented soybeans.

Three strains of B. subtilis have demonstrated therapeutic effects in humans and have been tested for safety as a food ingredient:

DE111: two placebo-controlled RCTs of Division 1 athletes during off season training found that B. subtilis DE111 was well tolerated. Female athletes saw greater reductions in body fat percentage; male athletes saw reduced blood TNFalpha, a marker of inflammation. There were no effects on physical performance.33,34 Other RCTs found that DE111 improved bowel irregularity35, increased anti-inflammatory immune cell population activity36, decreased fasting glucose37 and reduced total cholesterol in healthy adults.38 This strain is Generally Recognized as Safe (GRAS) by the FDA.

CU1 (“LifeinU”): one placebo-controlled RCT found that ten-day supplementation with B. subtilis CU1 was well tolerated and improved immune function (fecal and salivary sIgA) in elderly adults.39 It does not exhibit any antibiotic resistance and was shown to be absent of toxigenic activity in vitro.40 It is manufactured in France and has been granted the “Qualified Presumption of Safety” designation by the European Food Safety Authority.

MB40 (“OPTI-BIOME”): one placebo-controlled RCT found that this study was well tolerated in healthy adults, reduce bloating intensity and GI symptoms in male subjects, and modestly improved general health.41 This strain is Generally Recognized as Safe (GRAS) by the FDA.

Two additional strains have been well-studied in Asia, though most of the literature is not available in English:

R0179 (“Medilac-S”): this strain is found in the Asian probiotic formulation Medilac-S, which also contains Enterococcus faecium R0026. Several placebo-controlled RCTs found that the two-strain preparation reduced IBS-related abdominal pain42,43 and improved bowel preparation for colonoscopy.44 A recent Chinese systematic review and meta-analysis of 53 clinical trials concluded that Medilac-S is also effective for inducing remission in ulcerative colitis.45 Two RCTs also found that isolated B. subtilis R0179 was well-tolerated and survived passage through the human GI tract.46,47

TO-A (“BIO-THREE”): this strain of B. subtilis, in combination with E. faecalis T-110 and C. butyricum TO-A, has been fairly well studied as the probiotic BIO-THREE in Asia. In RCTs, these three strains have been shown to reduce postoperative infections in patients undergoing surgery48 and shorten hospital stay for children with acute diarrhea.49  See “Probiotic-3” section below for more on this formulation.

Verdict: Commonly studied strains of B. subtilis appear to be safe, well-tolerated, and with no reported adverse effects. Some strains appear to be particularly beneficial for improving immune function and bowel regularity.

Bacillus clausii

Bacillus clausii is a spore-forming, gram-positive bacterium known for its antimicrobial activity against Staphylococcus aureus and Clostridioides difficile. It is considered a commensal microbe, and has been recovered from the small intestine and stool of healthy individuals.50

There are only two combinations of strains that have been studied in humans:

OC, NR, SIN, & T: These four strains have been extensively studied and used since 1958 as the Italian pharmaceutical preparation Enterogermina. The strains have been shown to be acid and bile resistant,51 and can be recovered in stool for 4-12 days following a single oral administration in humans.52 Independent analyses have confirmed that Enterogermina indeed contains B. clausii, as labeled.53

Enterogermina may be particularly beneficial for those with allergies, reducing nasal congestion and the need for anti-histamines.54–56 It has also been shown to reduce side effects during antibiotic treatment for H. pylori.57,58

One study of 40 patients diagnosed with “SIBO” found that taking Enterogermina for one month resulted in a normalization of glucose breath test result in 47 percent of patients.59 While I have major reservations about the use of breath testing, its notable that this rate is comparable to the normalization seen with many antibiotics used for SIBO treatment. Only one patient reported a side effect of constipation.

Despite the many documented benefits and overall safety profile of Enterogermina, there have been sporadic case reports of sepsis from Bacillus clausii. Most reports have been following probiotic usage in the older, critically ill, or immunocompromised individuals, many of whom received high-dose Enterogermina following treatment with broad-spectrum antibiotics.60–62

UBBC-07: in a single placebo-controlled, randomized trial of children with acute diarrhea in India, this strain was shown to improve stool consistency and reduce the duration of diarrhea.63 This strain has undergone toxicology studies and was determined to be safe for human consumption.64

Verdict: Enterogermina has documented efficacy in numerous randomized, placebo-controlled trails, and may be particularly beneficial for those with allergies or irritable bowel syndrome. Since beginning this analysis, I have tried Enterogermina myself and noticed improved tolerance to foods. Isolated case reports of sepsis suggest that it may be contraindicated in the elderly, those that are critically ill or immunocompromised, and individuals who have recently taken broad-spectrum antibiotics.

Enterogermina can be purchased from international online pharmacies or from Amazon as either capsules or liquid vials. The vials contain no added inactive ingredients. Shipment should not be an issue since B. clausii is heat-stable and does not require refrigeration.

Bacillus (Metabacillus) indicus:

Bacillus indicus is a spore-forming bacterium has been touted for its ability to potently stimulate the immune system and produce high levels of carotenoids, vitamins, and quinols.

In vitro and animal studies failed to find any potential for toxicity or pathogenicity of B. indicus HU36, the strain most often used in probiotics, and no infections in humans have been reported.65

However, after an exhaustive search of the literature, I could find no scientific studies of Bacillus indicus in humans (with the exception of three studies that used a preparation of five different Bacillus species – see “MegaSporeBiotic” section below).

Verdict: Currently lacking evidence in humans.

Bacillus licheniformis

Bacillus licheniformis is a gram-positive, spore-forming bacterium commonly used for industrial enzyme production. Of all soil-based species used in probiotics, B. licheniformis is perhaps the most controversial. According to some reports, B. licheniformis may be an opportunistic pathogen, and can cause infection in immunocompromised hosts.

However, other reports have concluded that the virulence of B. licheniformis is very low. B. licheniformis is found in many fermented foods traditionally consumed in Korean culture, and it has been isolated from the GI tract of healthy human volunteers, so at least some strains appear to be commensal.50

The authors of a U.S. Environmental Protection Agency report write:

In order to achieve an infection, either the number of microorganisms must be very high or the immune status of the host low […] While there have been cases of acute, self-limited gastroenteritis associated with the isolation of large numbers of this species, a toxic or direct effect on intestinal epithelia has not been demonstrated. It is difficult to ascertain whether the species in these reported cases, which are quite limited in number, actively participated in the infection or were isolated in conjunction with an unidentified pathogen.”66

A literature search revealed only four human studies of isolated Bacillus licheniformis, none of which provided strain information, and only one of which was randomized and placebo controlled.

(Three additional studies included B. licheniformis in a preparation of five different Bacillus species – see “MegaSporeBiotic” section below).

Verdict: While traditional fermented foods containing B. licheniformis are almost undoubtedly safe, I believe there is currently insufficient evidence to support high-dose supplementation of B. licheniformis. I think it’s best to err on the side of caution and avoid probiotics that contain this species.

Enterococcus faecium

Enterococcus faecium is a gram-positive bacterium. Though it is not spore-forming, it is tolerant of a wide range of environmental conditions. E. faecium is a normal resident of the human gut, fermenting carbohydrates and produces lactic acid as a byproduct. Some strains of E. faecium can be found in traditional fermented foods, such as dadih, an Indonesian fermented buffalo milk.67

However, E. faecium can also be pathogenic, causing diseases like neonatal meningitis and endocarditis. Many strains of this bacterium have developed antibiotic resistance and virulence factors that allow it to aggregate and form biofilms. In the United States, 80-90 percent of medical device-associated infections can be attributed to antibiotic-resistant E. faecium.68 Thus, there are concerns about its use as a probiotic.

Many different strains have been studied, but only two are worth highlighting, as they have been studied in multiple human trials:

M-74: This strain has a number of “randomized” clinical trials associated with it, but every single one gave the probiotic in conjunction with 50 micrograms of selenium.69–72 Many probiotics point to these studies to suggest that E. faecium can reduce cholesterol, but the lack of a selenium control group means that it’s entirely plausible that the selenium alone provided the therapeutic effect.

R0026 (“Medilac-S”): this strain is found in the Asian probiotic formulation Medilac-S, which also contains Bacillus subtilis R0179 and has been very well-studied in China. As mentioned above, several RCTs found that the two-strain preparation reduced IBS-related abdominal pain42,43 and improved bowel preparation for colonoscopy.44 A recent Chinese systematic review and meta-analysis of 53 clinical trials (most of which are not available in English) concluded that Medilac-S is also effective for inducing remission in ulcerative colitis.45

Verdict: With the exception of the strains in Medilac-S, few well-designed RCTs have demonstrated the efficacy of E. faecium. Given its potential to acquire multi-drug antibiotic resistance and cause infection. I would exercise caution with high doses of isolated E. faecium.

Enterococcus faecalis

Enterococcus faecalis is a gram-positive bacterium. Similar to E. faecium, it is not capable of forming spores yet fairly tolerant of harsh environmental conditions.

E. faecalis is a normal resident of the human gut, present in around 90-95 percent of people.73 This bacterium is often one of the first microbes to colonize the human GI tract in the early stages of life and plays a significant role in the development of the gut immune system.

T-110 (“BIO-THREE”): this strain of E. faecalis, in combination with B. subtilis TO-A and C. butyricum TO-A, has been heavily used and somewhat well studied as the probiotic BIO-THREE in Asia. Together, these three strains have been shown in RCTs to reduce postoperative infections in patients undergoing surgery48 and shorten hospital stay for children with acute diarrhea.49 (See “Probiotic-3” section below for more on this formulation.)

YM0831: one crossover study found that a single administration of this strain to healthy human subjects acutely improved blood glucose response to a sucrose tolerance test.74

Verdict: With the exception of the strain in BIO-THREE, few well-designed RCTs have demonstrated the efficacy of E. faecalis as a probiotic.

Clostridium butyricum

Clostridium butyricum is a natural resident of the human GI tract. It is one of the many bacteria in the gut that ferments dietary fiber and produces the beneficial short-chain fatty acid butyrate. Butyrate serves as a source of energy for colon epithelial cells, helps maintain the gut barrier, has anti-inflammatory effects, and protects against colon cancer.

Three strains have been well studied in humans:

CBM 588 (“MIYAIRI 588”): This strain of C. butyricum has been used as a probiotic in Asia since as early as 1963 in a pharmaceutical preparation called Miyairisan. It has been evaluated for safety and does not carry any genes encoding any known toxins or virulence factors.75

Two RCTs found that this strain reduces side effects for abdominal symptoms and diarrhea incidence in patients undergoing H. pylori eradication therapy.76,77 Another placebo-controlled RCT in ulcerative colitis patients found that fewer subjects in the group receiving MIYAIRI 588 developed pouchitis, though the effects were not statistically significant, and the placebo group was given lactose, which can exacerbate colitis in many people.78

TO-A (“BIO-THREE”): this strain of C. butyricum, in combination with E. faecalis T-110 and B. subtilis TO-A, has been heavily used and somewhat well studied as a probiotic in Asia. The combined formula is called BIO-THREE and has been shown in RCTs to reduce postoperative infections in patients undergoing surgery48 and shorten hospital stay for children with acute diarrhea.49 One RCT of ulcerative colitis patients also found lower relapse rates in the group receiving BIO-THREE, though the difference was not statistically significant.79 No changes were observed in short-chain fatty acid levels.

A Tai Ning: this strain, contained in a product called A Tai Ning, was recently shown in a large-scale, multi-center, placebo-controlled RCT to have significant benefits for diarrhea-predominant IBS. The study included 200 patients. After four weeks, the probiotic group had significant improvement in overall IBS-D symptoms, stool frequency, and quality of life compared to placebo. Only six patients experienced mild to moderate adverse symptoms (abdominal pain, bloating, etc.) of 100 patients receiving the probiotic.

Several studies for which I could not find any strain information found that C. butyricum reduced the incidence of sepsis and diarrhea in premature infants,80 and improved antigen-specific immunotherapy.81 In animal studies, C. butyricum has been shown to improve intestinal homeostasis and attenuate colitis.82

Verdict: I really like the idea of being able to supplement with isolated C. butyricum. It’s a normal inhabitant of the gut, appears to be safe and well-tolerated in randomized trials, and could help increase butyrate levels in a way that is unlikely to induce toxicity.

Unfortunately, the only option for isolated C. butyricum, Miyarisan, is not currently available in the U.S., and I haven’t been able to find any international sources that I trust. Miyairisan also contains lactose, cornstarch, and talc – not the best inactive ingredients for those with gut issues. The only alternative is to use the three-probiotic formulation Probiotic-3, which I’ll discuss more in the next section.

Product analysis

I have no affiliation with any of these companies or products. None of the recommendations here should be taken as medical advice.

Like all supplements, probiotics are not regulated by any governing agency, so it’s important to do your homework regarding their claims, sourcing, and manufacturing methods. Many probiotic companies use species and strains that lack clinical evidence, make unsubstantiated statements, and cite highly questionable “research”.

In this section, I break down the ingredients, quality, claims, and evidence of ten of the most popular SBO products on the market.

While you might argue that a company’s marketing is less important than their product’s ingredients, I think it’s still a key factor to consider. If they can’t provide evidence-based claims on their website or even sound remotely scientific, I don’t trust them to be manufacturing a high-quality product that I’m going to take on a daily basis and recommend to readers and clients.

Probiotic-3 (Advanced Orthomolecular Research)

Soil-based species: Bacillus subtilis TO-A, E. faecium T-110, and C. butyricum TO-A (this combination is also known as “BIO-THREE”)

Colony-forming units: 1.2 million CFU / 36 million CFU / 1.2 million CFU

Other ingredients: contains lactose, potato starch, polyvinyl alcohol, and polyvinylpyrrolidone (may be an issue for many with gut symptoms)

What they claim on their website:

A clinically proven formula that works like a prebiotic, probiotic, symbiotic, and postbiotic all in one to support microbiome and gut health.

  • The only formula that has unique probiotics as well as supporting strains to increase colonization and effectiveness, and naturally produces short-chain fatty acids like butyrate and propionate
  • Reduces the growth of pathogenic bacteria while promoting the growth of beneficial bacteria like Bifidobacterium and Akkermansia
  • Normalizes the inflammatory response, promotes detoxification, supports immunity and provides relief from allergies”

They reference several studies of BIO-THREE.83–85

Verdict: Inclusion of E. faecium is questionable, but the formula has shown benefits in several randomized controlled trials. Not recommended to those sensitive to lactose, polyvinyl alcohol, or potato starch.

MegaSporeBiotic (Microbiome Labs)

Soil-based species: B. coagulans SC-208, B. subtilis HU58, B. clausii SC-109, B. indicus HU36, and B. licheniformis SL-307

Colony-forming units: 2 billion CFU

Other ingredients: cellulose, vegetable capsule (cellulose and water)

What they claim on their website: “MegaSporeBiotic™ is a 100% spore-based, broad-spectrum probiotic shown to maintain healthy gut barrier function. This unique all-spore formula effectively RECONDITIONS the gut by promoting microbial diversity and maintaining key health-promoting, commensal gut bacteria. MegaSporeBiotic™ boasts a 5-year shelf-life, does not require refrigeration, and maintains a healthy gut microbiome.”

Their clinical research:

In a 2017 study, MegaSporeBiotic was shown to reduce blood endotoxin, a measure of intestinal permeability, by 42 percent after a high-fat cheese pizza meal, compared to a 36 percent increase in volunteers receiving placebo.86  However, the researchers hand-selected a group of 25 endotoxin hyper-responders for the study – not the most translatable to the ability of MegaSporeBiotic to maintain or improve gut barrier function in a general population.

In a 2019 study, 90 irritable bowel syndrome patients without constipation were treated with the antibiotic rifaximin for ten days, followed by either a nutraceutical agent (containing Bifidobacterium longum W11, soluble fiber, and B vitamins), a low FODMAP diet, or MegaSporeBiotic for 34 days.87 IBS signs and symptoms decreased with each visit for all groups, with MegaSporeBiotic showing a modest difference at the third time point. The study was not blinded or placebo-controlled – a major limitation, especially for a study with IBS, where placebo response can be as high as 40-50 percent.88

In a 2020 study, 80 participants with high triglycerides (>150 mg/dL) were randomized to receive two capsules of MegaSporeBiotic or placebo for three months. Compared to the placebo group, participants consuming the probiotics had a significant reduction in non-fasting triglycerides levels. Other measures of metabolic health were not included. There were no reported adverse effects.

My comments: Currently, there is no evidence that this particular formulation increases microbial diversity, promotes diversity or maintains health-promoting, commensal gut bacteria, as their website might suggest.

Criticisms aside, I am really pleased that Microbiome Labs is making more of an effort to perform peer-reviewed research on their product. I hope that their future clinical research will emphasize randomized, placebo-controlled trials with a more rigorous design.

Verdict: Inclusion of B. licheniformis and B. indicus is questionable, as few studies have been performed on the safety or therapeutic benefit of these strains. Three clinical trials of the combined 5-strain formula showed modest benefits. Given a choice, I would still choose products that have more well-established safety profiles and more rigorous research to back their claims.

Just Thrive (Microbiome Labs)

Soil-based species: B. coagulans SC-208, B. subtilis HU58, B. clausii SC-109, B. indicus HU36 (same as MegaSporebiotic but without B. licheniformis)

Colony-forming units: 3 billion CFU

Other ingredients: cellulose, hydroxypropyl methyl cellulose capsule

What they claim on their website: “Our breakthrough, award-winning probiotic contains the proprietary strain, Bacillus Indicus Hu36, which produces antioxidants directly in the digestive system where they can be best absorbed by your body. […] The spores in Just Thrive have been successfully used to enhance digestive health in the progressive health and wellness space for more than 50 years.” 

What the evidence says: There is no research to confirm that Bacillus indicus HU36 produces antioxidants in humans, or that these can be absorbed by the digestive tract. While Bacillus species have been used as probiotics for more than 50 years, the specific strains in JustThrive have not been used or studied for very long.

Verdict: Contains B. indicus, which has little clinical evidence, though the included strain has been suggested to be safe for human consumption. Likely has some of the clinical benefits of MegaSporeBiotic but without the controversial inclusion of B. licheniformis. The language on their website has improved since I first wrote this analysis, but still makes claims that are not backed by any clinical evidence.

Proflora 4R (Bio-Botanical Research)

Soil-based species: B. coagulans SC-208, B. subtilis HU58, B. clausii SC-109 (similar to MegaSporebiotic and JustThrive but does not contain B. indicus or licheniformis)

Colony-forming units: 3 billion CFU

Other ingredients: 100mg quercetin, 100mg marshmallow root, 2mg aloe vera extract, microcrystalline cellulose, vegetable capsule (cellulose and water)

What they claim on their website: Proflora®4R is a unique spore-based probiotic with additional botanicals to support microbial balance and GI health. The combination of quercetin, marshmallow root, and aloe vera extract in Proflora® 4R provide additional nutritional support for healthy microbial balance, with just one capsule per day.”

Verdict: Contains a good selection of species, but the included strains have not been well-studied. The addition of quercetin, marshmallow root, and aloe may support gut barrier integrity.

ProBioSpore (Designs for Health) – NEW

Soil-based species: B. coagulans MTCC 5856 (Lactospore), B. coagulans SNZ 1969, B. coagulans Lacris-15, B. subtilis DE111, B. clausii CSI08

Colony-forming units: 10 billion CFU

Other ingredients: microcrystalline cellulose, hypromellose capsule, medium chain triglycerides, silicon dioxide

What they claim on their website: “ProbioSpore™ is an industry-leading, broad-spectrum, spore-based probiotic. It is comprised of a diverse combination of 5 different bacillus strains formulated to optimize gastrointestinal health.”

Verdict: Contains only well-studied species, but includes at least one strain (CSI08) that has never been studied in humans.

Gut Recovery (Jetson) – NEW

Soil-based species: B. coagulans MTCC 5856 (Lactospore), B. subtilis DE111, B. clausii CSI08

Other species: Saccharomyces boulardii DBVPG 6763, Lactobacillus rhamnosus GG

Colony-forming units: 15 billion CFU (per 2 packets)

Other ingredients: inulin, rice hull

What they claim on their website: “Gut Recovery is a powerful, multi-strain probiotic that maintains digestive balance during and after a course of antibiotics. By definition, antibiotics kill bacteria – which means they not only kill the bad, they kill the good too.”

“Gut Recovery is a flavorless powder that survives an antibiotic attack and replenishes the good bacteria wiped out by antibiotics. It can also combat uncomfortable antibiotic-related symptoms like nausea, diarrhea and yeast infections.”

What the science really says: The soil-based strains in this product will likely survive a course of antibiotics, at least in their spore form, but there is no evidence to suggest that they can replenish gut bacteria wiped out by antibiotics. I’ve written before about why we should think twice about taking high-dose probiotics with antibiotics, and other ways to support antibiotic recovery instead.

Verdict: Contains only well-studied species, but the strain of B. clausii this formula contains has never been studied in humans. It is also unclear how much of each strain is in this formula.

Digestive Health Probiotic (Doctor’s Best) – NEW

Soil-based species: B. coagulans MTCC 5856 (LactoSpore)

Colony-forming units: 2 billion CFU

Other ingredients: modified cellulose capsule, maltodextrin

What they claim on their website: “Doctor’s Best Digestive Health Probiotic contains LactoSpore, a shelf-stable probiotic capable of withstanding the acidic environment of the stomach. LactoSpore has been shown to improve digestive upset and constipation. It has also been shown to help prevent episodes of diarrhea.”

“LactoSpore (B. Coagulans strain) helps prevent the growth of bad bacteria (pathogenic microbes) and allows good bacteria (B. coagulans) to dominate the gut flora.”

My only comment: we really don’t want B. coagulans to dominate the gut flora. If anything, it should be a minor component of a healthy gut ecosystem.

Verdict: Contains LactoSpore, a well-studied strain of B. coagulans. Inclusion of maltodextrin is not ideal, as this food additive has been shown to alter microbiota and host functions.

Bacillus Coagulans (Thorne Research) – NEW

Soil-based species: B. coagulans MTCC 5856 (LactoSpore)

Note: the product label does not list the strain, but my communication with Thorne Research confirmed that the product contains LactoSpore.

Colony-forming units: 2 billion CFU

Other ingredients: microcrystalline cellulose, hypromellose capsule, silicon dioxide

What they claim on their website:“A stable probiotic bacteria that survives stomach acid and retains its potency in the intestines, where it can support GI upset, such as occasional gas, bloating, constipation or diarrhea.”

Verdict: Contains LactoSpore, a well-studied strain of B. coagulans. However, it also contains silicon dioxide, which has been shown to have negative effects on the gut microbiota and cause inflammatory damage in the gut.89

AFI LactoSpore Probiotic (America’s Finest, Inc.) – NEW

Soil-based species: B. coagulans MTCC 5856 (LactoSpore)

Colony-forming units: 2 billion CFU

Other ingredients: rice flour, hypromellose capsule

What they claim on their website: “Probiotic LactoSpore® helps normalize and maintain a healthy intestinal flora. [..] LactoSpore may be chosen as the probiotic of choice for several reasons including history of use, stability of spores, Generally Recognized as Safe (GRAS) status, documented clinical effectiveness and potential health benefits (normalizing intestinal flora/immune enhancement and non-GI tract conditions).”

“AFI products are produced in a GMP-certified and NSF-approved manufacturing facility.”

What the science says: it’s unclear whether the LactoSpore strain can “normalize” the intestinal microbiota in humans. Its documented health benefits are primarily for reducing IBS symptoms.

Verdict: Contains LactoSpore, a well-studied strain of B. coagulans, and no problematic inactive ingredients. A good overall choice, especially for those with irritable bowel syndrome that just want to try a single strain formula.

TOP CHOICE: CoreBiotic (Researched Nutritionals) – NEW

Soil-based species: B. coagulans SNZ1969, B. coagulans MTCC 5856 (“LactoSpore”), B. subtilis DE111

Colony-forming units: 5.5 billion CFU

Also contains: 330 mg of Organic VitaFiber®, a prebiotic from cassava root (Note: they also make another version, CoreBiotic Sensitive, that does not contain added fiber)

Other ingredients: capsule shell (hypromellose, water), low moisture rice dextrin, medium-chain triglycerides, rice bran

What they claim on their website: “CoreBiotic® combines three fully sequenced and registered spore-based probiotics along with VitaFiber® prebiotic to support a healthy microbiome. Each strain was specifically chosen for its mechanisms of action, backed by supporting research.”

“Each strain in CoreBiotic® is identified by genomic sequencing for specificity so that you know you are getting the same product every time. Only strain-specific probiotics have undergone rigorous genomic studies, guaranteeing accurate strain specificity, potency, and safety.”

Verdict: Contains three strains, all of which have been studied in human clinical trials and received Generally Recognized As Safe distinction! It also boasts a high CFU count compared to many probiotics on the market. The inclusion of rice dextrin isn’t ideal, but overall a solid choice that I’ll be excited to try myself and with clients. The strains in this product have been shown to be particularly beneficial for irritable bowel syndrome.

Note: CoreBiotics’ website only sells to healthcare practitioners, so you’ll need a practitioner to purchase or to get it from an outside seller.

Other Products:

To pre-empt questions on other formulas, here are a few quick notes on some other popular products:

Amy Myers Primal Earth Probiotic: contains the same un-studied strains as Proflora 4R

ATH Organics Gut Health Probiotics: contains Bacillus subtilis DE111, a well-studied strain, but no strain info for other species

Ancient Nutrition SBO Probiotics: no strain info

BodyBiotics SBO Probiotics: no strain info, contains Bacillus licheniformus

Codeage SBO Probiotic: no strain info

Dr. Ruscio Soil-Based Probiotic: no strain info

Enviromedica Terraflora: contains Bacillus pumilus and Bacillus megaterium, two species that have never been studied in humans

Garden of Life Primal Defense HSO Probiotic: does not actually contain SBOs

Klaire Labs Biospora: no strain info

Physician’s Choice SBO Probiotic: no strain info

Prescript-Assist – formula changed in 2017, contains many un-studied species

Primal Blueprint Primal Probiotics: formula changed, no longer contains SBOs

RealDose Nutrition RightBiotics RX: was originally my top choice, but unfortunately changed its formula and no longer contains SBOs

Schiff Digestive Advantage Daily Probiotics: contains Bacillus coagulans GBI-30, 6086, a well-studied strain, but also contains maltodextrin and titanium dioxide.

Smarter Nutrition Gut Health Probiotics: no strain info for B. clausii or B. subtilis

Swanson Soil-Based Organisms: does not actually contain SBOs

YouTheory Spore Probiotic: contains two un-studied strains

Conclusion

To sum up, soil-based organisms are quite well studied and have been shown in randomized clinical trials to be efficacious for a wide range of conditions. However, there is a lot of heterogeneity in soil-based microbes. I strongly advise choosing products that use high-quality manufacturing techniques and clinically-tested strains.

Currently, I am primarily using both Enterogermina and CoreBiotic Sensitive for myself and with my clients. I may occasionally try AFI LactoSpore, or Probiotic-3 in clients with low Clostridia or butyrate production. This is certainly subject to change, as more studies are available on particular species, strains, and formulas.

Note that every person will respond differently to probiotics. Response will depend on which probiotic you take, the dosage, which microbes you already have in your gut, and the health of your gut and immune system. When possible, choose probiotic strains that have been studied for your particular health condition. The right probiotic may not even be an SBO at all!

It’s possible that in some severe cases, we should look to heal the gut and treat gut pathologies before incorporating high-dose SBO probiotics. This may be especially true after antibiotics. I eagerly await more research on how individual strains and formulations of SBOs might impact the gut microbiota and gut environment in different contexts.

Additionally, I recommend avoiding SBOs completely if you are critically ill or immunocompromised. We still don’t have a good understanding of how these organisms act in vulnerable populations, and there have been case reports of adverse effects in those without sufficient immune function.

Of course, I also recommend getting exposure to SBOs the natural way – this means consuming organically grown vegetables, spending time in natural environments, and getting exposure to dirt through gardening or other outdoor activities!

It also means eating plenty of properly prepared fermented foods, if you tolerate them. Several popular kombucha brands now contain well-studied SBO strains. GTs kombucha contains Bacillus coagulans GBI-30, 6086, and a personal favorite, the new Kirkland brand kombucha, contains Bacillus subtilis DE111! As with all fermented foods, be sure to start slowly.

I will plan to update and reevaluate this guide periodically as more research is published and as companies (hopefully) become more transparent with their strains and evidence-based in their marketing claims. To be notified of any future updates, be sure to subscribe to my newsletter.

What soil-based probiotics do you take? Will this influence which products you use? Share your thoughts in the comments below!

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The complete guide to soil-based probiotics

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 subtilis

Bacillus clausii (Alkalihalobacillus clausii*)

Bacillus indicus (Metabacillus indicus*)

Bacillus licheniformis

Enterococcus faecium

Enterococcus faecalis

Clostridium butyricum

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:

Bacillus (Weizmannia) coagulans

Bacillus coagulans is a gram-positive bacterium that produces L-lactic acid and, as a result, was formerly misclassified as Lactobacillus sporogenes. It exhibits many characteristics typical of the Lactobacillaceae family, but unlike most lactic acid bacteria, B. coagulans can form spores.

Six strains of B. coagulans have been well-studied in human clinical trials:

GBI-30, 6086 (“Ganeden BC30”): with at least 10 human placebo-controlled, randomized controlled trials (RCTs), this is one of the most well-studied soil-based strains. GBI-30, 6086 has been shown to improve irritable bowel syndrome (IBS),5–7 immune function,8,9 and may beneficially modulate the gut microbiota.10,11 In vitro studies suggest that it may aid in the digestion of fructose and lactose.12

LBSC (DSM 17654): two placebo-controlled RCTs showed benefits of this strain on IBS patients13 and patients with acute diarrhea and abdominal discomfort.14

MTCC 5856 (“LactoSpore”): two placebo-controlled RCTs showed that this strain significantly reduced bloating, abdominal pain, and depressive symptoms in IBS patients.15,16

SANK 70258 (“Lacris-S”): one placebo-controlled RCT and one open-label study found that this strain improved stool frequency in healthy adults with reduced stool frequency, with no adverse effects.17,18 A recent study using a model system of the human gut found that this strain suppressed pro-inflammatory bacteria in the family Enterobacteriaceae and increased the abundance of butyrate-producing Lachnospiraceae in healthy individuals.19  The GRAS notice for this strain cites two additional RCTs (not available in English databases) that reported no adverse events. The strain has been used as a food ingredient in Japan since 1966.20 In 1973, the formulation and fermentation technology of this strain was offered to Sanzyme Ltd and became SNZ 1969.

SNZ 1969: one placebo-controlled RCT found that this strain significantly improved colonic transit time and reduced bowel discomfort in adults with mild intermittent constipation.21 It has also been shown to be effective for bacterial vaginosis.22 Another RCT using SNZ 1969 in a three-strain formula along with B. clausii and B. subtilis found reduced belching, bloating, pain, and total symptoms in adults with GI discomfort.23

Unique IS-2 (“ProDURA”): four human randomized, placebo-controlled RCTs have found this strain to be efficacious for bacterial vaginosis24 and IBS in both children25,26 and adults.27 This strain has been shown to metabolize fructose in vitro.28

All six of these strains have also been assessed for safety as a food ingredient and received “Generally Recognized as Safe” (GRAS) status by the FDA.

Verdict: These strains of Bacillus coagulans appear to be safe, well-tolerated, and may be especially beneficial for those with bacterial vaginosis or IBS.

Bacillus subtilis

Bacillus subtilis is spore-forming, gram-positive bacterium and recognized as a normal inhabitant of the human gut.29 It has long been considered the “type species” of the Bacillus genus, and is one of the earliest- and best-studied bacteria. Even before the introduction of antibiotics, cultures of B. subtilis were popularly used worldwide as an immune stimulant to aid in the treatment of urinary tract and gastrointestinal disease.30,31

B. subtilis produces an enzyme that can degrade oxalate32 and may also produce small amounts of Vitamin K2. B. subtilis is found naturally in natto, a traditional Japanese food made from fermented soybeans.

Three strains of B. subtilis have demonstrated therapeutic effects in humans and have been tested for safety as a food ingredient:

DE111: two placebo-controlled RCTs of Division 1 athletes during off season training found that B. subtilis DE111 was well tolerated. Female athletes saw greater reductions in body fat percentage; male athletes saw reduced blood TNFalpha, a marker of inflammation. There were no effects on physical performance.33,34 Other RCTs found that DE111 improved bowel irregularity35, increased anti-inflammatory immune cell population activity36, decreased fasting glucose37 and reduced total cholesterol in healthy adults.38 This strain is Generally Recognized as Safe (GRAS) by the FDA.

CU1 (“LifeinU”): one placebo-controlled RCT found that ten-day supplementation with B. subtilis CU1 was well tolerated and improved immune function (fecal and salivary sIgA) in elderly adults.39 It does not exhibit any antibiotic resistance and was shown to be absent of toxigenic activity in vitro.40 It is manufactured in France and has been granted the “Qualified Presumption of Safety” designation by the European Food Safety Authority.

MB40 (“OPTI-BIOME”): one placebo-controlled RCT found that this study was well tolerated in healthy adults, reduce bloating intensity and GI symptoms in male subjects, and modestly improved general health.41 This strain is Generally Recognized as Safe (GRAS) by the FDA.

Two additional strains have been well-studied in Asia, though most of the literature is not available in English:

R0179 (“Medilac-S”): this strain is found in the Asian probiotic formulation Medilac-S, which also contains Enterococcus faecium R0026. Several placebo-controlled RCTs found that the two-strain preparation reduced IBS-related abdominal pain42,43 and improved bowel preparation for colonoscopy.44 A recent Chinese systematic review and meta-analysis of 53 clinical trials concluded that Medilac-S is also effective for inducing remission in ulcerative colitis.45 Two RCTs also found that isolated B. subtilis R0179 was well-tolerated and survived passage through the human GI tract.46,47

TO-A (“BIO-THREE”): this strain of B. subtilis, in combination with E. faecalis T-110 and C. butyricum TO-A, has been fairly well studied as the probiotic BIO-THREE in Asia. In RCTs, these three strains have been shown to reduce postoperative infections in patients undergoing surgery48 and shorten hospital stay for children with acute diarrhea.49  See “Probiotic-3” section below for more on this formulation.

Verdict: Commonly studied strains of B. subtilis appear to be safe, well-tolerated, and with no reported adverse effects. Some strains appear to be particularly beneficial for improving immune function and bowel regularity.

Bacillus clausii

Bacillus clausii is a spore-forming, gram-positive bacterium known for its antimicrobial activity against Staphylococcus aureus and Clostridioides difficile. It is considered a commensal microbe, and has been recovered from the small intestine and stool of healthy individuals.50

There are only two combinations of strains that have been studied in humans:

OC, NR, SIN, & T: These four strains have been extensively studied and used since 1958 as the Italian pharmaceutical preparation Enterogermina. The strains have been shown to be acid and bile resistant,51 and can be recovered in stool for 4-12 days following a single oral administration in humans.52 Independent analyses have confirmed that Enterogermina indeed contains B. clausii, as labeled.53

Enterogermina may be particularly beneficial for those with allergies, reducing nasal congestion and the need for anti-histamines.54–56 It has also been shown to reduce side effects during antibiotic treatment for H. pylori.57,58

One study of 40 patients diagnosed with “SIBO” found that taking Enterogermina for one month resulted in a normalization of glucose breath test result in 47 percent of patients.59 While I have major reservations about the use of breath testing, its notable that this rate is comparable to the normalization seen with many antibiotics used for SIBO treatment. Only one patient reported a side effect of constipation.

Despite the many documented benefits and overall safety profile of Enterogermina, there have been sporadic case reports of sepsis from Bacillus clausii. Most reports have been following probiotic usage in the older, critically ill, or immunocompromised individuals, many of whom received high-dose Enterogermina following treatment with broad-spectrum antibiotics.60–62

UBBC-07: in a single placebo-controlled, randomized trial of children with acute diarrhea in India, this strain was shown to improve stool consistency and reduce the duration of diarrhea.63 This strain has undergone toxicology studies and was determined to be safe for human consumption.64

Verdict: Enterogermina has documented efficacy in numerous randomized, placebo-controlled trails, and may be particularly beneficial for those with allergies or irritable bowel syndrome. Since beginning this analysis, I have tried Enterogermina myself and noticed improved tolerance to foods. Isolated case reports of sepsis suggest that it may be contraindicated in the elderly, those that are critically ill or immunocompromised, and individuals who have recently taken broad-spectrum antibiotics.

Enterogermina can be purchased from international online pharmacies or from Amazon as either capsules or liquid vials. The vials contain no added inactive ingredients. Shipment should not be an issue since B. clausii is heat-stable and does not require refrigeration.

Bacillus (Metabacillus) indicus:

Bacillus indicus is a spore-forming bacterium has been touted for its ability to potently stimulate the immune system and produce high levels of carotenoids, vitamins, and quinols.

In vitro and animal studies failed to find any potential for toxicity or pathogenicity of B. indicus HU36, the strain most often used in probiotics, and no infections in humans have been reported.65

However, after an exhaustive search of the literature, I could find no scientific studies of Bacillus indicus in humans (with the exception of three studies that used a preparation of five different Bacillus species – see “MegaSporeBiotic” section below).

Verdict: Currently lacking evidence in humans.

Bacillus licheniformis

Bacillus licheniformis is a gram-positive, spore-forming bacterium commonly used for industrial enzyme production. Of all soil-based species used in probiotics, B. licheniformis is perhaps the most controversial. According to some reports, B. licheniformis may be an opportunistic pathogen, and can cause infection in immunocompromised hosts.

However, other reports have concluded that the virulence of B. licheniformis is very low. B. licheniformis is found in many fermented foods traditionally consumed in Korean culture, and it has been isolated from the GI tract of healthy human volunteers, so at least some strains appear to be commensal.50

The authors of a U.S. Environmental Protection Agency report write:

In order to achieve an infection, either the number of microorganisms must be very high or the immune status of the host low […] While there have been cases of acute, self-limited gastroenteritis associated with the isolation of large numbers of this species, a toxic or direct effect on intestinal epithelia has not been demonstrated. It is difficult to ascertain whether the species in these reported cases, which are quite limited in number, actively participated in the infection or were isolated in conjunction with an unidentified pathogen.”66

A literature search revealed only four human studies of isolated Bacillus licheniformis, none of which provided strain information, and only one of which was randomized and placebo controlled.

(Three additional studies included B. licheniformis in a preparation of five different Bacillus species – see “MegaSporeBiotic” section below).

Verdict: While traditional fermented foods containing B. licheniformis are almost undoubtedly safe, I believe there is currently insufficient evidence to support high-dose supplementation of B. licheniformis. I think it’s best to err on the side of caution and avoid probiotics that contain this species.

Enterococcus faecium

Enterococcus faecium is a gram-positive bacterium. Though it is not spore-forming, it is tolerant of a wide range of environmental conditions. E. faecium is a normal resident of the human gut, fermenting carbohydrates and produces lactic acid as a byproduct. Some strains of E. faecium can be found in traditional fermented foods, such as dadih, an Indonesian fermented buffalo milk.67

However, E. faecium can also be pathogenic, causing diseases like neonatal meningitis and endocarditis. Many strains of this bacterium have developed antibiotic resistance and virulence factors that allow it to aggregate and form biofilms. In the United States, 80-90 percent of medical device-associated infections can be attributed to antibiotic-resistant E. faecium.68 Thus, there are concerns about its use as a probiotic.

Many different strains have been studied, but only two are worth highlighting, as they have been studied in multiple human trials:

M-74: This strain has a number of “randomized” clinical trials associated with it, but every single one gave the probiotic in conjunction with 50 micrograms of selenium.69–72 Many probiotics point to these studies to suggest that E. faecium can reduce cholesterol, but the lack of a selenium control group means that it’s entirely plausible that the selenium alone provided the therapeutic effect.

R0026 (“Medilac-S”): this strain is found in the Asian probiotic formulation Medilac-S, which also contains Bacillus subtilis R0179 and has been very well-studied in China. As mentioned above, several RCTs found that the two-strain preparation reduced IBS-related abdominal pain42,43 and improved bowel preparation for colonoscopy.44 A recent Chinese systematic review and meta-analysis of 53 clinical trials (most of which are not available in English) concluded that Medilac-S is also effective for inducing remission in ulcerative colitis.45

Verdict: With the exception of the strains in Medilac-S, few well-designed RCTs have demonstrated the efficacy of E. faecium. Given its potential to acquire multi-drug antibiotic resistance and cause infection. I would exercise caution with high doses of isolated E. faecium.

Enterococcus faecalis

Enterococcus faecalis is a gram-positive bacterium. Similar to E. faecium, it is not capable of forming spores yet fairly tolerant of harsh environmental conditions.

E. faecalis is a normal resident of the human gut, present in around 90-95 percent of people.73 This bacterium is often one of the first microbes to colonize the human GI tract in the early stages of life and plays a significant role in the development of the gut immune system.

T-110 (“BIO-THREE”): this strain of E. faecalis, in combination with B. subtilis TO-A and C. butyricum TO-A, has been heavily used and somewhat well studied as the probiotic BIO-THREE in Asia. Together, these three strains have been shown in RCTs to reduce postoperative infections in patients undergoing surgery48 and shorten hospital stay for children with acute diarrhea.49 (See “Probiotic-3” section below for more on this formulation.)

YM0831: one crossover study found that a single administration of this strain to healthy human subjects acutely improved blood glucose response to a sucrose tolerance test.74

Verdict: With the exception of the strain in BIO-THREE, few well-designed RCTs have demonstrated the efficacy of E. faecalis as a probiotic.

Clostridium butyricum

Clostridium butyricum is a natural resident of the human GI tract. It is one of the many bacteria in the gut that ferments dietary fiber and produces the beneficial short-chain fatty acid butyrate. Butyrate serves as a source of energy for colon epithelial cells, helps maintain the gut barrier, has anti-inflammatory effects, and protects against colon cancer.

Three strains have been well studied in humans:

CBM 588 (“MIYAIRI 588”): This strain of C. butyricum has been used as a probiotic in Asia since as early as 1963 in a pharmaceutical preparation called Miyairisan. It has been evaluated for safety and does not carry any genes encoding any known toxins or virulence factors.75

Two RCTs found that this strain reduces side effects for abdominal symptoms and diarrhea incidence in patients undergoing H. pylori eradication therapy.76,77 Another placebo-controlled RCT in ulcerative colitis patients found that fewer subjects in the group receiving MIYAIRI 588 developed pouchitis, though the effects were not statistically significant, and the placebo group was given lactose, which can exacerbate colitis in many people.78

TO-A (“BIO-THREE”): this strain of C. butyricum, in combination with E. faecalis T-110 and B. subtilis TO-A, has been heavily used and somewhat well studied as a probiotic in Asia. The combined formula is called BIO-THREE and has been shown in RCTs to reduce postoperative infections in patients undergoing surgery48 and shorten hospital stay for children with acute diarrhea.49 One RCT of ulcerative colitis patients also found lower relapse rates in the group receiving BIO-THREE, though the difference was not statistically significant.79 No changes were observed in short-chain fatty acid levels.

A Tai Ning: this strain, contained in a product called A Tai Ning, was recently shown in a large-scale, multi-center, placebo-controlled RCT to have significant benefits for diarrhea-predominant IBS. The study included 200 patients. After four weeks, the probiotic group had significant improvement in overall IBS-D symptoms, stool frequency, and quality of life compared to placebo. Only six patients experienced mild to moderate adverse symptoms (abdominal pain, bloating, etc.) of 100 patients receiving the probiotic.

Several studies for which I could not find any strain information found that C. butyricum reduced the incidence of sepsis and diarrhea in premature infants,80 and improved antigen-specific immunotherapy.81 In animal studies, C. butyricum has been shown to improve intestinal homeostasis and attenuate colitis.82

Verdict: I really like the idea of being able to supplement with isolated C. butyricum. It’s a normal inhabitant of the gut, appears to be safe and well-tolerated in randomized trials, and could help increase butyrate levels in a way that is unlikely to induce toxicity.

Unfortunately, the only option for isolated C. butyricum, Miyarisan, is not currently available in the U.S., and I haven’t been able to find any international sources that I trust. Miyairisan also contains lactose, cornstarch, and talc – not the best inactive ingredients for those with gut issues. The only alternative is to use the three-probiotic formulation Probiotic-3, which I’ll discuss more in the next section.

Product analysis

I have no affiliation with any of these companies or products. None of the recommendations here should be taken as medical advice.

Like all supplements, probiotics are not regulated by any governing agency, so it’s important to do your homework regarding their claims, sourcing, and manufacturing methods. Many probiotic companies use species and strains that lack clinical evidence, make unsubstantiated statements, and cite highly questionable “research”.

In this section, I break down the ingredients, quality, claims, and evidence of ten of the most popular SBO products on the market.

While you might argue that a company’s marketing is less important than their product’s ingredients, I think it’s still a key factor to consider. If they can’t provide evidence-based claims on their website or even sound remotely scientific, I don’t trust them to be manufacturing a high-quality product that I’m going to take on a daily basis and recommend to readers and clients.

Probiotic-3 (Advanced Orthomolecular Research)

Soil-based species: Bacillus subtilis TO-A, E. faecium T-110, and C. butyricum TO-A (this combination is also known as “BIO-THREE”)

Colony-forming units: 1.2 million CFU / 36 million CFU / 1.2 million CFU

Other ingredients: contains lactose, potato starch, polyvinyl alcohol, and polyvinylpyrrolidone (may be an issue for many with gut symptoms)

What they claim on their website:

A clinically proven formula that works like a prebiotic, probiotic, symbiotic, and postbiotic all in one to support microbiome and gut health.

  • The only formula that has unique probiotics as well as supporting strains to increase colonization and effectiveness, and naturally produces short-chain fatty acids like butyrate and propionate
  • Reduces the growth of pathogenic bacteria while promoting the growth of beneficial bacteria like Bifidobacterium and Akkermansia
  • Normalizes the inflammatory response, promotes detoxification, supports immunity and provides relief from allergies”

They reference several studies of BIO-THREE.83–85

Verdict: Inclusion of E. faecium is questionable, but the formula has shown benefits in several randomized controlled trials. Not recommended to those sensitive to lactose, polyvinyl alcohol, or potato starch.

MegaSporeBiotic (Microbiome Labs)

Soil-based species: B. coagulans SC-208, B. subtilis HU58, B. clausii SC-109, B. indicus HU36, and B. licheniformis SL-307

Colony-forming units: 2 billion CFU

Other ingredients: cellulose, vegetable capsule (cellulose and water)

What they claim on their website: “MegaSporeBiotic™ is a 100% spore-based, broad-spectrum probiotic shown to maintain healthy gut barrier function. This unique all-spore formula effectively RECONDITIONS the gut by promoting microbial diversity and maintaining key health-promoting, commensal gut bacteria. MegaSporeBiotic™ boasts a 5-year shelf-life, does not require refrigeration, and maintains a healthy gut microbiome.”

Their clinical research:

In a 2017 study, MegaSporeBiotic was shown to reduce blood endotoxin, a measure of intestinal permeability, by 42 percent after a high-fat cheese pizza meal, compared to a 36 percent increase in volunteers receiving placebo.86  However, the researchers hand-selected a group of 25 endotoxin hyper-responders for the study – not the most translatable to the ability of MegaSporeBiotic to maintain or improve gut barrier function in a general population.

In a 2019 study, 90 irritable bowel syndrome patients without constipation were treated with the antibiotic rifaximin for ten days, followed by either a nutraceutical agent (containing Bifidobacterium longum W11, soluble fiber, and B vitamins), a low FODMAP diet, or MegaSporeBiotic for 34 days.87 IBS signs and symptoms decreased with each visit for all groups, with MegaSporeBiotic showing a modest difference at the third time point. The study was not blinded or placebo-controlled – a major limitation, especially for a study with IBS, where placebo response can be as high as 40-50 percent.88

In a 2020 study, 80 participants with high triglycerides (>150 mg/dL) were randomized to receive two capsules of MegaSporeBiotic or placebo for three months. Compared to the placebo group, participants consuming the probiotics had a significant reduction in non-fasting triglycerides levels. Other measures of metabolic health were not included. There were no reported adverse effects.

My comments: Currently, there is no evidence that this particular formulation increases microbial diversity, promotes diversity or maintains health-promoting, commensal gut bacteria, as their website might suggest.

Criticisms aside, I am really pleased that Microbiome Labs is making more of an effort to perform peer-reviewed research on their product. I hope that their future clinical research will emphasize randomized, placebo-controlled trials with a more rigorous design.

Verdict: Inclusion of B. licheniformis and B. indicus is questionable, as few studies have been performed on the safety or therapeutic benefit of these strains. Three clinical trials of the combined 5-strain formula showed modest benefits. Given a choice, I would still choose products that have more well-established safety profiles and more rigorous research to back their claims.

Just Thrive (Microbiome Labs)

Soil-based species: B. coagulans SC-208, B. subtilis HU58, B. clausii SC-109, B. indicus HU36 (same as MegaSporebiotic but without B. licheniformis)

Colony-forming units: 3 billion CFU

Other ingredients: cellulose, hydroxypropyl methyl cellulose capsule

What they claim on their website: “Our breakthrough, award-winning probiotic contains the proprietary strain, Bacillus Indicus Hu36, which produces antioxidants directly in the digestive system where they can be best absorbed by your body. […] The spores in Just Thrive have been successfully used to enhance digestive health in the progressive health and wellness space for more than 50 years.” 

What the evidence says: There is no research to confirm that Bacillus indicus HU36 produces antioxidants in humans, or that these can be absorbed by the digestive tract. While Bacillus species have been used as probiotics for more than 50 years, the specific strains in JustThrive have not been used or studied for very long.

Verdict: Contains B. indicus, which has little clinical evidence, though the included strain has been suggested to be safe for human consumption. Likely has some of the clinical benefits of MegaSporeBiotic but without the controversial inclusion of B. licheniformis. The language on their website has improved since I first wrote this analysis, but still makes claims that are not backed by any clinical evidence.

Proflora 4R (Bio-Botanical Research)

Soil-based species: B. coagulans SC-208, B. subtilis HU58, B. clausii SC-109 (similar to MegaSporebiotic and JustThrive but does not contain B. indicus or licheniformis)

Colony-forming units: 3 billion CFU

Other ingredients: 100mg quercetin, 100mg marshmallow root, 2mg aloe vera extract, microcrystalline cellulose, vegetable capsule (cellulose and water)

What they claim on their website: Proflora®4R is a unique spore-based probiotic with additional botanicals to support microbial balance and GI health. The combination of quercetin, marshmallow root, and aloe vera extract in Proflora® 4R provide additional nutritional support for healthy microbial balance, with just one capsule per day.”

Verdict: Contains a good selection of species, but the included strains have not been well-studied. The addition of quercetin, marshmallow root, and aloe may support gut barrier integrity.

ProBioSpore (Designs for Health) – NEW

Soil-based species: B. coagulans MTCC 5856 (Lactospore), B. coagulans SNZ 1969, B. coagulans Lacris-15, B. subtilis DE111, B. clausii CSI08

Colony-forming units: 10 billion CFU

Other ingredients: microcrystalline cellulose, hypromellose capsule, medium chain triglycerides, silicon dioxide

What they claim on their website: “ProbioSpore™ is an industry-leading, broad-spectrum, spore-based probiotic. It is comprised of a diverse combination of 5 different bacillus strains formulated to optimize gastrointestinal health.”

Verdict: Contains only well-studied species, but includes at least one strain (CSI08) that has never been studied in humans.

Gut Recovery (Jetson) – NEW

Soil-based species: B. coagulans MTCC 5856 (Lactospore), B. subtilis DE111, B. clausii CSI08

Other species: Saccharomyces boulardii DBVPG 6763, Lactobacillus rhamnosus GG

Colony-forming units: 15 billion CFU (per 2 packets)

Other ingredients: inulin, rice hull

What they claim on their website: “Gut Recovery is a powerful, multi-strain probiotic that maintains digestive balance during and after a course of antibiotics. By definition, antibiotics kill bacteria – which means they not only kill the bad, they kill the good too.”

“Gut Recovery is a flavorless powder that survives an antibiotic attack and replenishes the good bacteria wiped out by antibiotics. It can also combat uncomfortable antibiotic-related symptoms like nausea, diarrhea and yeast infections.”

What the science really says: The soil-based strains in this product will likely survive a course of antibiotics, at least in their spore form, but there is no evidence to suggest that they can replenish gut bacteria wiped out by antibiotics. I’ve written before about why we should think twice about taking high-dose probiotics with antibiotics, and other ways to support antibiotic recovery instead.

Verdict: Contains only well-studied species, but the strain of B. clausii this formula contains has never been studied in humans. It is also unclear how much of each strain is in this formula.

Digestive Health Probiotic (Doctor’s Best) – NEW

Soil-based species: B. coagulans MTCC 5856 (LactoSpore)

Colony-forming units: 2 billion CFU

Other ingredients: modified cellulose capsule, maltodextrin

What they claim on their website: “Doctor’s Best Digestive Health Probiotic contains LactoSpore, a shelf-stable probiotic capable of withstanding the acidic environment of the stomach. LactoSpore has been shown to improve digestive upset and constipation. It has also been shown to help prevent episodes of diarrhea.”

“LactoSpore (B. Coagulans strain) helps prevent the growth of bad bacteria (pathogenic microbes) and allows good bacteria (B. coagulans) to dominate the gut flora.”

My only comment: we really don’t want B. coagulans to dominate the gut flora. If anything, it should be a minor component of a healthy gut ecosystem.

Verdict: Contains LactoSpore, a well-studied strain of B. coagulans. Inclusion of maltodextrin is not ideal, as this food additive has been shown to alter microbiota and host functions.

Bacillus Coagulans (Thorne Research) – NEW

Soil-based species: B. coagulans MTCC 5856 (LactoSpore)

Note: the product label does not list the strain, but my communication with Thorne Research confirmed that the product contains LactoSpore.

Colony-forming units: 2 billion CFU

Other ingredients: microcrystalline cellulose, hypromellose capsule, silicon dioxide

What they claim on their website:“A stable probiotic bacteria that survives stomach acid and retains its potency in the intestines, where it can support GI upset, such as occasional gas, bloating, constipation or diarrhea.”

Verdict: Contains LactoSpore, a well-studied strain of B. coagulans. However, it also contains silicon dioxide, which has been shown to have negative effects on the gut microbiota and cause inflammatory damage in the gut.89

AFI LactoSpore Probiotic (America’s Finest, Inc.) – NEW

Soil-based species: B. coagulans MTCC 5856 (LactoSpore)

Colony-forming units: 2 billion CFU

Other ingredients: rice flour, hypromellose capsule

What they claim on their website: “Probiotic LactoSpore® helps normalize and maintain a healthy intestinal flora. [..] LactoSpore may be chosen as the probiotic of choice for several reasons including history of use, stability of spores, Generally Recognized as Safe (GRAS) status, documented clinical effectiveness and potential health benefits (normalizing intestinal flora/immune enhancement and non-GI tract conditions).”

“AFI products are produced in a GMP-certified and NSF-approved manufacturing facility.”

What the science says: it’s unclear whether the LactoSpore strain can “normalize” the intestinal microbiota in humans. Its documented health benefits are primarily for reducing IBS symptoms.

Verdict: Contains LactoSpore, a well-studied strain of B. coagulans, and no problematic inactive ingredients. A good overall choice, especially for those with irritable bowel syndrome that just want to try a single strain formula.

TOP CHOICE: CoreBiotic (Researched Nutritionals) – NEW

Soil-based species: B. coagulans SNZ1969, B. coagulans MTCC 5856 (“LactoSpore”), B. subtilis DE111

Colony-forming units: 5.5 billion CFU

Also contains: 330 mg of Organic VitaFiber®, a prebiotic from cassava root (Note: they also make another version, CoreBiotic Sensitive, that does not contain added fiber)

Other ingredients: capsule shell (hypromellose, water), low moisture rice dextrin, medium-chain triglycerides, rice bran

What they claim on their website: “CoreBiotic® combines three fully sequenced and registered spore-based probiotics along with VitaFiber® prebiotic to support a healthy microbiome. Each strain was specifically chosen for its mechanisms of action, backed by supporting research.”

“Each strain in CoreBiotic® is identified by genomic sequencing for specificity so that you know you are getting the same product every time. Only strain-specific probiotics have undergone rigorous genomic studies, guaranteeing accurate strain specificity, potency, and safety.”

Verdict: Contains three strains, all of which have been studied in human clinical trials and received Generally Recognized As Safe distinction! It also boasts a high CFU count compared to many probiotics on the market. The inclusion of rice dextrin isn’t ideal, but overall a solid choice that I’ll be excited to try myself and with clients. The strains in this product have been shown to be particularly beneficial for irritable bowel syndrome.

Note: CoreBiotics’ website only sells to healthcare practitioners, so you’ll need a practitioner to purchase or to get it from an outside seller.

Other Products:

To pre-empt questions on other formulas, here are a few quick notes on some other popular products:

Amy Myers Primal Earth Probiotic: contains the same un-studied strains as Proflora 4R

ATH Organics Gut Health Probiotics: contains Bacillus subtilis DE111, a well-studied strain, but no strain info for other species

Ancient Nutrition SBO Probiotics: no strain info

BodyBiotics SBO Probiotics: no strain info, contains Bacillus licheniformus

Codeage SBO Probiotic: no strain info

Dr. Ruscio Soil-Based Probiotic: no strain info

Enviromedica Terraflora: contains Bacillus pumilus and Bacillus megaterium, two species that have never been studied in humans

Garden of Life Primal Defense HSO Probiotic: does not actually contain SBOs

Klaire Labs Biospora: no strain info

Physician’s Choice SBO Probiotic: no strain info

Prescript-Assist – formula changed in 2017, contains many un-studied species

Primal Blueprint Primal Probiotics: formula changed, no longer contains SBOs

RealDose Nutrition RightBiotics RX: was originally my top choice, but unfortunately changed its formula and no longer contains SBOs

Schiff Digestive Advantage Daily Probiotics: contains Bacillus coagulans GBI-30, 6086, a well-studied strain, but also contains maltodextrin and titanium dioxide.

Smarter Nutrition Gut Health Probiotics: no strain info for B. clausii or B. subtilis

Swanson Soil-Based Organisms: does not actually contain SBOs

YouTheory Spore Probiotic: contains two un-studied strains

Conclusion

To sum up, soil-based organisms are quite well studied and have been shown in randomized clinical trials to be efficacious for a wide range of conditions. However, there is a lot of heterogeneity in soil-based microbes. I strongly advise choosing products that use high-quality manufacturing techniques and clinically-tested strains.

Currently, I am primarily using both Enterogermina and CoreBiotic Sensitive for myself and with my clients. I may occasionally try AFI LactoSpore, or Probiotic-3 in clients with low Clostridia or butyrate production. This is certainly subject to change, as more studies are available on particular species, strains, and formulas.

Note that every person will respond differently to probiotics. Response will depend on which probiotic you take, the dosage, which microbes you already have in your gut, and the health of your gut and immune system. When possible, choose probiotic strains that have been studied for your particular health condition. The right probiotic may not even be an SBO at all!

It’s possible that in some severe cases, we should look to heal the gut and treat gut pathologies before incorporating high-dose SBO probiotics. This may be especially true after antibiotics. I eagerly await more research on how individual strains and formulations of SBOs might impact the gut microbiota and gut environment in different contexts.

Additionally, I recommend avoiding SBOs completely if you are critically ill or immunocompromised. We still don’t have a good understanding of how these organisms act in vulnerable populations, and there have been case reports of adverse effects in those without sufficient immune function.

Of course, I also recommend getting exposure to SBOs the natural way – this means consuming organically grown vegetables, spending time in natural environments, and getting exposure to dirt through gardening or other outdoor activities!

It also means eating plenty of properly prepared fermented foods, if you tolerate them. Several popular kombucha brands now contain well-studied SBO strains. GTs kombucha contains Bacillus coagulans GBI-30, 6086, and a personal favorite, the new Kirkland brand kombucha, contains Bacillus subtilis DE111! As with all fermented foods, be sure to start slowly.

I will plan to update and reevaluate this guide periodically as more research is published and as companies (hopefully) become more transparent with their strains and evidence-based in their marketing claims. To be notified of any future updates, be sure to subscribe to my newsletter.

What soil-based probiotics do you take? Will this influence which products you use? Share your thoughts in the comments below!

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