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The Best Soil-Based Probiotics

Soil-based probiotics are probiotics that are often found in soil and that confer a health benefit to humans. Remember, we evolved with constant contact with soil and the bacteria soil contains. However, there is confusion regarding what soil-based probiotics are safe and effective.  Let’s discuss the best soil-based probiotics based upon what the scientific evidence shows.

In This Episode

Episode Intro … 00:01:50
Prescript Assist Changed … 00:02:20
Categories of Probiotics … 00:02:49
Product Recommendations … 00:09:03
Dosage … 00:12:32
Clinical Studies … 00:15:13
Soil-based Probiotic Benefits … 00:17:48
Clausii and Licheniformis … 00:19:50
Probiotics Containing Prebiotics … 00:20:50
Prescript Assist … 00:22:00
Episode Wrap-up … 00:24:50

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Episode Intro

Dr. Michael Ruscio, DC: Hey, everyone. Welcome to Dr. Ruscio Radio. This is Dr. Ruscio. Today, let’s talk about soil-based probiotics and what the best soil-based probiotics are. There are two points here, a background that is important to be aware of.

Point one is soil-based probiotics are essentially bacterium that are found predominantly in the soil and, of course, that we have evolved in constant contact with and therefore may have a beneficial effect on the human host.

Dr. Ruscio’s Fast Facts Summary

Categories of Probiotics

Lactobacillus and bifidobacterium

  • Well studied, numerous clinical trials

Saccharomyces Boulardii

  • A healthy type of fungus

Soil-based probiotics

  • Usually start with bacillus
    • B. coagulans (most studied)
    • B. subtilis (second most studied)
    • B. clausii (third most studied)
    • B. licheniformis (hovers around the third most studied)

E. coli Nissle 1917

  • Has shown benefit in clinical trials for IBD
  • Trade name Mutaflor
  • Not available in the U.S.

Enterococcus faecalis

  • Has shown some benefit, worth considering

Product Recommendations

  • FMF Soil-Based Probiotic – contains B. subtilis and B. coagulans
  • Megaspore contains Coagulans and Subtilis + B. clausii and B. licheniformis
  • Just Thrive contains B. Indicus, B. Subtilis, B. Clausii, B. Coagulans
  • Biocidin’s ProFlora4R contains B. subtilis, B. coagulans + B. clausii plus it also contains marshmallow, quercetin and aloe.
  • BioSpora from Klaire contains B. coagulans and B. subtilis
  • AOR Probiotic 3 – contains E. faecium, Clostridium butyricum, B. subtilis
  • All fairly comparable

Recommended Dosage

  • 2-8 billion per day, upper end of dose range
    • Start with a lower dose, see how you feel after a few days. If feeling good, stay with that, if no change, increase dose. After a month or 2-3 months, try to titrate down to the minimum dose to maintain improvement or completely off the probiotic.

How many probiotics strains are helpful?

  • Best data is for one strain preparation. However, a more diverse probiotic might be better, purely speculative but IBS literature has concluded this with lacto-bifido preparations.
  • In theory, a multi-strain soil-based probiotic might be best. I would start with 2 strain (1st B. coagulan, 2nd B. subtilis), it’s a compromise, then consider a trial on a multi-strain with more than 2.

What other strains to include?

  • Could draw an inference based upon what strains are found most abundantly in human stool – B. clausii and B. licheniformis
  • See product recommendations above

Clinical Trials  

  • B. coagulans showing benefit
    • See Links section

Benefits of Soil-based Probiotics

  • Improved diarrhea, abdominal pain, bloating and stool consistency
  • Increase secretory IgA
  • Decreased leaky gut
  • Decrease respiratory tract infection
  • Healthier microbiota
  • Decreased inflammation
  • Improvement in IBS severity
  • Decreased post-exercise muscle soreness
  • Secrete antimicrobial peptides
  • Aids in Abx treatment of H. pylori
  • Decreases AE from antibiotics

Slight benefit on constipation

  • Effect on constipation is unclear, some studies show non-significant improvement, others show no improvement. Another study found laxative combined with SBO more effective than a laxative alone
    • See Link section

Studies that show no benefit from soil-based probiotic

  • These studies are few and far between
    • See Link section

Don’t buy cheap, no-name probiotics. Formulas matter.


  • The benefits of soil-based probiotics are not unique to soil-based probiotics ONLY, benefits have been shown in other probiotics. They are one of 3-5 categories of probiotics.

Prescript Assist Changed

Point two is a more popular or one of the most popular versions of a soil-based probiotics, specifically, Prescript-Assist has recently had a formula change that many people are not happy with and are now looking for an alternative recommendation. So we will, today, review what the actual clinical trial outcome data with soil-based probiotics has shown. And we will also use that to be able to then see what strains are the most well-studied and the most efficacious. And that clearly leads us to a few product recommendations.

Categories of Probiotics

Okay. So let’s jump in. One of the first things that is probably important to understand here is that we can break probiotics down into a few different categories. And, really, you can break them down into about three to five categories.

Category one, the most well-studied, contains predominantly Lactobacillus and Bifidobacterium strains. That’s the most well-studied type of probiotics. There have been numerous clinical trials using a Lactobacillus and Bifidobacterium predominant probiotic.

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Category two, Saccharomyces boulardii, which is a healthy type of fungus. Category three are soil-based probiotics and they mostly start with Bacillus, so you have Bacillus coagulans, Bacillus subtilis, Bacillus clausii, Bacillus licheniformis. Most of the soil-based probiotics that have been used in clinical trials in humans start with the designation of Bacillus.

The Best Soil-Based Probiotics - SBoulardii New L

Category three are soil based probiotics, and they mostly start with Bacillus. So you have Bacillus coagulans, Bacillus subtilis, Bacillus clausii, Bacillus lichenformis. Most of the soil-based probiotics that have been used in clinical trials in humans start with the decimation of Bacillus.

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And then the fourth category is E. coli Nissle 1917. E. coli Nissle 1917 has been used in a number of clinical trials and shown benefit most namely for inflammatory bowel disease. This trades name has one product known as Mutaflor. It is not available in the United States. So it’s not something that is used typically, unfortunately. And then category five, Enterococcus faecium, which has also been used in a number of studies and has shown some benefit, lesser so than the others but something worth considering also.

Now, it’s important to understand those categories because if you understand that there are these three to five categories of probiotics, you can try, you can experiment, either on yourself or, if you’re a clinician, with someone that you’re working with, a probiotic from each of these categories and attempt to see if you can elucidate benefit from a probiotic. Now, why that helps is because it can prevent you from trying just different formulations of the same category, right? Someone may try a Lactobacillus-Bifidobacterium predominant blend called Bifidobacteria 10; and it’s got Bifidobacterium plus a few Lactobacillus strains, and they have a negative reaction. So then they try another one called Gut Restore 5. It’s got three Lactobacillus strains and two Bifidobacterium strains. And they have the same kind of reaction, right? Then they try another one called Leaky Gut Complete and it’s got four Bifidobacterium and four different Lactobacillus. And guess what? They had the same reaction again.

So they keep pounding their head against the wall trying a different formula within the same category not understanding that they’re doing so. So understanding the categories can be very helpful so that you can try one probiotic from each category, assess if it’s helpful or if you have a reaction. If you have a reaction, you can move on. If it’s helpful, you can continue. So that’s why it’s helpful to understand those categories of probiotics.

Okay. So when we look at the soil-based probiotics specifically, we see the best clinical data clearly for Bacillus coagulans, that is the most well-studied strain. Now second to that would be Bacillus subtilis, or Bacillus clausii, or Bacillus licheniformis, or Enterococcus faecium. They’re all kind of tied for second or third.

We may be able to say that the best data out of all those is Bacillus subtilis and then the others follow. But those are really the players to consider when trying to find a soil-based probiotic. So Bacillus coagulans, most well studied. Second to that Bacillus subtilis followed by Bacillus clausii, Bacillus licheniformis, and Enterococcus faecium.

Now, specifically regarding the studies using soil-based probiotics, the best data does appear, in terms of the randomized clinical trials for one strain of probiotic. However, when we look at the body of literature on probiotics more broadly, we see that the consensus emerging suggests that a multi-strain form of probiotic seems to be better than a single strain form.

So this pulls me to not only go by what the evidence shows here and not just be evidence-limited so as to make a recommendation to use what—I’m making a bit of an inference to generate but the recommendation of using a two-strain soil-based probiotic or higher. Again, because I do think that the better stimulus to provide someone’s microbiota, someone’s gut would be a multi-strain stimulus. I think you have a higher probability of benefiting from that. That is mostly taken from the studies on Lactobacillus and Bifidobacterium probiotics where we have a wealth of data to kind of mine from. So that is my thinking there.

Sponsored Resources

Hey, everyone. I just wanted to say thank you to Biocidin, who has helped make this podcast possible. If you’re not familiar with Biocidin, they have a quality line of products, including anti-microbials, a soil-based probiotic, and a gut detox formula, amongst other things.

And how I came to learn about Biocidin was actually after a few patients of mine—who had been reacting to all other forms of anti-microbials—went out, did some experimentation, and actually found the only anti-microbial formula that they did not negatively react to was Biocidin. So this got me to open my eyes and give them a further look.

And they have a few products I think are worth mentioning. One is their anti-microbial Biocidin, which comes in a few different forms. They also have Proflora®4R, which is one of the few soil-based probiotics that I recommend. And also they have Dentalcidin, which is their Biocidin in the toothpaste form. And this may actually help with the removal of oral biofilms.

Now, if you go to and you use the code RUSCIO, they will give you free shipping and a free bottle of Dentalcidin when you purchase their comprehensive cleansing program. They do have wholesale pricing available for licensed healthcare practitioners if you email [email protected]

So Biocidin definitely has some helpful products for improving your gut health. And I would definitely recommend checking out Biocidin for more information on a few of these tools that can help you in optimizing your gut health.

Product Recommendations

Okay. So we’ve covered kind of the theory behind the soil-based probiotics, which is the organisms that we theoretically have had a lot of contact with in soil, dirt, food coming from the dirt, what have you. We’ve talked about the categories of probiotics. We’ve talked about the main players for a soil-based probiotic. Now, let’s briefly touch on some specific product recommendations, and then I want to come back to some of the trials that have been down that help craft those specific recommendations.

So like I mentioned, the two-strain probiotic I think is the best compromise, at least initially, for a soil-based probiotic. So I use a probiotic in the book and in the clinic specifically called Soil-Based Probiotic. And it contains Bacillus coagulans and Bacillus subtilis, probably the two most well studied.

The Best Soil-Based Probiotics - SoilB 2s L

Now, there is another formula that’s very similar to this. It also offers the two strains. And this is BioSporafrom Klaire Labs. It contains Bacillus coagulans and Bacillus subtilis. Now, if you wanted to go to a higher number of strains with a soil-based probiotic then you could use MegaSpore, which contains Bacillus coagulans, Bacillus subtilis, Bacillus clausii, and Bacillus licheniformis.

Let me shut my windows today. I’m trying to record with my window open because it’s sunny. And, of course, that’s not going to happen.

So, MegaSpore will give you essentially a four-strain probiotic: coagulans, subtilis, clausii, and licheniformis. And we have at least one study to support the use of each of these strains in there. Now, there’s also a comparable formula known as Just Thrive Probiotic. This contains B. Indicus, B. Subtilis, B. Clausii, B. Coagulans. So it’s a three-strain, soil-based probiotic; whereas MegaSpore is four-strain probiotic. There is also Biocidin’s Proflora 4R, which contains Bacillus subtilis, Bacillus coagulans, and Bacillus clausii plus marshmallow, quercetin, and aloe. And finally, there is AOR Probiotic-3, which contain Enterococcus faecium, Clostridium butyricum—I believe it’s pronounced—and B. subtilis.

So, those are really the best players on the board regarding soil-based probiotics. Now, is one of these clearly better than the others? You’ll hear lots of claims, but I think they’re all fairly comparable, which is a good thing, right? These are all good probiotics. Are they better than no-name brands or brands that you may find that are half the cost? Very likely, because one of the things you do see with probiotics is major challenges with meeting the label claims and the viability in terms of the number of probiotics that are actually contained in there.

So sometimes you don’t have what’s in there or sometimes you don’t have as much of what’s in there. This is very important with the soil-based probiotics because some soil-based probiotics—none of these, but some soil-based—they’re not really soil-based probiotics. They’re soil-based organisms. Some soil-based organisms can be pathogenic and can harm you. So working with a company that has good quality assurance is important. So these are all the good formulations.


Now, regarding the dose, a dosage of two to eight billion per day is what’s been used in a number of the studies. (123456789101112131415) Now, that’s a broad range, right? And that may give you a range of anywhere from one capsule once a day to two capsules twice a day, right? So, one total capsule a day versus four total capsules a day.

And sometimes people have a hard time with this concept. And it’s actually a good thing. It means that we don’t have to be incredibly precise with the dose, right? So what I typically have people do is start with a lower dose and give that a few days.

And if they’re feeling great from that, I’ll have them just continue with that. And if they’re not feeling much, we’ll have them try to work up to the full dose, see how they do. And then after a time, usually a month, or two, or three, we have them try to wean down to the minimum dose needed to maintain improvement, or off completely if they notice that they maintain the improvement once they come off.

So these dose ranges tell us that these things are not high prescriptive, which, again, makes some people uncomfortable because they need a very specific number. But that’s just not the way this stuff works. There are ranges. We can work within the ranges. Some people do better on less. Some people do better on more. A little bit of experimentation goes a long way in determining where you may fall in there.

Clinical Studies

So let’s talk about some of the clinical studies with some of these probiotics. Like I mentioned a moment ago, the best data is really for Bacillus coagulans. There are—one, two, three, four, five, six, seven—eight trials using single strain Bacillus coagulans showing benefit in humans. (1617181920212223) And I’ll put the link to all these studies in the notes.

There is one study with just Bacillus subtilis. That’s our kind of pseudo, second-rated strain showing benefit. And there are few clinical trials with other strains, usually one to two strains, showing benefit. And here, this is where we see the kind of bidding for the second or third position between Bacillus subtilis, Bacillus clausii, Bacillus licheniformis, and Enterococcus faecium.

So Bacillus subtilis has six studies, clinical trials. (252627282930) Bacillus clausii has three. (313233) Bacillus licheniformis has two. (3435) And Enterococcus faecium has five. (3637383940)

And, again, most of these are using two. Some of these are using three strains for the most part. And this is why I hover around two as a starting point because we have a number of studies showing benefit with one and a small number of studies showing benefit with two to three. So I kind of position my specific probiotic recommendation at least where I start with the soil-based probiotic to about two. It seems to be a middle ground there.

Clinical Trials

So there’s also been one trial specifically with a formulation that is MegaSporeBiotic, and this is a nice trial. The one thing I would have liked to have seen is a clinical outcome tied to this. They showed reduced leaky gut, which is a nice first step. However, I’m very wary of leaky gut because, you see, for example, literatures showing people who eat a lower-carb, higher-fat diet have increased leaky gut.

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However, these people also tend to lose more weight and have better improvements in body composition than people eating a higher-carb, lower-fat diet. And, again, it’s not to say one diet is better than the other. But if the higher-fat, lower-carb diet that is “causing leaky gut” was so detrimental for one’s health, we wouldn’t see it tied to the improved health outcomes that we see it tied to. So I think there’s a little bit more to leaky gut than we fully understand. Leaky gut is clearly only an intermediary between a health problem in the gut and intestinal damage. Leaky gut is not the cause as what I’m saying another way. So I don’t put a huge amount of stock in findings regarding leaky gut.

But anyway, there we have a review of the studies. And there are a number of trials that had been published here. Again, you have seven or eight with Bacillus coagulans. You have one with specifically Bacillus subtilis. Then—one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen—about thirteen with some of these other strains. And so, there’s definitely some data here to substantiate at least a trial.

View Dr. Ruscio’s Additional Resources

Soil-based Probiotic Benefits

Now, in terms of mechanism, soil-based probiotics have been shown to impart numerous benefits in the host. Improvements in diarrhea, abdominal pain, bloating, and stool consistency have been reported. Increases in secretory IgA, the protective mucous membrane in the gut. Decreased leaky gut. Decreased respiratory tract infections. A healthier microbiota. Decreased inflammation. Improvements in IBS severity. Decreased post-exertional muscle soreness. Secretion of antimicrobial peptides, meaning probiotics are actually antimicrobial, which I think is one of the major—like one of the major benefits from probiotics. And they also decrease adverse events from antibiotics. So a lot of nice benefits here.

And I should also mention that there’s a slight benefit on constipation. Not all the studies show this but there does seem to be a hint toward a benefit in constipation with soil-based probiotics also. (434445)

But there’s another really important to note because I can envision someone reading or listening to this and saying, “Gosh, I need to get myself on a soil-based probiotic, stat.” But these benefits are not unique to soil-based probiotics, right? These benefits have been shown with the other forms of probiotics also. So, just because I’m giving you some data about the mechanisms regarding soil-based probiotics, don’t let that fool you into thinking that this is the best form of probiotic. I don’t think it is. I think they are all viable. I think we have the best data for Lactobacillus-Bifidobacterium blends class I, and for Saccharomyces boulardii probiotics class II. But there’s also some good data here. So just contextualize this. Don’t let the fact that there are some nice-looking mechanisms there throw you too off.

And there are also some studies showing no benefit from a soil-based probiotic. There’s about, let’s see, four or five that I was able to find. And I’ll also put a reference in here for you, again, a published peer-reviewed study showing that quality of the formulation is important because label claims don’t always match. (46474849)

Clausii and Licheniformis

Now, there’s one other thing here that I want to speak to, which is we see very good data for coagulans. Secondary to that may be subtilis. But what about clausii and licheniformis? Well, part of where the recommendation to you is Bacillus clausii and Bacillus licheniformis is likely because those appear to be the most common strains found in human stool. So what may have actually happened here is when trying to find the best probiotic of the soil-based family, looking at stool gave us a starting point and that fueled some studies and that seemed to have panned out. So I just want to make people aware of that that B. clausii and B. licheniformis are the most commonly found strains in stool. So just an interesting observation there.

Probiotics Containing Prebiotics

Now, the question also comes up—and I’ll put a table in here from a study that was a review paper on soil-based probiotics. The question comes up, what about using a probiotic that contains, let’s say, a prebiotic, some Lactobacillus, some Bifidobacterium, some Saccharomyces boulardii, and something like B. coagulans or one of our soil-based probiotics? What about getting an all-in-one? And I’m certainly open to that. However, it’s not something that I do. And the reason for this is because I’m always trying to minimize the level of reactivity to anything that I’m using, okay? So the more you combine into one formula the higher the likelihood that someone will react negatively to something in that formula and then therefore not be able to use it.

So what I like to do is break these formulas apart as I recommended it in the book and you’ll see this reflected in the products that I recommended in the online store into different categories, so that someone can try these different categories and find their benefit or even reaction to each one.

Sometimes people react negatively to a Lactobacillus-Bifidobacterium probiotic. Sometimes people react negatively to a Saccharomyces boulardii probiotic. So if we bundle these all into one formula, we increase the chance of having a reaction to one of the categories or one of the class types and therefore having to throw out the entire formulation. So it’s not to say the combination formulas are bad, right? It’s just I prefer not to start there so as to minimize the amount of troubleshooting and minimize the difficulty in identifying where a potential reaction is coming from.

Prescript Assist

And then coming to Prescript-Assist specifically, there was only one controlled trial that showed benefit with the former formula of Prescript-Assist (50 and 51).

And when I look into this more deeply, I was a little bit perplexed why Prescript-Assist had such a lofty, I guess, stereotypical recommendation of it being the best soil-based probiotic. And I have no quarrel with the former formula of Prescript-Assist. I use it in the clinic. I use it myself. This is not a dig. But it was interesting when doing this comparative analysis of the different studies on different types of probiotics.

You clearly see that there’s not a ton of benefit for…Or I’m sorry. I shouldn’t say a ton of benefit. There’s only really one good study showing benefit from the formula of Prescript-Assist. So some of these may have been where the theory was far ahead of what the actual science showed. It doesn’t mean that if we had additional comparative trials with the old Prescript-Assist formula and some of these other formulas that I think are better recommendations that Prescript-Assist wouldn’t outperform those. But it’s just interesting to see that, I guess, if there’s enough fanfare around one product, you can have the opinion at large recommending a given probiotic even though it’s not what’s really truest to the science.

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And in this case, we’re talking good science. We’re talking randomized clinical trials in human showing benefit in conditions and in symptoms, which is very, very high quality. So it was just interesting to kind of see that. And it’s another reason why I really reserve my opinion until I’ve had a chance to fact-check. Because oftentimes, unfortunately—and I really do think it’s fair to say oftentimes—the popular opinion in that, which is actually true based upon the best clinical literature that we have, are disparate from one another.

So, there’s couple other thoughts here regarding probiotics or soil-based probiotics, specifically. The classification of soil-based probiotics fall into the phylum of Firmicutes and then we go all the way down to the genus Bacillus. And regarding the dosing, again, we reviewed a number of clinical trials looking at the dosing and the dosing comes out at about two to eight billion per day. So that’s your rundown on soil-based probiotics. Hopefully, that all makes sense.

Episode Wrap Up

But, again, a few summary points and important takeaways. Soil-based probiotics are one of three to five major classes or categories of probiotics. Those categories are Lactobacillus-Bifidobacterium predominant formulas; that’s class or category one. Class or category two, Saccharomyces boulardii. Category three is your soil-based probiotics oftentimes including various Bacillus strains, Bacillus coagulans, Bacillus subtilis, Bacillus clausii, Bacillus licheniformis, and Enterococcus faecium. And then category four would be your E. coli Nissle 1917. And you could theoretically put the Enterococcus in the category five or to category three. Really what you see in the research literature is a suggestion of anywhere from a three to a five category classification system. But in any case, we have those different categories of probiotics. We reviewed the best strains, and the best evidence, and the best formulas for the soil-based class or category, specifically.

And we also discussed that there is a—I think there’s solid theory behind soil-based probiotics. These are probiotics that we come into contact to or at least we used to come into contact to on a daily basis. And we also talked about the dosage. And a few tips for using minimally bundled formulas, if you will, so that if someone has a reaction you can identify where that reaction is coming from.

So that’s the breakdown on soil-based probiotics. Again, the soil-based probiotic from Functional Medicine Formulations is what I recommend in the book and I use in the clinic. A comparable formula to that is the BioSpora from Klaire, MegaSpore, and Just Thrive Probiotics, and also Biocidin’s Proflora 4 are all fairly solid three to four-strain, soil-based probiotic formulas. I think any of those are reasonable in addition to the AOR Probiotic-3, which contains Enterococcus faecium, Clostridium butyricum, and Bacillus subtilis.

So there are definitely a few good options out there for soil-based probiotics. I wouldn’t overthink it. I would find a formula that resonates with you. I would use that. And if it works well for you, great. If not, I wouldn’t go crazy trying a bunch of different reiterations of the same class. You may just simply not do well with this class.

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If you don’t react well to it, that’s okay. That happens. I move on to the others. And if you’re still struggling and you want kind of the specific step-by-step guide of exactly what to do to improve your gut health, check out the book, Healthy Gut, Healthy You. It’ll walk you through all this and help you piece it all together in the bigger picture and greater context.

And that’s it, guys. I will talk to you next time. Hopefully, you found this helpful.

Research ➕



Clinical Studies with Bacillus Coagulans


Clinical Studies with Bacillus Subtilis


Clinical Studies with Bacillus Clausii


Clinical Studies with Bacillus Licheniformis


Clinical Studies with Enterococcus Faecium


Clinical Study with Megaspore


Soil-based Probiotic Benefits


Clinical Studies Showing No Benefits


Clinical Studies with Prescrip Assist ➕


I care about answering your questions and sharing my knowledge with you. Leave a comment or connect with me on social media asking any health question you may have and I just might incorporate it into our next listener questions podcast episode just for you!