The complete guide to soil-based probiotics
BY LUCY MAILING, MD/PHD STUDENT
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.
Until recently, I recommended Prescript Assist as the best soil-based probiotic. While some of the microbes in the old probiotic formula were not well-studied, Prescript Assist had been used in several clinical trials with excellent results and no reported adverse events.1,2 It was also well tolerated, even by those with IBS, severe gut dysbiosis, or other gut pathologies.
In late 2017, the manufacturer made major changes to the ingredients of Prescript Assist, so it is no longer using the formulation that was studied in clinical trials. While the original formula contained 29 different strains, the new formula contains 28 strains, only 9 of which are from the original formula. There’s very limited evidence for most of the strains included in the new formula.
I’ve been asked by many people what my new recommended alternative to Prescript Assist is, so I decided to do some digging. This guide is a result of 50+ hours of independent research on soil-based organisms and the products commercially available today.
First, though, I’ll review what soil-based organisms are, the controversy, and the evidence for the most commonly used strains.
What are soil-based organisms?
The term soil-based organism (SBO) encompasses over 100 different species of microbes naturally found in soil. Some of these have been isolated and adapted for use as probiotics. Most SBO used in soil-based probiotics are spore-forming. This means that when they replicate, they form a small spore that is protected by a hard coating, making them resistant to heat, acid, and most antibiotics. This also means that they are more likely to survive the upper gastrointestinal tract and reach the large intestine compared to other commonly used probiotic strains.
The controversy and the evidence
There is currently a lot of 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.
On the other hand, opponents of SBOs argue that because of their spore-forming nature, they proliferate rapidly, and may compete with our resident gut microbes, rather than helping to bring the gut microbiota back to normalcy. In some individuals, opportunistic SBOs could overgrow, with the potential to become pathogenic.
My take: Several individual SBO strains have been shown to be beneficial, with no adverse effects, in dozens of randomized, placebo-controlled, human clinical trials. However, other strains have very limited or no clinical evidence and may be able to cause infection in people with a compromised immune system.
Rather than labeling all SBOs as good or bad, I think we need a more nuanced discussion – one that considers the evidence for each particular strain, microbe, and formula. That’s what I’ll try to provide in the next few sections. 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:
Before I do an analysis of the soil-based probiotic formulations on the market, it’s important to understand which species are most commonly used.
I searched PubMed and Google Scholar for every available human clinical trial on the seven most commonly used soil-based microbes:
Bacillus coagulans
Bacillus subtilis
Bacillus clausii
Bacillus indicus
Bacillus licheniformis
Enterococcus faecium
Clostridium butyricum
Before I share my findings below, it’s important to note that microbes are denoted by their genus, species, and strain. The list above provides the genus and species but does not tell you anything about the strain. Strain is incredibly important since two strains of the same species can have very different characteristics.3 Unfortunately, most probiotic formulations do not provide information about which strains they contain.
To see my full analysis of the available clinical trial literature for each strain, click here to download my Excel spreadsheet. For just the key findings, read on:
Bacillus 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.
There are three strains of B. coagulans that have been heavily studied:
GBI-30, 6086 (“Ganeden BC30”): with over 8 human randomized, placebo-controlled trials, this is one of the most well-studied Bacillus strains. GBI-30, 6086 has been shown to improve IBS,4–6 immune function,7,8 and beneficially modulate the gut microbiota.9,10 In cell culture experiments, this strain has been shown to stimulate production of anti-inflammatory cytokines and regenerative markers.11
Unique IS-2 (“ProDURA”): three human clinical trials have found this strain to be efficacious for bacterial vaginosis12 and children with IBS.13,14 Cell culture studies have also found that it inhibits the proliferation of cancer cells.15
MTCC 5856 (“LactoSpore”): two randomized controlled trials showed that MTCC 5856 significantly reduced bloating, abdominal pain, and depressive symptoms in IBS patients.16,17
Verdict: These three strains of Bacillus coagulans appear to be safe, well-tolerated, and may be especially beneficial for those with IBS.
Bacillus subtilis
Bacillus subtilis is recognized as a normal inhabitant of the human gut.18 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.19,20
B. subtilis produces an enzyme that can degrade oxalate, which may be particularly helpful for people with hyperoxaluria,21 and may also produce small amounts of Vitamin K-2. B. subtilis is found naturally in natto, a traditional Japanese food made from fermented soybeans.
Only four strains of B. subtilis have been studied in humans:
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.22,23 Another study found that DE111 improved bowel irregularity in otherwise healthy adults.24
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.25 It does not exhibit any antibiotic resistance and was shown to be absent of toxigenic activity in vitro.26
R0179: one study found B. subtilis R0179 to be well tolerated in healthy adults at a dose of 1 or 10 billion CFU per day, and confirmed that it survived passage through the GI tract.27
IP 5832: one Croatian study found that B. subtilis IP 5832 given during parenteral rehydration therapy for acute nontyphoid Salmonella gastroenteritis reduced patient-weeks of carrier state and resulted in fewer positive stool cultures at week four.28
Several studies for which I could not find strain information also showed benefits from B. subtilis: One Chinese study found that B. subtilis plus lactulose was more effective at treating functional constipation than lactulose alone.29 Several other studies found that B. subtilis + Enterococcus faecium reduced IBS-related abdominal pain30,31 and improved bowel preparation for colonoscopy.32
Verdict: Commonly studied strains of B. subtilis appear to be safe, well-tolerated, and with no adverse effects. Some strains appear to be particularly beneficial for improving immune function and bowel regularity.
Bacillus clausii
Bacillus clausii has been studied extensively and used for many years as the Italian pharmaceutical preparation Enterogermina for the treatment of a wide range of gastrointestinal diseases. B. clausii has been shown to have antimicrobial activity against Staphylococcus aureus and Clostridium difficile.
Enterogermina is the only formulation of B. clausii that has been studied in controlled human clinical trials and is made up of four different strains (OC, NR, SIN, and T). These strains have been shown to be acid and bile resistant,33 and can be recovered in stool for up to 12 days after a single administration.34
Enterogermina has found to be particularly beneficial for those with allergies, reducing nasal congestion and the need for anti-histamines.35–37 It has also been shown to reduce side effects during antibiotic treatment for H. pylori.38
One study of 40 patients diagnosed with SIBO found that taking Enterogermina for 1 month resulted in a normalization of glucose breath test result in 47 percent of patients.39 This is comparable to the rate observed with many antibiotics commonly used for SIBO treatment. Only one patient reported a side effect of constipation.
Verdict: Very well-studied and well-tolerated, with clear efficacy documented in several randomized, placebo-controlled trials. May be particularly beneficial for those with allergies or symptoms associated with SIBO. Since beginning this analysis, I have also tried Enterogermina myself and noticed improved tolerance to foods.
Enterogermina can be purchased from international online pharmacies as either capsules or liquid vials. Shipment should not be an issue since B. clausii is extremely heat-stable and does not require refrigeration.
Bacillus indicus:
Bacillus indicus has been touted for its ability to potently stimulate the immune system and produce high levels of carotenoids, vitamins, and quinols.
However, after an exhaustive search of the literature, I could find no scientific studies of Bacillus indicus in humans (with the exception of one study that used a preparation of 5 Bacillus strains – see “MegaSporeBiotic” section below).
Verdict: Currently lacking scientific evidence. This does not necessarily mean that B. indicus is not beneficial – it just means we have little to no evidence to speak to its safety and efficacy in humans.
Bacillus licheniformis
Bacillus licheniformis is commonly used in the fermentation history. 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: “In order to achieve an infection, either the number of microorganisms must be very high or the immune status of the host low.”40
The same EPA report further notes: “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.”40
A literature search only revealed only three human studies of Bacillus licheniformis – two from Russia and one from China – none of which were placebo-controlled. I could not determine which strain was used in any of these studies, and the results were largely unimpressive.
Nonetheless, B. licheniformis is found in many fermented foods traditionally consumed in Korean culture. Certain strains found in these foods have been found to enhance the longevity of worms by upregulating serotonin signaling.41
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 isolated B. licheniformis. I think it’s best to err on the side of caution and avoid probiotics that contain this species, especially if they can provide no strain information and/or do not regularly test the genetic identity of their strains.
Enterococcus faecium
Enterococcus faecium is a normal resident of the human gut, metabolizing carbohydrates and producing 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.42
However, it can also be pathogenic, causing diseases like neonatal meningitis and endocarditis. Many strains of this bacterium have developed multi-drug 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.43 Thus, there are concerns about its use as a probiotic.
Many different strains have been studied:
M-74: This strain has the most “randomized” clinical trials associated with it, but every single one gave the probiotic in conjunction with 50 micrograms of selenium.44–47 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 was reducing cholesterol levels.
L3: one Russian randomized controlled trial found that this strain of E. faecium reduced the frequency of infectious complications in premature infants on antibiotic therapy, reduced persistence of C. difficile, and increased abundance of Bifidobacterium and Lactobacillus spp.48
IS 27526: one Indonesian randomized, placebo-controlled study found that this strain of E. faecium increased salivary sIgA and weight gain in underweight preschool children.42
WB 2000: one Japanese study found that a combination of E. faecium with fish oil, lactoferrin, and several vitamins and minerals improved clinical symptoms of dry eye.49 However, the effects of probiotic cannot be separated because it was not adequately controlled.
SF68: one Italian randomized crossover study found that cirrhosis patients taking this strain of E. faecium had a greater reduction in blood ammonia than those taking lactulose.50 There was no control group taking neither E. faecium or lactulose.
CRL 183: one study performed in Brazil found that a combination of isoflavone-supplemented soy fermented with E. faecium and Lactobacillus helveticus was better than soy alone at improving total cholesterol, but again, we cannot separate out the effects of E. faecium from L. helveticus and the isoflavone supplementation.51
As mentioned above, several studies found that B. subtilis + E. faecium reduced IBS-related abdominal pain30,31 and improved bowel preparation for colonoscopy,32 but I could not determine which strains were used in these studies.
To make matters more complicated, Streptococcus faecium was reclassified to Enterococcus faecium several years ago. However, Enterococcus faecalis (previously known as Streptococcus faecalis) is an entirely separate organism. Unfortunately, I believe this delineation has been smudged in studies of these organisms.
Verdict: Very few well-designed RCTs have demonstrated the efficacy of E. faecium, and all seem to use different strains. E. faecium also has the potential to acquire multi-drug antibiotic resistance and cause infection. Until more studies can be performed, I would exercise caution with high doses of isolated E. faecium.
Clostridium butyricum
Clostridium butyricum is a natural resident of the human GI tract. It is one of the many important microbes in the gut that ferments dietary fiber and produces the beneficial short-chain-fatty acid butyrate. Butyrate is an important source of energy for colon epithelial cells, helps maintain the gut barrier, has anti-inflammatory effects, and protects against colon cancer.
MIYAIRI 588: This strain of C. butyricum has been used as a probiotic in Asia since as early as 1963. It does not carry any genes encoding any known toxins or virulence factors.
Two randomized controlled trials showed that this strain alone reduces side effects for abdominal symptoms and diarrhea incidence in patients undergoing H. pylori eradication therapy.52,53 Another randomized, placebo-controlled trial 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 given was lactose, which can exacerbate colitis in many people.54
TO-A: this strain of C. butyricum, in combination with E. faecium and B. subtilis, has been heavily used and somewhat well studied as a probiotic in Asia. The combined product is called BIO-THREE and has been shown in randomized controlled trials to reduce postoperative infections in patients undergoing surgery55 and shorten hospital stay for children with acute diarrhea.56
In cell culture studies, C. butyricum TO-A has been shown to reduce expression of TLR4, a gene involved in the inflammatory immune response. One randomized trial of ulcerative colitis patients found lower relapse rates in the group receiving BIO-THREE, but the difference was not statistically significant.57 No changes were observed in SCFA levels with probiotic supplementation.
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,58 and improved antigen-specific immunotherapy.59 In animal studies, C. butyricum has been shown to improve intestinal homeostasis and attenuate colitis.60
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, isolated forms of either of the strains listed above are not currently available in the United States, and I haven’t been able to find any international sources that I trust. The only alternative is to use the three-probiotic formulation BIO-THREE, which I’ll discuss more in the next section.
Product analysis
Note: I have no affiliation with any of these companies or products. This is the objective analysis that I used to determine which products I wanted to use for myself and with my clients.
Like all supplements, probiotics are not regulated by any governing agency (FDA, FTC, etc.), so it’s important to do your homework regarding their claims, sourcing, etc. Many companies that sell probiotics 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 the top eight most popular SBO products on the market.
While you might argue that a company’s marketing is less important than its ingredients or strains, I think it’s a key component. 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 my readers and clients.
Probiotic-3 (Advanced Orthomolecular Research)
Soil-based species: Bacillus subtilis TO-A, E. faecium T-100, and C. butyricum TO-A, (also known as BIO-THREE)
Colony-forming units: 19.2 million CFU
Other ingredients: contains lactose, polyvinyl alcohol, and potato starch (may be an issue for many with gut symptoms
What they claim on their website:
“Probiotic-3 is a probiotic formula that has been used clinically for more than 50 years in Japan and across Asia.”
- Reduces the growth of pathogenic bacteria while promoting the growth of beneficial bacteria
- Normalizes the inflammatory response, promotes detoxification and supports immunity
They reference several studies of BIO-THREE.61–63
Verdict: Inclusion of E. faecium is questionable, but the formula has shown benefits in several randomized clinical trials. Not recommended for those sensitive to lactose, 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
Colony-forming units: 4 billion CFU
What they claim on their website: “MegaSporeBiotic™ is the first 100% spore-based, broad-spectrum probiotic clinically shown to improve leaky gut by 60% in just 30 days. This unique all-spore formula effectively RECONDITIONS the gut by increasing microbial diversity and encouraging the growth of key health-promoting, commensal gut bacteria. MegaSporeBiotic™ boasts a 5-year shelf-life, does not require refrigeration, and maintains efficacy during antibiotic therapy.”
What their single research study actually found: In a “randomized”, placebo-controlled trial, 30 days of supplementation with MegaSporeBiotic reduced endotoxin (a measure of bacterial translocation into the blood) by 42 percent after a high-fat cheese pizza meal, compared to a 36 percent increase in endotoxin in the group receiving placebo. However, the subjects included in the “randomized” trial were really a hand-picked group of endotoxin hyper-responders.64 So yes, MegaSporeBiotic may reduce leaky gut by 60 percent if you are a dietary endotoxin hyper-responder and you happen to eat cheese pizza regularly.
Furthermore, there is NO evidence that this particular formulation increases microbial diversity, promotes health-promoting, commensal gut bacteria, or maintains efficacy during antibiotics.
Verdict: Inclusion of B. licheniformis and B. indicus is questionable, as few studies have been performed on the safety and efficacy of these strains. One clinical trial showed some benefit in hyper-responders, but the findings are heavily exaggerated on their website.
Just Thrive (Microbiome Labs)
Soil-based species: B. coagulans, B. subtilis HU58, B. clausii, B. indicus HU36
Colony-forming units: 3 billion CFU
What they claim on their website:
“With Just Thrive™ […] the body becomes a super-antioxidant factory right in the digestive system at the site where these important nutrients are most needed and absorbed.”
“Just Thrive® is the only product on the shelf to contain the patented Bacillus Indicus HU36®, a strain that produces high levels of antioxidants.”
What the evidence says:
There is absolutely no evidence to suggest that your gut becomes a “super-antioxidant factory”. In fact, any antioxidants produced by this probiotic are likely negligible if you consume a nutrient-dense diet rich in fruits and vegetables.
Moreover, Just Thrive is not the only product on the shelf to contain Bacillus indicus HU36, since MegaSporeBiotic also contains this strain.
Verdict: Contains B. indicus, which has little clinical evidence. Their website makes some pretty glorified claims that are clearly not backed by any real evidence. Supposedly they have about 10 clinical trials underway, so I’ll be happy to reevaluate Just Thrive when I see the data.
Primal Probiotics (Primal Blueprint):
Soil-based microbes: B. coagulans, B. subtilis, B. clausii (no strain information; quality assurance team said it was proprietary information)
Other probiotics: B. bifidus, L. plantarum, S. boulardii
Colony-forming units: 5 billion CFU soil-based, 5 billion CFU other probiotics
Other ingredients: microcrystalline cellulose, magnesium stearate, silicon dioxide, and 50 mg potato starch. Potato starch may be an issue for some people with gut issues. Resistant starch deserves an article on its own, but for now, I’ll say that I do not recommend supplementing with raw potato starch if you have gut dysbiosis, intestinal permeability, or autoimmunity.
What they claim on their website:
Like every probiotic, they make some lofty claims, such as:
“A simple daily dose of Primal Probiotics can help rebalance and restore gut health and improve immune function*”.
However, they are careful to note that:
“* There is no guarantee of specific results and results can vary from person to person.”
Verdict: A good mix of species with high CFU count but no strain information. No supporting clinical evidence for this formula, and not suitable for those who can’t tolerate potato starch.
Biospora (Klaire Labs):
Soil-based species: B. coagulans, B. subtilis (no strain information; no response to my inquiry)
Colony-forming units: 2 billion CFU
Other ingredients: coconut oil powder
What they claim on their website:
“BioSpora™ is recommended for enhanced support of normal GI and immune function. […] Each lot of Bacillus species used in BioSpora™ undergoes independent DNA testing using 16S ribosomal RNA sequencing to verify genetic identity.”
What the science really says:
You can’t verify genetic identity with 16S rRNA gene sequencing at anything below the genus level – only occasionally can you get to the species level with this type of sequencing. So, the only thing they are “verifying” is that each lot has some form of Bacillus.
Verdict: Contains only well-studied species. Website claims are largely scientific, but their genetic identity verification is highly questionable. No studies on this formulation have been done and no strain information is provided. However, Klaire Labs is NSF certified, which means their products do undergo independent testing.
Proflora 4R (Bio-Botanical Research):
Soil-based species: B. coagulans, B. subtilis HU58, B. clausii (no response to my inquiry about strains)
Colony-forming units: 3 billion CFU cells
Other ingredients: 100mg quercetin, 100mg marshmallow root, and aloe vera extract
What they claim on their website: “Proflora 4R replaces beneficial flora: Evidence suggests that the increase of inflammatory gastrointestinal (GI) disorders and intestinal permeability may, in part, be attributed to a under-consumption of these vital spore-producing flora. The combination of Quercetin, Marshmallow Root, and Aloe Vera extract in Proflora 4R™ provide additional nutritional support for “leaky gut” and a healthy microbial balance, with just one capsule a day.”
Verdict: Contains a good selection of species, but strains are not provided or have not been studied in human clinical trials. Website claims are largely scientific, and the addition of quercetin, marshmallow root, and aloe may help soothe a damaged gut.
TOP CHOICE: RightBiotics RX (RealDose Nutrition)
Soil-based species: B. subtilis DE111, Bacillus coagulans Lactospore (MTCC 5856) (both clinically validated strains!)
Colony-forming units: 5.36 billion CFU soil-based organisms, 15 billion CFU other
Other probiotics: B. lactis B1-04, B. longum BB536, L. helveticus Lafti L10, L. gasseri Lg-36, L. acidophilus DDS-1, L. plantarum Lp-115, Gnosis® S. boulardii (also all clinically validated strains) *Despite inclusion of Lactobacillus strains, this product should not cause histamine issues.
Other ingredients: vegetable capsule, organic rice bran extract, organic rice hull concentrate.
Allergens: “RightBiotics Rx includes one probiotic strain (L. helveticus LAFTI® L10) that contains a trace amount of soy from the culture media and may contain a trace amount of milk (including lactose) as it is sourced from dairy, according to the product’s Allergen Statement. For this reason, the label includes a caution statement for people with soy or milk allergy.”
Website claims: “Like people, no two probiotic strains are exactly alike. Each has a unique genetic makeup that determines its special health benefits. Verifying the strain ID ensures the formula delivers the unique strains shown in clinical research to deliver health benefits.”
Manufactured in the USA and third-party lab tested for potency and purity: “Our 3rd party laboratory is Atlas Bioscience Labs in Tucson, AZ. Atlas is DEA registered, and members of several industry-wide organizations including AOAC (Association of Official Analytical Chemists), and currently undergoing accreditation with ACLASS for ISO:17025 certification. We send every batch of product to Atlas Bioscience to test for active ingredients, as well as heavy metals, residual solvents, organochlorides, organophosphates and microbiology.”
Verdict: This is by far the best soil-based probiotic supplement I have seen on the market to date. I currently have NO affiliation with RightBiotics RX but am excited to have finally come across a product that is so well-supported by the evidence, independently tested, etc. I had not even heard of RealDose Nutrition before conducting this independent analysis, but if I continue to find success with this product with my clients, I may discuss affiliate options with RealDose Nutrition so that I can offer a discounted rate to my readers and clients.
For now, you can purchase it on their website or on Amazon.
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, I strongly advise choosing products that use high-quality manufacturing techniques and clinically-tested strains.
Currently, I am primarily using both Enterogermina and RightBiotics RX for myself and with my clients. I may occasionally try Probiotic-3 (BIO-THREE) in patients 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. This is part of the reason I recommend gut testing or working with someone with expertise in rebalancing the gut microbiota.
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.
Of course, I also recommend getting exposure to SBOs the natural way – this means consuming organically grown vegetables and getting exposure to dirt through gardening or other outdoor activities where you’re getting your hands and feet in the dirt! It also means eating plenty of properly prepared fermented foods. Interestingly, I’ve noticed that many popular kombucha brands, such as GTs, contain Bacillus coagulans GBI-30, 6086.
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!
Sources:
- Bittner, A. C., Croffut, R. M. & Stranahan, M. C. Prescript-Assist probiotic-prebiotic treatment for irritable bowel syndrome: a methodologically oriented, 2-week, randomized, placebo-controlled, double-blind clinical study. Clin Ther 27, 755–761 (2005).
- Bittner, A. C., Croffut, R. M., Stranahan, M. C. & Yokelson, T. N. Prescript-assist probiotic-prebiotic treatment for irritable bowel syndrome: an open-label, partially controlled, 1-year extension of a previously published controlled clinical trial. Clin Ther 29, 1153–1160 (2007).
- De Clerck, E. et al. Polyphasic Characterization of Bacillus coagulans Strains, Illustrating Heterogeneity within this Species, and Emended Description of the Species. Systematic and Applied Microbiology 27, 50–60 (2004).
- Hun, L. Bacillus coagulans significantly improved abdominal pain and bloating in patients with IBS. Postgrad Med 121, 119–124 (2009).
- Dolin, B. J. Effects of a proprietary Bacillus coagulans preparation on symptoms of diarrhea-predominant irritable bowel syndrome. Methods Find Exp Clin Pharmacol 31, 655–659 (2009).
- Kalman, D. S. et al. A prospective, randomized, double-blind, placebo-controlled parallel-group dual site trial to evaluate the effects of a Bacillus coagulans-based product on functional intestinal gas symptoms. BMC Gastroenterol 9, 85 (2009).
- Baron, M. A patented strain of Bacillus coagulans increased immune response to viral challenge. Postgrad Med 121, 114–118 (2009).
- Yang, O. O., Kelesidis, T., Cordova, R. & Khanlou, H. Immunomodulation of Antiretroviral Drug-Suppressed Chronic HIV-1 Infection in an Oral Probiotic Double-Blind Placebo-Controlled Trial. AIDS Research and Human Retroviruses 30, 988–995 (2014).
- Nyangale, E. P. et al. Bacillus coagulans GBI-30, 6086 Modulates Faecalibacterium prausnitzii in Older Men and Women. J. Nutr. 145, 1446–1452 (2015).
- Nyangale, E. P., Farmer, S., Keller, D., Chernoff, D. & Gibson, G. R. Effect of prebiotics on the fecal microbiota of elderly volunteers after dietary supplementation of Bacillus coagulans GBI-30, 6086. Anaerobe 30, 75–81 (2014).
- Jensen, G. S., Cash, H. A., Farmer, S. & Keller, D. Inactivated probiotic Bacillus coagulans GBI-30 induces complex immune activating, anti-inflammatory, and regenerative markers in vitro. J Inflamm Res 10, 107–117 (2017).
- Sudha, M. R., Bhonagiri, S. & Kumar, M. A. Efficacy of Bacillus clausii strain UBBC-07 in the treatment of patients suffering from acute diarrhoea. Benef Microbes 4, 211–216 (2013).
- Sudha, M. R., Jayanthi, N., Aasin, M., Dhanashri, R. D. & Anirudh, T. Efficacy of Bacillus coagulans Unique IS2 in treatment of irritable bowel syndrome in children: a double blind, randomised placebo controlled study. Benef Microbes 9, 563–572 (2018).
- Saneian, H., Pourmoghaddas, Z., Roohafza, H. & Gholamrezaei, A. Synbiotic containing Bacillus coagulans and fructo-oligosaccharides for functional abdominal pain in children. Gastroenterol Hepatol Bed Bench 8, 56–65 (2015).
- Madempudi, R. S. & Kalle, A. M. Antiproliferative Effects of Bacillus coagulans Unique IS2 in Colon Cancer Cells. Nutr Cancer 69, 1062–1068 (2017).
- Majeed, M. et al. Bacillus coagulans MTCC 5856 supplementation in the management of diarrhea predominant Irritable Bowel Syndrome: a double blind randomized placebo controlled pilot clinical study. Nutr J 15, 21 (2016).
- Majeed, M., Nagabhushanam, K., Arumugam, S., Majeed, S. & Ali, F. Bacillus coagulans MTCC 5856 for the management of major depression with irritable bowel syndrome: a randomised, double-blind, placebo controlled, multi-centre, pilot clinical study. Food Nutr Res 62, (2018).
- Hong, H. A. et al. Bacillus subtilis isolated from the human gastrointestinal tract. Res. Microbiol. 160, 134–143 (2009).
- Graebner, H. F. [Supplemental treatment of radiogenic enterocolitis using Bacillus subtilis]. Med Klin 64, 1080–1084 (1969).
- Pillen, D. [Treatment of intestinal diseases with Bacillus strain 5832]. Med Welt 7, 266–268 (1971).
- Langman, C. B. et al. A Double-Blind, Placebo Controlled, Randomized Phase 1 Cross-Over Study with ALLN-177, an Orally Administered Oxalate Degrading Enzyme. Am. J. Nephrol. 44, 150–158 (2016).
- Toohey, J. C. et al. Effects of Probiotic (Bacillus subtilis) Supplementation During Offseason Resistance Training in Female Division I Athletes. J Strength Cond Res (2018). doi:10.1519/JSC.0000000000002675
- Townsend, J. R. et al. Effects of Probiotic (Bacillus subtilis DE111) Supplementation on Immune Function, Hormonal Status, and Physical Performance in Division I Baseball Players. Sports (Basel) 6, (2018).
- Cuentas, A. M., Deaton, J., Davidson, J., Ardita, C. & Khan, S. The Effect of <em>Bacillus subtilis</em> DE111 on the Daily Bowel Movement Profile for People with Occasional Gastrointestinal Irregularity. Journal of Probiotics & Health 5, 1–4 (2017).
- Lefevre, M. et al. Probiotic strain Bacillus subtilis CU1 stimulates immune system of elderly during common infectious disease period: a randomized, double-blind placebo-controlled study. Immun Ageing 12, 24 (2015).
- Lefevre, M. et al. Safety assessment of Bacillus subtilis CU1 for use as a probiotic in humans. Regul. Toxicol. Pharmacol. 83, 54–65 (2017).
- Hanifi, A. et al. Evaluation of Bacillus subtilis R0179 on gastrointestinal viability and general wellness: a randomised, double-blind, placebo-controlled trial in healthy adults. Benef Microbes 6, 19–27 (2015).
- Vuković, M. [Bacillus subtilis IP 5832 (Flonivin BS) shortens the duration of the carrier state in patients with acute non-typhoid salmonella enteritis]. Med. Pregl. 54, 62–68 (2001).
- Liu, Y.-P., Liu, X. & Dong, L. [Lactulose plus live binary Bacillus subtilis in the treatment of elders with functional constipation]. Zhonghua Yi Xue Za Zhi 92, 2961–2964 (2012).
- Choi, C. H. et al. Efficacy of combination therapy with probiotics and mosapride in patients with IBS without diarrhea: a randomized, double-blind, placebo-controlled, multicenter, phase II trial. Neurogastroenterol. Motil. 27, 705–716 (2015).
- Kim, Y. G., Moon, J. T., Lee, K. M., Chon, N. R. & Park, H. [The effects of probiotics on symptoms of irritable bowel syndrome]. Korean J Gastroenterol 47, 413–419 (2006).
- Lee, H. et al. A feasibility study of probiotics pretreatment as a bowel preparation for colonoscopy in constipated patients. Dig. Dis. Sci. 55, 2344–2351 (2010).
- Cenci, G., Trotta, F. & Caldini, G. Tolerance to challenges miming gastrointestinal transit by spores and vegetative cells of Bacillus clausii. J. Appl. Microbiol. 101, 1208–1215 (2006).
- Ghelardi, E. et al. Survival and persistence of Bacillus clausii in the human gastrointestinal tract following oral administration as spore-based probiotic formulation. J. Appl. Microbiol. 119, 552–559 (2015).
- Ciprandi, G., Vizzaccaro, A., Cirillo, I. & Tosca, M. A. Bacillus clausii exerts immuno-modulatory activity in allergic subjects: a pilot study. Eur Ann Allergy Clin Immunol 37, 129–134 (2005).
- Ciprandi, G., Vizzaccaro, A., Cirillo, I. & Tosca, M. A. Bacillus clausii effects in children with allergic rhinitis. Allergy 60, 702–703 (2005).
- Ciprandi, G., Tosca, M. A., Milanese, M., Caligo, G. & Ricca, V. Cytokines evaluation in nasal lavage of allergic children after Bacillus clausii administration: a pilot study. Pediatr Allergy Immunol 15, 148–151 (2004).
- Nista, E. C. et al. Bacillus clausii therapy to reduce side-effects of anti-Helicobacter pylori treatment: randomized, double-blind, placebo controlled trial. Aliment. Pharmacol. Ther. 20, 1181–1188 (2004).
- Gabrielli, M. et al. Bacillus clausii as a Treatment of Small Intestinal Bacterial Overgrowth. The American Journal of Gastroenterology 104, 1327–1328 (2009).
- EPA: Bacillus Licheniformis Final Risk Assessment – Biotechnology Program Under Toxic Substances Control Act (TSCA). Available at: http://widit.knu.ac.kr/epa/ebtpages/Pollutants/Toxics/Microorganisms/siteout/s1out8.htm. (Accessed: 21st September 2018)
- Park, M. R. et al. Bacillus licheniformis Isolated from Traditional Korean Food Resources Enhances the Longevity of Caenorhabditis elegans through Serotonin Signaling. J. Agric. Food Chem. 63, 10227–10233 (2015).
- Surono, I. S. et al. Novel probiotic Enterococcus faecium IS-27526 supplementation increased total salivary sIgA level and bodyweight of pre-school children: a pilot study. Anaerobe 17, 496–500 (2011).
- Agudelo Higuita, N. I. & Huycke, M. M. Enterococcal Disease, Epidemiology, and Implications for Treatment. in Enterococci: From Commensals to Leading Causes of Drug Resistant Infection (eds. Gilmore, M. S., Clewell, D. B., Ike, Y. & Shankar, N.) (Massachusetts Eye and Ear Infirmary, 2014).
- Mego, M. et al. Prevention of febrile neutropenia in cancer patients by probiotic strain Enterococcus faecium M-74. Pilot study phase I. Neoplasma 52, 159–164 (2005).
- Hlivak, P. et al. One-year application of probiotic strain Enterococcus faecium M-74 decreases serum cholesterol levels. Bratisl Lek Listy 106, 67–72 (2005).
- Hlivak, P. et al. Long-term (56-week) oral administration of probiotic Enterococcus faecium M-74 decreases the expression of sICAM-1 and monocyte CD54, and increases that of lymphocyte CD49d in humans. Bratisl Lek Listy 106, 175–181 (2005).
- Mego, M. et al. Prevention of febrile neutropenia in cancer patients by probiotic strain Enterococcus faecium M-74. Phase II study. Support Care Cancer 14, 285–290 (2006).
- Lo Skiavo, L. A., Gonchar, N. V., Fedorova, M. S. & Suvorov, A. N. [Dynamics of contamination and persistence of Clostridium difficile in intestinal microbiota in newborn infants during antibiotic therapy and use of probiotic strain enterococcus faecium L3]. Antibiot. Khimioter. 58, 13–18 (2013).
- Kawashima, M., Nakamura, S., Izuta, Y., Inoue, S. & Tsubota, K. Dietary Supplementation with a Combination of Lactoferrin, Fish Oil, and Enterococcus faecium WB2000 for Treating Dry Eye: A Rat Model and Human Clinical Study. Ocul Surf 14, 255–263 (2016).
- Loguercio, C. et al. Long-term effects of Enterococcus faecium SF68 versus lactulose in the treatment of patients with cirrhosis and grade 1-2 hepatic encephalopathy. J. Hepatol. 23, 39–46 (1995).
- Cavallini, D. C. U. et al. Probiotic Soy Product Supplemented with Isoflavones Improves the Lipid Profile of Moderately Hypercholesterolemic Men: A Randomized Controlled Trial. Nutrients 8, (2016).
- Shimbo, I. et al. Effect of Clostridium butyricum on fecal flora in Helicobacter pylori eradication therapy. World J Gastroenterol 11, 7520–7524 (2005).
- Imase, K. et al. Efficacy of Clostridium butyricum preparation concomitantly with Helicobacter pylori eradication therapy in relation to changes in the intestinal microbiota. Microbiol. Immunol. 52, 156–161 (2008).
- Yasueda, A. et al. The effect of Clostridium butyricum MIYAIRI on the prevention of pouchitis and alteration of the microbiota profile in patients with ulcerative colitis. Surg. Today 46, 939–949 (2016).
- Nomura, T. et al. Probiotics reduce infectious complications after pancreaticoduodenectomy. Hepatogastroenterology 54, 661–663 (2007).
- Chen, C.-C. et al. Probiotics have clinical, microbiologic, and immunologic efficacy in acute infectious diarrhea. Pediatr. Infect. Dis. J. 29, 135–138 (2010).
- Yoshimatsu, Y. et al. Effectiveness of probiotic therapy for the prevention of relapse in patients with inactive ulcerative colitis. World J Gastroenterol 21, 5985–5994 (2015).
- Ren, Y.-F. & Wang, L.-L. [Effects of probiotics on intestinal bacterial colonization in premature infants]. Zhongguo Dang Dai Er Ke Za Zhi 12, 192–194 (2010).
- Liao, H.-Y. et al. Clostridium butyricum in combination with specific immunotherapy converts antigen-specific B cells to regulatory B cells in asthmatic patients. Sci Rep 6, (2016).
- Kanai, T., Mikami, Y. & Hayashi, A. A breakthrough in probiotics: Clostridium butyricum regulates gut homeostasis and anti-inflammatory response in inflammatory bowel disease. J. Gastroenterol. 50, 928–939 (2015).
- Tsuda, H., Ochiai, K., Suzuki, N. & Otsuka, K. Butyrate, a bacterial metabolite, induces apoptosis and autophagic cell death in gingival epithelial cells. J. Periodont. Res. 45, 626–634 (2010).
- Horie, H. et al. Probiotic mixture decreases DNA adduct formation in colonic epithelium induced by the food mutagen 2-amino-9H-pyrido[2,3-b]indole in a human-flora associated mouse model. Eur. J. Cancer Prev. 12, 101–107 (2003).
- Hua, M.-C. et al. Probiotic Bio-Three induces Th1 and anti-inflammatory effects in PBMC and dendritic cells. World J. Gastroenterol. 16, 3529–3540 (2010).
- McFarlin, B. K., Henning, A. L., Bowman, E. M., Gary, M. A. & Carbajal, K. M. Oral spore-based probiotic supplementation was associated with reduced incidence of post-prandial dietary endotoxin, triglycerides, and disease risk biomarkers. World J Gastrointest Pathophysiol 8, 117–126 (2017).
The complete guide to soil-based probiotics
BY LUCY MAILING, MD/PHD STUDENT
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.
Until recently, I recommended Prescript Assist as the best soil-based probiotic. While some of the microbes in the old probiotic formula were not well-studied, Prescript Assist had been used in several clinical trials with excellent results and no reported adverse events.1,2 It was also well tolerated, even by those with IBS, severe gut dysbiosis, or other gut pathologies.
In late 2017, the manufacturer made major changes to the ingredients of Prescript Assist, so it is no longer using the formulation that was studied in clinical trials. While the original formula contained 29 different strains, the new formula contains 28 strains, only 9 of which are from the original formula. There’s very limited evidence for most of the strains included in the new formula.
I’ve been asked by many people what my new recommended alternative to Prescript Assist is, so I decided to do some digging. This guide is a result of 50+ hours of independent research on soil-based organisms and the products commercially available today.
First, though, I’ll review what soil-based organisms are, the controversy, and the evidence for the most commonly used strains.
What are soil-based organisms?
The term soil-based organism (SBO) encompasses over 100 different species of microbes naturally found in soil. Some of these have been isolated and adapted for use as probiotics. Most SBO used in soil-based probiotics are spore-forming. This means that when they replicate, they form a small spore that is protected by a hard coating, making them resistant to heat, acid, and most antibiotics. This also means that they are more likely to survive the upper gastrointestinal tract and reach the large intestine compared to other commonly used probiotic strains.
The controversy and the evidence
There is currently a lot of 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.
On the other hand, opponents of SBOs argue that because of their spore-forming nature, they proliferate rapidly, and may compete with our resident gut microbes, rather than helping to bring the gut microbiota back to normalcy. In some individuals, opportunistic SBOs could overgrow, with the potential to become pathogenic.
My take: Several individual SBO strains have been shown to be beneficial, with no adverse effects, in dozens of randomized, placebo-controlled, human clinical trials. However, other strains have very limited or no clinical evidence and may be able to cause infection in people with a compromised immune system.
Rather than labeling all SBOs as good or bad, I think we need a more nuanced discussion – one that considers the evidence for each particular strain, microbe, and formula. That’s what I’ll try to provide in the next few sections. 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:
Before I do an analysis of the soil-based probiotic formulations on the market, it’s important to understand which species are most commonly used.
I searched PubMed and Google Scholar for every available human clinical trial on the seven most commonly used soil-based microbes:
Bacillus coagulans
Bacillus subtilis
Bacillus clausii
Bacillus indicus
Bacillus licheniformis
Enterococcus faecium
Clostridium butyricum
Before I share my findings below, it’s important to note that microbes are denoted by their genus, species, and strain. The list above provides the genus and species but does not tell you anything about the strain. Strain is incredibly important since two strains of the same species can have very different characteristics.3 Unfortunately, most probiotic formulations do not provide information about which strains they contain.
To see my full analysis of the available clinical trial literature for each strain, click here to download my Excel spreadsheet. For just the key findings, read on:
Bacillus 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.
There are three strains of B. coagulans that have been heavily studied:
GBI-30, 6086 (“Ganeden BC30”): with over 8 human randomized, placebo-controlled trials, this is one of the most well-studied Bacillus strains. GBI-30, 6086 has been shown to improve IBS,4–6 immune function,7,8 and beneficially modulate the gut microbiota.9,10 In cell culture experiments, this strain has been shown to stimulate production of anti-inflammatory cytokines and regenerative markers.11
Unique IS-2 (“ProDURA”): three human clinical trials have found this strain to be efficacious for bacterial vaginosis12 and children with IBS.13,14 Cell culture studies have also found that it inhibits the proliferation of cancer cells.15
MTCC 5856 (“LactoSpore”): two randomized controlled trials showed that MTCC 5856 significantly reduced bloating, abdominal pain, and depressive symptoms in IBS patients.16,17
Verdict: These three strains of Bacillus coagulans appear to be safe, well-tolerated, and may be especially beneficial for those with IBS.
Bacillus subtilis
Bacillus subtilis is recognized as a normal inhabitant of the human gut.18 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.19,20
B. subtilis produces an enzyme that can degrade oxalate, which may be particularly helpful for people with hyperoxaluria,21 and may also produce small amounts of Vitamin K-2. B. subtilis is found naturally in natto, a traditional Japanese food made from fermented soybeans.
Only four strains of B. subtilis have been studied in humans:
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.22,23 Another study found that DE111 improved bowel irregularity in otherwise healthy adults.24
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.25 It does not exhibit any antibiotic resistance and was shown to be absent of toxigenic activity in vitro.26
R0179: one study found B. subtilis R0179 to be well tolerated in healthy adults at a dose of 1 or 10 billion CFU per day, and confirmed that it survived passage through the GI tract.27
IP 5832: one Croatian study found that B. subtilis IP 5832 given during parenteral rehydration therapy for acute nontyphoid Salmonella gastroenteritis reduced patient-weeks of carrier state and resulted in fewer positive stool cultures at week four.28
Several studies for which I could not find strain information also showed benefits from B. subtilis: One Chinese study found that B. subtilis plus lactulose was more effective at treating functional constipation than lactulose alone.29 Several other studies found that B. subtilis + Enterococcus faecium reduced IBS-related abdominal pain30,31 and improved bowel preparation for colonoscopy.32
Verdict: Commonly studied strains of B. subtilis appear to be safe, well-tolerated, and with no adverse effects. Some strains appear to be particularly beneficial for improving immune function and bowel regularity.
Bacillus clausii
Bacillus clausii has been studied extensively and used for many years as the Italian pharmaceutical preparation Enterogermina for the treatment of a wide range of gastrointestinal diseases. B. clausii has been shown to have antimicrobial activity against Staphylococcus aureus and Clostridium difficile.
Enterogermina is the only formulation of B. clausii that has been studied in controlled human clinical trials and is made up of four different strains (OC, NR, SIN, and T). These strains have been shown to be acid and bile resistant,33 and can be recovered in stool for up to 12 days after a single administration.34
Enterogermina has found to be particularly beneficial for those with allergies, reducing nasal congestion and the need for anti-histamines.35–37 It has also been shown to reduce side effects during antibiotic treatment for H. pylori.38
One study of 40 patients diagnosed with SIBO found that taking Enterogermina for 1 month resulted in a normalization of glucose breath test result in 47 percent of patients.39 This is comparable to the rate observed with many antibiotics commonly used for SIBO treatment. Only one patient reported a side effect of constipation.
Verdict: Very well-studied and well-tolerated, with clear efficacy documented in several randomized, placebo-controlled trials. May be particularly beneficial for those with allergies or symptoms associated with SIBO. Since beginning this analysis, I have also tried Enterogermina myself and noticed improved tolerance to foods.
Enterogermina can be purchased from international online pharmacies as either capsules or liquid vials. Shipment should not be an issue since B. clausii is extremely heat-stable and does not require refrigeration.
Bacillus indicus:
Bacillus indicus has been touted for its ability to potently stimulate the immune system and produce high levels of carotenoids, vitamins, and quinols.
However, after an exhaustive search of the literature, I could find no scientific studies of Bacillus indicus in humans (with the exception of one study that used a preparation of 5 Bacillus strains – see “MegaSporeBiotic” section below).
Verdict: Currently lacking scientific evidence. This does not necessarily mean that B. indicus is not beneficial – it just means we have little to no evidence to speak to its safety and efficacy in humans.
Bacillus licheniformis
Bacillus licheniformis is commonly used in the fermentation history. 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: “In order to achieve an infection, either the number of microorganisms must be very high or the immune status of the host low.”40
The same EPA report further notes: “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.”40
A literature search only revealed only three human studies of Bacillus licheniformis – two from Russia and one from China – none of which were placebo-controlled. I could not determine which strain was used in any of these studies, and the results were largely unimpressive.
Nonetheless, B. licheniformis is found in many fermented foods traditionally consumed in Korean culture. Certain strains found in these foods have been found to enhance the longevity of worms by upregulating serotonin signaling.41
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 isolated B. licheniformis. I think it’s best to err on the side of caution and avoid probiotics that contain this species, especially if they can provide no strain information and/or do not regularly test the genetic identity of their strains.
Enterococcus faecium
Enterococcus faecium is a normal resident of the human gut, metabolizing carbohydrates and producing 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.42
However, it can also be pathogenic, causing diseases like neonatal meningitis and endocarditis. Many strains of this bacterium have developed multi-drug 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.43 Thus, there are concerns about its use as a probiotic.
Many different strains have been studied:
M-74: This strain has the most “randomized” clinical trials associated with it, but every single one gave the probiotic in conjunction with 50 micrograms of selenium.44–47 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 was reducing cholesterol levels.
L3: one Russian randomized controlled trial found that this strain of E. faecium reduced the frequency of infectious complications in premature infants on antibiotic therapy, reduced persistence of C. difficile, and increased abundance of Bifidobacterium and Lactobacillus spp.48
IS 27526: one Indonesian randomized, placebo-controlled study found that this strain of E. faecium increased salivary sIgA and weight gain in underweight preschool children.42
WB 2000: one Japanese study found that a combination of E. faecium with fish oil, lactoferrin, and several vitamins and minerals improved clinical symptoms of dry eye.49 However, the effects of probiotic cannot be separated because it was not adequately controlled.
SF68: one Italian randomized crossover study found that cirrhosis patients taking this strain of E. faecium had a greater reduction in blood ammonia than those taking lactulose.50 There was no control group taking neither E. faecium or lactulose.
CRL 183: one study performed in Brazil found that a combination of isoflavone-supplemented soy fermented with E. faecium and Lactobacillus helveticus was better than soy alone at improving total cholesterol, but again, we cannot separate out the effects of E. faecium from L. helveticus and the isoflavone supplementation.51
As mentioned above, several studies found that B. subtilis + E. faecium reduced IBS-related abdominal pain30,31 and improved bowel preparation for colonoscopy,32 but I could not determine which strains were used in these studies.
To make matters more complicated, Streptococcus faecium was reclassified to Enterococcus faecium several years ago. However, Enterococcus faecalis (previously known as Streptococcus faecalis) is an entirely separate organism. Unfortunately, I believe this delineation has been smudged in studies of these organisms.
Verdict: Very few well-designed RCTs have demonstrated the efficacy of E. faecium, and all seem to use different strains. E. faecium also has the potential to acquire multi-drug antibiotic resistance and cause infection. Until more studies can be performed, I would exercise caution with high doses of isolated E. faecium.
Clostridium butyricum
Clostridium butyricum is a natural resident of the human GI tract. It is one of the many important microbes in the gut that ferments dietary fiber and produces the beneficial short-chain-fatty acid butyrate. Butyrate is an important source of energy for colon epithelial cells, helps maintain the gut barrier, has anti-inflammatory effects, and protects against colon cancer.
MIYAIRI 588: This strain of C. butyricum has been used as a probiotic in Asia since as early as 1963. It does not carry any genes encoding any known toxins or virulence factors.
Two randomized controlled trials showed that this strain alone reduces side effects for abdominal symptoms and diarrhea incidence in patients undergoing H. pylori eradication therapy.52,53 Another randomized, placebo-controlled trial 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 given was lactose, which can exacerbate colitis in many people.54
TO-A: this strain of C. butyricum, in combination with E. faecium and B. subtilis, has been heavily used and somewhat well studied as a probiotic in Asia. The combined product is called BIO-THREE and has been shown in randomized controlled trials to reduce postoperative infections in patients undergoing surgery55 and shorten hospital stay for children with acute diarrhea.56
In cell culture studies, C. butyricum TO-A has been shown to reduce expression of TLR4, a gene involved in the inflammatory immune response. One randomized trial of ulcerative colitis patients found lower relapse rates in the group receiving BIO-THREE, but the difference was not statistically significant.57 No changes were observed in SCFA levels with probiotic supplementation.
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,58 and improved antigen-specific immunotherapy.59 In animal studies, C. butyricum has been shown to improve intestinal homeostasis and attenuate colitis.60
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, isolated forms of either of the strains listed above are not currently available in the United States, and I haven’t been able to find any international sources that I trust. The only alternative is to use the three-probiotic formulation BIO-THREE, which I’ll discuss more in the next section.
Product analysis
Note: I have no affiliation with any of these companies or products. This is the objective analysis that I used to determine which products I wanted to use for myself and with my clients.
Like all supplements, probiotics are not regulated by any governing agency (FDA, FTC, etc.), so it’s important to do your homework regarding their claims, sourcing, etc. Many companies that sell probiotics 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 the top eight most popular SBO products on the market.
While you might argue that a company’s marketing is less important than its ingredients or strains, I think it’s a key component. 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 my readers and clients.
Probiotic-3 (Advanced Orthomolecular Research)
Soil-based species: Bacillus subtilis TO-A, E. faecium T-100, and C. butyricum TO-A, (also known as BIO-THREE)
Colony-forming units: 19.2 million CFU
Other ingredients: contains lactose, polyvinyl alcohol, and potato starch (may be an issue for many with gut symptoms
What they claim on their website:
“Probiotic-3 is a probiotic formula that has been used clinically for more than 50 years in Japan and across Asia.”
- Reduces the growth of pathogenic bacteria while promoting the growth of beneficial bacteria
- Normalizes the inflammatory response, promotes detoxification and supports immunity
They reference several studies of BIO-THREE.61–63
Verdict: Inclusion of E. faecium is questionable, but the formula has shown benefits in several randomized clinical trials. Not recommended for those sensitive to lactose, 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
Colony-forming units: 4 billion CFU
What they claim on their website: “MegaSporeBiotic™ is the first 100% spore-based, broad-spectrum probiotic clinically shown to improve leaky gut by 60% in just 30 days. This unique all-spore formula effectively RECONDITIONS the gut by increasing microbial diversity and encouraging the growth of key health-promoting, commensal gut bacteria. MegaSporeBiotic™ boasts a 5-year shelf-life, does not require refrigeration, and maintains efficacy during antibiotic therapy.”
What their single research study actually found: In a “randomized”, placebo-controlled trial, 30 days of supplementation with MegaSporeBiotic reduced endotoxin (a measure of bacterial translocation into the blood) by 42 percent after a high-fat cheese pizza meal, compared to a 36 percent increase in endotoxin in the group receiving placebo. However, the subjects included in the “randomized” trial were really a hand-picked group of endotoxin hyper-responders.64 So yes, MegaSporeBiotic may reduce leaky gut by 60 percent if you are a dietary endotoxin hyper-responder and you happen to eat cheese pizza regularly.
Furthermore, there is NO evidence that this particular formulation increases microbial diversity, promotes health-promoting, commensal gut bacteria, or maintains efficacy during antibiotics.
Verdict: Inclusion of B. licheniformis and B. indicus is questionable, as few studies have been performed on the safety and efficacy of these strains. One clinical trial showed some benefit in hyper-responders, but the findings are heavily exaggerated on their website.
Just Thrive (Microbiome Labs)
Soil-based species: B. coagulans, B. subtilis HU58, B. clausii, B. indicus HU36
Colony-forming units: 3 billion CFU
What they claim on their website:
“With Just Thrive™ […] the body becomes a super-antioxidant factory right in the digestive system at the site where these important nutrients are most needed and absorbed.”
“Just Thrive® is the only product on the shelf to contain the patented Bacillus Indicus HU36®, a strain that produces high levels of antioxidants.”
What the evidence says:
There is absolutely no evidence to suggest that your gut becomes a “super-antioxidant factory”. In fact, any antioxidants produced by this probiotic are likely negligible if you consume a nutrient-dense diet rich in fruits and vegetables.
Moreover, Just Thrive is not the only product on the shelf to contain Bacillus indicus HU36, since MegaSporeBiotic also contains this strain.
Verdict: Contains B. indicus, which has little clinical evidence. Their website makes some pretty glorified claims that are clearly not backed by any real evidence. Supposedly they have about 10 clinical trials underway, so I’ll be happy to reevaluate Just Thrive when I see the data.
Primal Probiotics (Primal Blueprint):
Soil-based microbes: B. coagulans, B. subtilis, B. clausii (no strain information; quality assurance team said it was proprietary information)
Other probiotics: B. bifidus, L. plantarum, S. boulardii
Colony-forming units: 5 billion CFU soil-based, 5 billion CFU other probiotics
Other ingredients: microcrystalline cellulose, magnesium stearate, silicon dioxide, and 50 mg potato starch. Potato starch may be an issue for some people with gut issues. Resistant starch deserves an article on its own, but for now, I’ll say that I do not recommend supplementing with raw potato starch if you have gut dysbiosis, intestinal permeability, or autoimmunity.
What they claim on their website:
Like every probiotic, they make some lofty claims, such as:
“A simple daily dose of Primal Probiotics can help rebalance and restore gut health and improve immune function*”.
However, they are careful to note that:
“* There is no guarantee of specific results and results can vary from person to person.”
Verdict: A good mix of species with high CFU count but no strain information. No supporting clinical evidence for this formula, and not suitable for those who can’t tolerate potato starch.
Biospora (Klaire Labs):
Soil-based species: B. coagulans, B. subtilis (no strain information; no response to my inquiry)
Colony-forming units: 2 billion CFU
Other ingredients: coconut oil powder
What they claim on their website:
“BioSpora™ is recommended for enhanced support of normal GI and immune function. […] Each lot of Bacillus species used in BioSpora™ undergoes independent DNA testing using 16S ribosomal RNA sequencing to verify genetic identity.”
What the science really says:
You can’t verify genetic identity with 16S rRNA gene sequencing at anything below the genus level – only occasionally can you get to the species level with this type of sequencing. So, the only thing they are “verifying” is that each lot has some form of Bacillus.
Verdict: Contains only well-studied species. Website claims are largely scientific, but their genetic identity verification is highly questionable. No studies on this formulation have been done and no strain information is provided. However, Klaire Labs is NSF certified, which means their products do undergo independent testing.
Proflora 4R (Bio-Botanical Research):
Soil-based species: B. coagulans, B. subtilis HU58, B. clausii (no response to my inquiry about strains)
Colony-forming units: 3 billion CFU cells
Other ingredients: 100mg quercetin, 100mg marshmallow root, and aloe vera extract
What they claim on their website: “Proflora 4R replaces beneficial flora: Evidence suggests that the increase of inflammatory gastrointestinal (GI) disorders and intestinal permeability may, in part, be attributed to a under-consumption of these vital spore-producing flora. The combination of Quercetin, Marshmallow Root, and Aloe Vera extract in Proflora 4R™ provide additional nutritional support for “leaky gut” and a healthy microbial balance, with just one capsule a day.”
Verdict: Contains a good selection of species, but strains are not provided or have not been studied in human clinical trials. Website claims are largely scientific, and the addition of quercetin, marshmallow root, and aloe may help soothe a damaged gut.
TOP CHOICE: RightBiotics RX (RealDose Nutrition)
Soil-based species: B. subtilis DE111, Bacillus coagulans Lactospore (MTCC 5856) (both clinically validated strains!)
Colony-forming units: 5.36 billion CFU soil-based organisms, 15 billion CFU other
Other probiotics: B. lactis B1-04, B. longum BB536, L. helveticus Lafti L10, L. gasseri Lg-36, L. acidophilus DDS-1, L. plantarum Lp-115, Gnosis® S. boulardii (also all clinically validated strains) *Despite inclusion of Lactobacillus strains, this product should not cause histamine issues.
Other ingredients: vegetable capsule, organic rice bran extract, organic rice hull concentrate.
Allergens: “RightBiotics Rx includes one probiotic strain (L. helveticus LAFTI® L10) that contains a trace amount of soy from the culture media and may contain a trace amount of milk (including lactose) as it is sourced from dairy, according to the product’s Allergen Statement. For this reason, the label includes a caution statement for people with soy or milk allergy.”
Website claims: “Like people, no two probiotic strains are exactly alike. Each has a unique genetic makeup that determines its special health benefits. Verifying the strain ID ensures the formula delivers the unique strains shown in clinical research to deliver health benefits.”
Manufactured in the USA and third-party lab tested for potency and purity: “Our 3rd party laboratory is Atlas Bioscience Labs in Tucson, AZ. Atlas is DEA registered, and members of several industry-wide organizations including AOAC (Association of Official Analytical Chemists), and currently undergoing accreditation with ACLASS for ISO:17025 certification. We send every batch of product to Atlas Bioscience to test for active ingredients, as well as heavy metals, residual solvents, organochlorides, organophosphates and microbiology.”
Verdict: This is by far the best soil-based probiotic supplement I have seen on the market to date. I currently have NO affiliation with RightBiotics RX but am excited to have finally come across a product that is so well-supported by the evidence, independently tested, etc. I had not even heard of RealDose Nutrition before conducting this independent analysis, but if I continue to find success with this product with my clients, I may discuss affiliate options with RealDose Nutrition so that I can offer a discounted rate to my readers and clients.
For now, you can purchase it on their website or on Amazon.
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, I strongly advise choosing products that use high-quality manufacturing techniques and clinically-tested strains.
Currently, I am primarily using both Enterogermina and RightBiotics RX for myself and with my clients. I may occasionally try Probiotic-3 (BIO-THREE) in patients 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. This is part of the reason I recommend gut testing or working with someone with expertise in rebalancing the gut microbiota.
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.
Of course, I also recommend getting exposure to SBOs the natural way – this means consuming organically grown vegetables and getting exposure to dirt through gardening or other outdoor activities where you’re getting your hands and feet in the dirt! It also means eating plenty of properly prepared fermented foods. Interestingly, I’ve noticed that many popular kombucha brands, such as GTs, contain Bacillus coagulans GBI-30, 6086.
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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Check out Dr. Ruscio – 3 strain soil probiotic
Can anyone recommend a good soil based probiotic? I was on the Xifaxin/Neomycin treatment a few weeks ago for my SIBO-C. It didn’t work. In fact, I feel worse & my acid reflux is worse. My doctor said a second course in Dec will be needed. Have to wait a month.
I tried Megaspore a few months back. It caused skin rashes & joint pain that never went away. This wasn’t die off. Can some people not tolerate spore probiotics? Is it the Bacillus Licheniformis that’s the issue? I’m desperate for something to help me. Any suggestions?
I cannot do any probiotics containing soy or any dairy. I’m very sensitive.
Thanks,
Suzette
Hi Lucy,
I also found out that “RightBiotics RX” is not available anymore (wonder why?) – what would be your second best choice? Might it be “Bacillus coagulans Lactospore (MTCC 5856)” by itself? Or does it not provide enough variety?
RightBiotics RX at the Real Dose Nutrition website has different strains than mentioned in your article and no bacillus. It seems they have changed the formula they use?:
https://www.realdosenutrition.com/products/rightbiotics-rx
Hi Lucy-
Thank you for all the research that went into this article!
It looks like Rightbiotics Rx has completely changed their formula. The only strain that is the same is Lactobacillus plantarum Lp-115, and it now contains NO soil-based bacillus strains. Does that just leave us with the single bacillus strain of Enterogermina? Or is there another soil-based or bacillus blend that you would recommend now?
Hi Lucy I had the same concern as Evan when he wrote below,
“Hi Lucy, first of all I’d just like to say thank you for writing such a great article! It can get very overwhelming trying to dig through all the information out there on probiotics, and articles like yours really make a difference. Keep up the good work!
My comment is in regards to your top choice probiotic – Rightbiotics RX. It seems that the manufacturer may have changed the ingredients since you wrote your article. Instead of the ingredients you have listed, it now says it contains only 5 strains – none of which are soil based. The strains are: Saccharomyces boulardii, Lactobacillus acidophilus LA-14, Bifidobacterium longum BI-05, Lactobacillus plantarum LP-115 & Bifidobacterium lactis HN019.
Just wondering if you are aware of this change, and what your thoughts are on it?”
I thought since blog post settled on Rightbiotics RX( which is now just called Rightbiotics) as the top choice and so much hard work went into writing this blog post, that the readers could get your opinion on this change to the product.
Thanks for all of your hard work!
You mentioned reevaluating Just Thrive based on new research and I’m curious to find out if new studies have been released and if so, your review of the results? I recently bought several bottles for my family and myself and now I’d like to wait before using them. Thanks!
It’s working well for me! I’ve been taking it for about 50 days now. Gut is much more calm. I am personally more calm as well, feel like I have better blood sugar control or something. Don’t get hunger pangs and cravings anymore. Little to no fatigue after eating or a BM anymore either. I had a giant 6 x 6″ patch of bad eczema that has been clearing up steadily as well.
Hi Lucy, first of all I’d just like to say thank you for writing such a great article! It can get very overwhelming trying to dig through all the information out there on probiotics, and articles like yours really make a difference. Keep up the good work!
My comment is in regards to your top choice probiotic – Rightbiotics RX. It seems that the manufacturer may have changed the ingredients since you wrote your article. Instead of the ingredients you have listed, it now says it contains only 5 strains – none of which are soil based. The strains are: Saccharomyces boulardii, Lactobacillus acidophilus LA-14, Bifidobacterium longum BI-05, Lactobacillus plantarum LP-115 & Bifidobacterium lactis HN019.
Just wondering if you are aware of this change, and what your thoughts are on it?
Kind regards
Thanks for your comment, Evan! And thanks to all those who pointed out the change with RightBiotics RX! I’m not sure why they changed their formula and will be reaching out to them to see if they plan to release their soil-based formula again.
I’ll hope to update this article sometime in the next few months. In the meantime, Enterogermina is still a good option. The new Kirkland (Costco brand) kombucha also contains Bacillus subtilis DE111 and is quite tasty :)
Hi Lucy,
My apologies for all the questions.
Do you have any feedback or recommendations regarding Saccharomyces Cerevisiae by EpiCor? I researched it a bit and it seems like there are 5+ human clinical trials out there regarding this yeast. I wanted to know if you had any knowledge or experience with it?
Best,
Kirk
Hi Lucy,
Do you currently still recommend RightBiotics RX? If so, are you also still taking them? Have you or any of your patients experience any sort of “die off” effects from taking this probiotic?
Lastly, I noticed that they were sold out on both Amazon and on their website. Do you have any insight into if there were any issues with the product causing them to take it off the shelves.
Any help you can provide would be appreciated!
Will the lactic acid probiotics in RightBiotic colonize in The small intestine and worsen SIBO? That would be my hesitation on it vs a simple SBO probiotic.
Thanks for your thorough research! I wonder why some of these companies use the strains that aren’t studied and the same ones? SC 208 coagulans and HU58 subtillis instead of the studies ones… Is it cost or their own independent research?
I don’t see Amy Meyers Primal Earth probiotic mentioned here. I like that hers includes only the 3 well studied species, but unfortunately not the right strains. I wish RightBiotic was a simpler formula.
Do you have any experience with Body Biotics?
Hi Hannah – Body Biotics does not provide any strain info, and also contains B. licheniformis.
Thanks so much for the great information Lucy! I have Candida and leaky gut and also sensitivity to soy and dairy which I see both are in RightBiotics. The enterogermina is also currently unavailable. Based on your research would you then recommend Proflora4 for someone with leaky gut or best to wait for the enterogermina and take that on its own without RightBiotics? Thanks for your guidance!
Thank you for your very informative website!
I have 2 questions:
1) I am curious as to why you have not included the well-researched Bacillus coagulans SNZ1969 in your section about Bacillus coagulans (above) – it appears to be heavily studied and safely used for more than 40 years…
2) Perhaps it would be possible to connect as professionals? I am a German RD based in Berlin and would love to exchange knowledge and expertise with someone like you!
Thanks for your time!
Hi Martina, I can’t find any human clinical studies on B. coagulans SNZ1969, with the exception of this one published last November: https://link.springer.com/article/10.1007/s00384-019-03416-w. If there are others, please point me to them! And feel free to email me to connect :)
This is an amazing resource… I was wondering why, despite the branding differences between MegaSporeBiotic and JustThrive, the products seemed so similar… I love to know more about the science, and did not realize one ought to know the specific strain as indicated by the number, otherwise, the product is suspect. My probiotic literacy is expanding! Before reading this article, I started using MegaSporeBiotic after seeing it recommended by Jolene Brighten– I noticed a positive change literally within 1 day of my BM’s and was really impressed so started looking into spore/soil based probiotics to learn more, and found the Phoenix Helix podcast episode you were on. Bookmarking this, and sharing with others, for sure.
Thanks for your comment, Lara! The strains are definitely very important. Hope you found one that works for you!
This article is by far far the most well-informed, researched and informative one yet, and l have read a lot. Best part is writer is not connected with a particular product he’s promoting.
Thanks, Elaine! I hope to always remain independent and objective.
Hi Lucy, very interesting article! Currently I consume conventional sauerkraut for my gut health that I prepare in a conventional mason jar using salt. I would like to know what are your thougths if instead of using filtered water in the fermentation process one uses dirty water full of SBOs. Could that be safe, and do I expose to parasites eggs in this way?
Hi Maxi, good question! Traditional ferments with gently washed vegetables are very unlikely to be harmful, as people have been consuming these for hundreds of years.
However, the strains contained in these foods will vary from batch to batch and may lack the specific therapeutic qualities that an isolated, well-characterized and carefully chosen probiotic supplement would have.
I’d generally err on the side of caution and avoid using dirty water, as you don’t really know what you might be introducing, and in what quantities, without getting your soil tested. You could potentially expose yourself to parasites in this way.
I just wanted to say that I used this review to make a probiotic purchase because I have been suffering from multiple issues this year and last year. I am HLA-B27+ and that has always skewed (but I never knew until 3/2019) my gut bacteria towards a subset of species that are quite pro-inflammatory. We now know that specific receptors on the surface of cells in those with HLA-B27 will bind KIR-3DL2, increasing its expression in CD4 T-Cells. This expression increases both the longevity of cells undergoing inflammations as well as the response to produce inflammatory markers in the blood (some study somewhere mentioned up to 4x the response of inflammatory markers.)
I have recently contracted (and recovered from) a pretty horrendous intestinal infection from my time traveling in Mexico. The person that I traveled with was fine, so I blame an inflamed and non-standard gut makeup from my genetics. Curing the imbalance took me some months, and after finally starting to feel better…I started to feel MUCH worse. I found out that I began having the reaction that many HLA-B27 sufferers will experience after certain types of infections…and that was Ankylosing Spondylitis, Sceleritis, and Reactive Arthritis (of course IBS/IBD as well.)
I have also just torn my meniscus (90% tear) while in bed, so this indicated to me that the quality of my tendons from years of being HLA-B27+ (body attacks collagen in the body due to molecular mimicry, they think, between certain fragments of the bacteria Klebsiella Pneumoniae’s genetic makeup and that of collagen in the body) was severely degraded and inflamed. I have had inflammation and pain in the insertion points of most of my muscles (for years.) Needless to say, this all has been building up over the years and I am only 33 years old as I write this post.
After reading around 20-30 hours of medical journals, after having read nearly 50 in the past, because my symptoms have always seemed to return quite quickly after treating my intestines with probiotics and using antimicrobials (Candibactin AR/BR) I decided to give Rightbiotics a try after reading this review. I don’t even know how to describe the effects this stuff is having on me. I also purchased psyllium seed powder to enhance its proliferation inside me. While I may have taken too much the first day (yesterday) and this caused me a little discomfort at night, I have reduced the amount of powder I put in a cup of water and that seems to be just fine. As for the effects I’m having this morning I’d like to document the following:
1) I am feeling like colors are brighter (and so is my disposition). My scleritis flares up with a lot of carbs/starches I eat, and while I am specifically staying away from them…the vascularity in my eyes was always present when it never used to be. My vision would sometimes blur on flare-ups and I could feel mild to moderate irritation in the sides of my eyes. I woke up today with a little “pressure” in my eyes but nothing uncomfortable at all. This may actually be related to sinus bacteria being modulated due to immune modulating effects of the probiotics in Righbiotics’ blend. I actually am smiling and more mobile today even though I have a completely jacked up and painful knee.
2) The nerve in my knee would drive me crazy at random intervals almost every day (12 days of injury so far). It is doing that significantly less today and I have increased mobility, though I can’t really put much weight on it obviously.
3) I have had extreme difficulty in digesting leafy greens and fleshy roots for quite some time. I had some pho last night (without the noodles,) so let’s call it a beef soup. There were quite a few leafy greens, some authentic Vietnamese greens that you would not see in most restaurants, so my digestive system is obviously not accustomed to breaking them down in any way. I have eaten Pho before (made by my Vietnamese friend) and had a slightly hard time breaking down some of these substances. Woke up today with my stool almost completely normalized in both color and consistency and the veggies were digested. To me…this is huge! I know I am having malabsorption issues when I am not digesting veggies for so long. This is why I’ve looked to shilajit as a way to almost completely support my trace mineral requirements. This may become less necessary after using this Rightbiotics blend.
These are the things I am feeling almost over-night. I’ll admit this isn’t a long time to have used the probiotic to make a statistically significant claim…but these effects are PROFOUND and I felt them almost immediately. Funny enough, when I take the psyllium husk in water…I always get a thermogenic reaction and feel VERY warm for quite a while. I don’t feel bad, just warm, and this makes me get tired a little faster. This could be due to a lot of different bacterial colonies being reproportioned inside me, or some other byproduct of its breakdown/absorption…but it is indeed another indicator that SOMETHING is happening.
Just reporting these findings for those who may be HLA-B27+ and looking for a good strain combination to help them. This is certainly helping me! I also have been taking Lactobacillus Rhamnosus GG as it is highly recommended for those with my genetics as it evades detection by the immune system through producing a particular polysaccharide that is not flagged by our immune system as a pathogen. I still have a LONG battle ahead of me and my ankylosing spondylitis pain in my back has JUST begun after taking pain killers for me knee (knew it was gonna mess with the lining of my gut and have an adverse reaction…but initially after they forced my leg extended…the pain was just too great)
I also wanted to say “Thank You” for writing such a great article that helped me make a decision that I believe will be extremely beneficial for me in the weeks/months/years to come. I am so happy to find someone who is as thorough in reporting their findings as I like to be and doesn’t jump to conclusions or broad generalities…this helped me trust in the strains you chose to look at a little more when you were critical of them in a fair way. Keep up the GREAT work and I’m sure I’ll have more updates in the near future!
Jacob, my most sincere apologies that it took me so long to see and respond to this. Thank you so much for sharing your story and your experience with RightBiotics, and for your kind words about my work! I always hope that people will learn and benefit from the time it takes me to research and publish articles like this, but don’t always get feedback from people who actually try the products or interventions I suggest. I can’t tell you how rewarding it is to hear that my efforts are helping people like you to make educated decisions that can so dramatically improve their health!
The effects that you noted are certainly profound, and n=1 experimentation is often the best way to assess our response to various interventions. If you have a moment, I’d love to hear if you have continued to take RightBiotics RX and what you have experienced over the last few months!
Amazing write-up! Really appreciate your careful review of the literature, especially in vivo studies. Also glad you clarified the species vs strain issue (so much inappropriate use of the description ‘strain’ in marketing and much misunderstanding about this issue).
Thanks for your kind words, Christy! I’m glad you enjoyed my write-up and am hoping to do a similar analysis for other types of probiotics in the future!
Very helpful as I’ve gotten conflicting advice on soil based probiotics. One of my GI’s had recommended Primal Earth Probiotics by Dr Amy Myers when treating my sibo and IBS. . However, in looking at the ingredients, the strains of the cagulans, clausii, and subtilis were not shown except for subtilis, which was HU58 strain. She writes an article, too about the preference for Soil based at early ages of treating SIBO, but the research cited was limited.
Link below if anyone wants to see more –
https://www.amymyersmd.com/2018/02/soil-based-probiotics-best-sibo/
https://store.amymyersmd.com/products/primal-earth-probiotic
Glad you found this helpful, Brad! Transparency in strains is so important.
The strains are shown on the image of the bottle:
https://store.amymyersmd.com/products/primal-earth-probiotic
Bacillus subtilis HU58
Bacillus clausii (SC-109)
Bacillus coagulans (SC-208)
Microbiome Labs private labels for Amy Myers, Biocidin, and a few others.
Lucy
It’s refreshing to see that Integrative and Functional Medicine is gaining exposure. Big Pharma has had a stranglehold on conventional medicine for far too long. Too many lives lost far too soon due to the way patients have been treated for over one hundred years. Keep up the great work girl.
Thanks for your kind words, Daniel. I’m committed to bringing more of this approach into the mainstream!
You state the following:
Verdict: This is by far the best probiotic supplement I have seen on the market to date. I currently have NO affiliation with RightBiotics RX but am excited to have finally come across a product that is so well-supported by the evidence, independently tested, etc.
You are just starting out in the medical field beings you state you are a student, with that being said it’s obvious you don’t realize that many study results in the Drug Industry and Supplement industry can and are falsified all the time. Ones on results with a product is really the ONLY way to tell what works and what doesn’t.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340084/
https://www.theguardian.com/science/2017/jun/05/dozens-of-recent-clinical-trials-contain-wrong-or-falsified-data-claims-study
Dan, great point! Clinical trials are constantly being conducted, and MANY initial findings are subsequently falsified. Thirty years ago, we had to completely guess with probiotics, try random strains, and hope that they were safe and had the intended health benefits. Now, we have enough clinical evidence that I believe it is worth doing an analysis like this to identify strains that have been tested in trials, as products that contain these strains are the MOST likely to be safe and have specific therapeutic qualities that will benefit health. I agree that having studies on a product formula itself is ideal as opposed to studies that look at the individual strains, and hope to see more of this in the future. I acknowledge that some of what is included in the article above may be falsified in later clinical trials. I am presenting the evidence we have now so that people can consider these therapeutic tools appropriately, and will continue to refine and update this as we learn more!
There’s always some new hothead that shows up out of the blue and tries to disprove established research so they can start their own health coaching practice and convince people that they have the answers. I am seeing this constantly now
Why are you being so negative? ‘Established research’ for the microbiome doesn’t exist, this is a new area of health. Her research and analysis is straight to the point and referenced very well. Let her be.
Hello,
I’ve been researching how to heal a leaky gut. I am getting confused when reading about transient versus resident forming bacteria strains versus soil-based organism’s. Could you possibly explain the differences? I do consume on a daily basis a variety of Kombucha’s. Would you recommend any of the above probiotics for someone who has two auto-immune diseases: Celiac, and Hashimoto’s? There is so much information available on the Web that it can be quite overwhelming. I would appreciate your input?
Hi Lisa! The most recent research suggests that probiotic colonization is very individual – meaning that certain probiotics appear to colonize in some people, but not in others. We don’t yet understand what characteristics make it more likely that your gut is permissive to colonization. However, probiotics still have lots of beneficial effects while in transit through the GI tract, even when they don’t colonize. You might want to check out this article on leaky gut: https://lucymailing.com/probiotics-helpful-or-harmful-for-leaky-gut/ to understand how probiotics can influence the gut barrier. I’d typically recommend Visbiome as a good probiotic for celiac disease, for reasons I discuss in this article: https://lucymailing.com/gluten-intolerance-or-gut-dysbiosis/. You could also try the two soil-based probiotics I recommend in this article.
I reached out to the company that makes Terraflora about research and was told that they will be running human clinical trials shortly. I’m interested to see the outcomes. They did indicate that there have been tests on the megaterium and pumilis, but they are not currently in the public domain. We shall see.
Thanks for such an in depth analysis – much appreciated.
Thanks for sharing, Eva! I’ll be very interested to see the trials when they come out!
Excellent article on the “dirt” probiotics Lucy, you put in some time. :) I was wondering your thoughts on another SBO I found called Terraflora? My reading concludes that it is soil-based with many of these Bacillus strains, but it also has a prebiotic complex. Many of the aforementioned do not contain prebiotic fiber in addition to the Bacillus strains and I was interested in your take.
Hi Frank,
That’s a great question, and at some point, I should definitely add TerraFlora to this analysis! From a quick look, TerraFlora contains Bacillus megaterium and Bacillus pumulus, two species that have not been well studied in humans. One study (Alkaya et al. 2017) used these two species in a probiotic toothpaste, but found no statistically significant benefits compared to placebo. The formula also contains B. coagulans, B. subtilis, and B. clausii, but has no strain information available for these species. So overall, I don’t think there is evidence to support the use of TerraFlora, though I do like the synbiotic concept and hope that more companies consider incorporating prebiotics into their formulas!
[…] Probiotics, especially a good soil-based probiotic. […]
probiotic-3 contains lactose. most people with gut problems cannot tolerate any dairy. i dont get why these probiotic compabies constantly put dairy in their products . are yo uaware of any other brands that contain these strains and are dairy and gluten free?
Any traces of dairy and soy in probiotics are typically leftover from the fermentation process, but for Probiotic-3, it seems that they have intentionally put lactose into the product as well. I’m not sure why either, as it is definitely an issue for those with gut problems! Unfortunately, that’s the only probiotic with C. butyricum that I am aware of.
Oh boy…would sure love to get you in a room with Kiran Krishnan for a couple hours and be a fly on the wall!!! Look forward to receiving your updates on this topic!
there’s always some new expert that pops up who challenges things previously established. in the end a treatment is highly individualized and people need to do what works best for them not what others tell them
Any thoughts on Progurt probiotics? They’re human-derived (isolated from breast milk, from what I can gather) and contain 1 trillion Colony-Forming Units. Said to colonise better than SBOs because the microbes are intuitive to the human GIT. Apparently Progurt is favoured by a number of practitioners/clinicians who report great results. Have personally used them and felt the benefits. Interested in your professional take.
Hi Ronnie. Progurt isn’t soil-based, it contains Lactobacillus and Bifidobacteria, so I did not include it in this post. I am planning to do a deep dive on the best species and strains of Lactobacillus and Bifidobacterium in the near future, so I’ll be able to speak more to it then!
Great work!I too was impressed by Prescript Assist and disappointed when the formulation was changed. The one that I see missing is Bifidobacterium infantis and apparent benefits for those with autism not just infants.
Absolutely. My intention with this article was to focus solely on soil-based species, but I will certainly be doing a similar analysis in the future that will discuss the benefits of Lactobacillus and Bifidobacterium-based probiotics :)
Lucy, thank you for providing this very insightful research into SBO options available.
As with most topics surrounding gut health these days, there are alternative opinions. I was wondering if you have considered comments made by Natasha Trenev of Natren and others surrounding the unknown, long-term impact of SBO’s A friend of mine has a site discussing related topics and reviews Natasha’s comments here: https://fixyourgut.com/hso-probiotics-not-as-safe-as-they-are-believed-to-be/
Thanks…
Thanks for offering your perspective, Gary. I have read the entire HSO series on fixyourgut.com and am familiar with the arguments made there. As I mentioned in the article, I think we need a more nuanced discussion as “all good” or “all bad”, since there are clearly certain strains that show efficacy in RCTs with no significant adverse events, and some of these species are normal inhabitants of the human gut microbiome.
Great article! I’ll add the B. clausii UBBC 07 as another potential option besides Enterogermina. Certainly not as much research as those strains, but possibly useful. Here’s one of their studies on the strain: https://www.wageningenacademic.com/doi/abs/10.3920/BM2012.0034
Thanks, Kelsey! I have seen that study and did include it in my analysis, but it isn’t a controlled study. They gave 27 patients with acute diarrhea B. clausii UBBC 07, and their diarrhea resolved over time, but we have no idea if the B. clausii improved recovery since there was no placebo or control group that did not receive the probiotic. And as I’m sure you’re well aware, most acute diarrhea resolves on its own with time and fluids. I’m certainly keeping my eye out for more controlled studies on that strain, though!
Yeah, I’m looking forward to more research too. It would be nice to have another B.clausii option on the market if it actually worked!
This is freaking awesome! You rock Lucy. I had been taking Just Thrive for a few months after meeting a rep at AHS last year and looking at the study they did on leaky gut. Did you see that one? The results seemed pretty impressive, but I’ll admit I more or less trusted the face-value results and didn’t dig deeper into how impressive they actually were (apparently I’m not as much of a skeptic as I thought!).
Anyway, I haven’t noticed any huge difference while taking it (I never really do with probiotics), so I might skip a month and instead try the two you recommended. Thanks so much for doing the hard leg-work!
Thanks, Alyssa! Just Thrive and Megasporebiotic are actually both manufactured by Microbiome Labs, so the leaky gut study that I discussed under the Megasporebiotic section is the same as the one cited on the Just Thrive website. My biggest issue is that they hand-picked dietary endotoxin hyper-responders for the study (not a big deal in and of itself) but then used the study to say that it is “clinically proven to improve leaky gut in 30 days”.
I’d love to hear what your experience is if you try these two!
Ah, interesting! Well I’ve ordered both of the probiotics you recommended, and I’ll definitely let you know if I notice a difference!
Did they make a difference?
Enterogermina is also available on Amazon for those who may not want to risk customs clearance issues when purchasing from international pharmacies: https://www.amazon.com/gp/offer-listing/B07H7QTPCM/
I didn’t realize that, thanks Nita!