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Soil Based Probiotic Dangers: Overgrowth, Dysbiosis and Disease! Oh My!

What are soil based probiotics (A.K.A. sbo probiotics)? Is a soil based probiotic right for you? I have my concerns

“The human body houses somewhere in the neighborhood of one hundred trillion bacteria—about 3.5 pounds worth.”

But don’t think of that fact as a reason to lose weight – rather turn on the porch light and lay out the guest towels. Those bacteria, including 400-500 different species in the gut alone, are responsible for your health as much or more than food.

Bacteria in your body outnumber your own cells ten to one. Some of these bacteria are friendly, but research is still pending on soil based probiotic dangers.

RELATED: Pathogen Cleanse Fast + What Probiotics are Best


What Actually Are Probiotics?

This term is thrown around a lot, but what IS a probiotic? How does it work in the body and why is it there? Our gut is a complex arena of bacteria, yeast, and other organisms… most of which have a mind of their own. They all live and work together, sometimes not so peacefully.

In simple terms, probiotics are live bacteria and yeasts which benefit the body. The problem is, which bacteria are helpful and which ones are harmful? Research is still developing on probiotic supplements, and all signs point toward bio-individuality on this one. As in, it depends on the person and their specific health concerns.

So what are soil based probiotics? Before cover that you should know…. 

RELATED: Seed Synbiotic Probiotic Review

Where Does Our Gut Flora Come From?

It’s widely believed that, at birth, babies’ guts are sterile of all bacteria. Beginning at birth and continuing through the first two years of life, the tiny human being becomes residence for various bacteria, beneficial or detrimental, depending on the environment provided in the gut and what the baby comes into contact with (source).

Think it’s a good idea to let baby have sugar before age two?

My first two babies didn’t have desserts until after age one, and as I got smarter, John and Gabe didn’t have any refined sugar until age two! Sugars and refined flours are food for pathogens, dangerous bacteria. If you feed them, they will come.

My oldest son clearly has bacterial issues and has needed antibiotics numerous times. He had antibiotics at birth, had sugar and flour in things like Cheerios well before age one, and has certainly had his fair share of white flour in his lifetime. Le sigh. I doubt it’s a coincidence, and we continue to work on building his gut health with probiotics and other measures.

Are Probiotic Supplements Helpful? From an MD

View my entire interview with Dr. Lauren Jefferis here.

The Danger Lurking Below

Some of the microorganisms in our guts aren’t so friendly, like pathogenic bacteria, certain yeasts and overgrowths, and parasites. Certain strains of bacteria and yeast found naturally in our body, like e. coli and candida, only become a problem when their balance is disrupted. It’s like Invasion of the Body Snatchers, but in your gut.

“Pathogens have found really clever ways of taking over the normal processes of our cells. Often they know more about our own cells than we do…” –Source
The dangers of soil based probiotics

What are Soil Based Probiotics?

There are over 100 different species of soil based probiotics we know of and many form spores. These spores have a hard coating on them which helps them survive the trip through stomach acid down to the gut better than other probiotics. (source).

Soil based probiotics (or soil based organisms) are different than the strains found in dairy and most fermented foods. SBOs occur naturally in the soil and used to be a big part of our diets before factory farms and large chain grocery stores.

The History of Soil Based Probiotics

When food processing got between farmers and eaters, the food chain was interrupted, and SBO consumption plummeted. Our clean-to-the-point-of-sterile society reduced our interaction and further removed SBOs from the gut.

Baby + Dirt = Good

I always wondered aloud while watching my babies put everything in their mouths how that could possibly be a good thing. Maybe the good Lord made a little “oops” on that one.

Now, I understand.

kids playing in the dirt

Human babies are made to crawl in the dirt and get intimate with soil-based organisms. Putting everything in the world in their mouths is a unique form of inoculation, brilliant in its simplicity. Those babies are hard at work populating their guts with healthy bacteria, and who knew?

Like RN Jena Halman-Kincaid taught us, our immune system is strengthened by exposure to a little dirt. That’s part of the theory behind SBOs and one of a few reasons my husband and I took a few different brands of soil based probiotics years ago.

They were supposed to be helpful for Crohn’s Disease, which my husband had…and then I was told by a naturopath that they might actually turn against us! I immediately switched brands and types of probiotic, and now I’m digging in (pun intended) to the dirty research.

Soil Based Probiotic Dangers

While SBOs have been around for a while, the issue isn’t black and white. Some experts are gung-ho on soil based probiotics because they say it can help re-seed gut microbes. On the other hand, other experts warn of soil based probiotic dangers.

The idea is if a person does not have enough of their own healthy gut flora to compete with the SBO spores, it opens the door for them to become pathogenic (source), (source).

You read that right.

Supplements you take to improve your health and gut could turn against you and become harmful bacteria themselves.

Isn’t that lovely?

Who Should Use Soil Based Organisms?

Before you freak out and run to wash all the vegetables in your fridge again, there are actually some benefits to soil based probiotics.

Many people, most notably Jordan Rubin of The Maker’s Diet and Ancient Nutrition supplements, credit soil-based organisms (SBOs) for their miraculous recovery. In Rubin’s case, he saw nearly 70 specialists globally for his severe Crohn’s Disease and related complications. Rubin says SBO probiotics finally brought him back from the brink of death (quite literally).


There are several well-tested soil based probiotic strains that are beneficial in human trials. This doesn’t mean everyone everywhere should take them though.

Do Soil Based Probiotics Stay in our Gut?

There’s been some debate about how probiotics work in the body. Do they stay and start a homestead or are they passing travelers that do their job then make their way to the exit? The research is still pending on this one.

Scientists with the human microbiome project are still mapping out which microbes have set up house in our guts. What they’ve found so far is like our outsides, our insides are just as unique.

“Every human being appears to carry their own, largely individual, suite of microbial strains which are acquired early in life.” –Source

We all have different gut microbes and which ones depend on where we’re born, how we’re born (c-section, antibiotics early in life, etc.), and the earliest years. These are also a few reasons why some babies need a probiotic. Think back to babies putting everything in their mouths, including dirt and rocks.

What does all that have to do with taking probiotics? Because we’re all different, certain probiotics strains stick around and start a family in some people, but the same exact strain won’t in others.

On that same note, certain probiotic strains, including soil based probiotics, can help one person, but hurt another. Those with compromised immune systems like leaky gut could get infections from SBO spores taking over their gut.

RELATED: High Quality Fish Oil

woman with heart over belly

Can’t Live With ‘em, Can’t Live Without ‘em (Sigh)

“A deficiency of medicinal ‘superbugs’ – known as Soil Based Organisms (SBO) – from our soil and food chain may be responsible for intestinal illnesses and diseases such as irritable bowel syndrome (IBS), Crohn’s disease, colitis, candidiasis, and colon cancer.” source

Because we’re already deficient in soil based organisms, some people can’t handle them when they come, which causes gut dysbiosis and disease.

As one anecdote, Dr. Kathryn Doran-Fisher, a local naturopath, has clients who took a turn for the worse after they started SBO supplements. These same clients improved once they used non-SBO refrigerated strains.

Since our sanitized society is deficient in soil-based organisms, we get sick. Because we’re sick and out of balance, some can’t handle taking SBOs that could help and instead get sicker. #irony

It’s that kind of info that I found after that visit with a naturopath that caused me to ditch the soil based probiotics, even though the research is clear that it’s traditional to be inoculated by soil.

The Dangers of Soil Based Probiotics

The FDA doesn’t really regulate supplements, just their claims, which can be a good and bad thing. Soil based probiotics strains don’t have to be tested and shown to be helpful or safe before they’re sold. Certain SBO strains on the market haven’t been tested at all so we have no idea if they’re harmful or not.

Some dangers of soil based probiotics lie in the fact that many formulas don’t list the exact strain used, so you’re not sure what you’re getting, plus some strains help certain diseases while hurting others, so you almost need to be strain-specific to your exact physiology (source). (Yep, bio-individuality again!)

soil based probiotic, SBO probiotic pills

Here’s a breakdown of some common SBO strains, the soil based probiotic dangers, and who shouldn’t use them.

Soil Based Probiotic Dangers by Strain

Bacillus indicus

There’s only one human study so far that includes this SBO, however, the study was a combination of 5 different strains. We don’t know how this one performs on its own and there’s almost no information to show if it’s safe or effective.

There have been a few animal studies on B. indicus, including this one that concluded it should be safe to supplement with. The researchers did have some concerns that B. indicus was resistant to certain antibiotics.

However, the bottom line is that we don’t really know how this strain affects the complex human microbiome and any potential side effects and dangers.

Bacillus licheniformis

This soil based probiotic species has more research behind it, but it’s not very reassuring.

Some researchers say it becomes an invading pathogen in the gut and can cause infection for those with poor immune systems. Other scientists say not to worry because it probably won’t hurt you unless your immune system isn’t stellar (source).

News flash: If we have poor gut health and take probiotics to try and fix the problem, then we probably don’t have a stellar immune system. The EPA reports they’re not sure if this SBO is to blame for harmful infections or not.

You can naturally find B. lichenformis in Korean fermented foods so some get it through diet. However, probiotic strains found in these same foods are known to help worms live longer (can you say parasite party??).

gut microbes

Enterococcus faecium

This probiotic naturally lives in our gut, helps break down carbs and is in some fermented foods. That alone doesn’t mean it’s safe to supplement with though!

E. faecium can be pathogenic and cause serious diseases, like meningitis in babies and infections in the heart lining. It’s quickly becoming antibiotic resistant and forms biofilms in the body that are hard to get rid of. About 90% of medical device infections are thought to be caused by this soil based probiotic! (source)

RELATED: The truth about antibacterial resistance and how it works from a biologist and my own experiment to prove that antibacterial soap isn’t better.

There’s not a lot of clear studies on this soil based probiotic showing its benefits. There are human trials, however there aren’t many that compare a group taking E. faecium to a placebo group, or the probiotic is given along with other supplements. It’s hard to tell if the benefits are coming from the supplements, the probiotic, or a combination (source, source, source).

To make matters even more confusing, a different strain, S. faecium, was renamed E. faecium and some are getting E. faeciulis confused with E. faecium. The research waters are murky and lacking on this one.

Clostridium butyricum

Naturally found in the GI tract, studies show promise with this soil based probiotic. There’s a catch though. The specific strains with the most safety info aren’t available in the US.

Lucy from Nextgen medicine does recommend BIO-THREE, which includes C. butyricum. Finding a safe strain outside of that supplement may prove difficult.

Some of the studies for this strain showed definite health benefits for certain conditions, however other research wasn’t as clear. In this study and this one, researchers looked at C. butyricum’s ability to reduce complications for patient’s with ulcerative colitis. Unfortunately, the study groups were very small and the results weren’t statistically significant.

The Bottom Line on Soil Based Probiotics

  • Soil based probiotics survive the trip through the stomach and make it to the intestines, so they may be more effective than other probiotic strains.
  • Humans used to be exposed to soil bacteria regularly, but we live in a sanitized culture and are disconnected from the dirt now.
  • That means that sometimes, the human gut isn’t ready for soil based probiotics, and they feel worse after taking them because the bacteria become pathogenic in their gut.
  • Some credit SBOs for healing Crohn’s Disease, however — so bio-individuality is key here!
  • Various strains of soil based organisms have been tested against certain health issues, but other strains are not well-tested at all.

There are some benefits to soil based organisms and some people swear by them. It all boils down to choosing the right one. Working with a trained practitioner will be your best bet — someone who can check the research for your particular issue and determine the best strain(s) for your health.

This complete guide to soil-based probiotics from Lucy Mailing, PhD student, is an incredible feat after over 50 hours digging through research. Any questions you don’t have answered here, that’s where you go!

What kind of probiotic do you take? Have you tried a SBO probiotic? Do you notice a difference if you stop taking it?

If you’re looking for a probiotic, here are my personal recommendations after trying many, many brands and types over the years!

Some Quality Probiotics

Some of these I’ve used, some I’m planning to use, and some have been recommended by friends and professionals alike. It’s good to remember a few things about probiotics: 1. People should get different colonies of probiotics, so switching brands/strains every so often (6 weeks?) is good practice. 2. What works great for one person’s needs doesn’t always work for another.  I’ve personally tried:
  • Just Thrive Probiotics – this one can be taken during antibiotics and not be rendered ineffective, which almost all other probiotics are! It’s the top-recommended probiotic overall by Paleo Mom Sarah Ballantyne. 😮 (Be sure to use the code Katie15 for 15% off; also found on Amazon and from Perfect Supplements where you can use the coupon KS10 for 10% off!)
  • Seed Daily Synbiotic – the new player in the field but recommended by superstars like Chris Kresser for its unique probiotic/prebiotic synergy. Here’s my full review including a number of surprises for my thinking and a 15% off code!
  • Note: If you’re struggling with digestion, especially constipation, or you feel like you really need to populate your gut with healthy probiotics, I would recommend Saccharomyces Boulardii in addition to any other you choose (except any above which include this strain). Saccharomyces Boulardii is research-proven to get through the digestive tract without being killed, which is rare. 
  • Balance One probiotics with a unique time-release formula (use the code KITCHENS15 at either Balance One’s site or even Amazon to save 15% either place! Wow! Use the code at checkout on Amazon btw.)

For Little Ones (we use all of these):

  • Mary Ruth’s liquid probiotic is a liquid probiotic that doesn’t need to be refrigerated and tastes like…nothing! It’s my new favorite for administering to kids! (Use code KCRF15 for 15% off!)
  • WellBelly by WellFuture (9 strains of probiotics in apple and banana carrier – it’s a powder)
  • Buddies in my Belly probiotic powder (2 strains of probiotics + potato starch carrier and prebiotics) or chewable tablets
Recommended by experts I trust:

Unless otherwise credited, photos are owned by the author or used with a license from Canva or Deposit Photos.
Category: Natural Health

14 thoughts on “Soil Based Probiotic Dangers: Overgrowth, Dysbiosis and Disease! Oh My!”

  1. My research found the opposite of yours: s. boulardii is more known for helping with diarrhea and to cause constipation in some, than it is to help with motility. You don’t use the word ‘motility’ but I think I got the impression that you believe constipation is what it primarily helps. B. coagulans on the other hand is good for increasing motility in sluggish intestines by my research and even experience but I’ve just begun to try it…. and is more known for that than helping with diarrhea but it has helped with both. I wouldn’t take s. boulardii simply because of its reputation as useful for diarrhea and the reputation it has also for causing constipation.

    I won’t be reading followup comments if any. These are just thoughts to clarify s. boulardii from another person’s perspective and to make a suggestion for those who do want something to help with slow motility, a sense of retention. These would include older people; b. coagulans is research proven to assist in the areas many people find it impossible to resolve that I mention. It used to be known as lactobacilllus sporogenes and also has the trade name Lactospore.

    The only question for older people in relying on sbo that personally is influential is the fact that bifidobacteria decline rapidly with the age of the person and need to be there for normal gut function. They also affect mood, at least some of them do and probably all to some degree. SBO’s help with increasing bifidobceria that may already be there – b. coagulans does this I believe…. but can’t guarantee it does but I know some strains do and b. coagulans is the only strain I’ve been researching intently.

    Other thoughts on SBO for me center around amount. Through experience I see I can go higher than the 1 or 2 billion CFU usually mentioned….. these low amounts are the result of FDA GRAS petitions in my opinion anyway…. once a bacillus is approved as GRAS at a certain very very low but reflected in research level, most product manufacturers will want to err on the side of safety – as will web sites like Healthline, RXList, etc….. because they do not want to be liable or responsible for trouble in my opinion. Some SBO products and reputable makers do have the courage to suggest much higher amounts of for example b. coagulans – 100 Billion CFU or more. This sounds astonishing…. but is not necessarily so. One has to find a way to verify using lower amounts, much lower amounts. I find 6 billion CFU once a day, at night, of b. coagulans really does help with motility. And, adding anoth6r 6 billion or two has not caused harm. B. coagulans is incapable of colonizing the ‘gut.’ That is according to an article in sciencedirect, which is part of publisher Elsevier (very respected) about the life cycle of b. coagulans.

    B. coagulans is a champ. S. boulardii is….. worth caution and is not a ‘jack of all trades.’

  2. Hi. I stared up asking a liquid soil based spore probiotic and developed thrush in my oesophagus, is this a common problem?

    1. Carolyn @ Kitchen Stewardship

      I’ve never heard of that happening! I have seen probiotics recommended for help treating thrush often though. Are you sure it’s connected? I hope you’re able to treat it quickly and I would definitely be cautious trying any probiotics in the future.

    2. I don’t get your question ? You started taking probiotic and had thrush in your eosophogus ? How did you even know you had thrush in your eosophogus?

      Did you get an endoscopy done.

      But I have the same thing , feel like my eosophogus is on fire . Do you feel the same ? I also took a liquid probiotic

  3. Hi,

    I noticed you recommend Mary Ruth’s soil based probiotic. Is this different from other SBOs? I’m asking because my 5 year old son is seeing a new nutritionist who really wants him to take a soil based probiotic, but after reading this, I’m scared ? My poor little guy is already taking his new diet hard and I don’t want to give him anything that will make him worse off.


    1. Carolyn @ Kitchen Stewardship

      Hi Heidi, I just checked on Mary Ruth’s website and it looks like they’re reformulated and are no longer a soil-based probiotic. I’ll have to update that information! I’m sorry your son is struggling, specific diets with little kids are tough!

  4. I take Garden of Life Primal Defense and I go to the bathroom great 3 pills everyday on empty stomach. I highly recommend I buy them at Vitamin Shoppe

  5. Hi there, I used to have chronic diarrhea so I took a probiotic with strains of

    Bacillus Clausii and bacillus subtillus .

    I am however experiencing severe acid reflux after using these probiotics. Could you please help in regards to stopping my reflux

    1. Carolyn @ Kitchen Stewardship

      Hi Breen, I would suggest trying a different probiotic. I’ve heard of that happening to people where they just react negatively to certain strains. Some people just don’t do well with a probiotic supplement at all. If you don’t want to buy multiple types to try out or can’t seem to find one that you can handle perhaps incorporating more fermented food into your diet would be the most beneficial. I hope you’re able to find one that works for you!

  6. Hi there,

    thank you for the informative read. I think I have SIBO/& candida after 1 year of high dose PPIs. I have tried several probiotics (s.boulardii, bascillus coagulans,high CFU broad spectrum probiotics -nutralife brand) and all seem to make my digestive symptoms worse. Diarrhea/reflux/nausea – like a war is going on in my gut

    Could I be taking too many too soon? or making the SIBO worse? I feel better taking anti-microbials but I don’t know how long to take those for, or whether to turn to prebiotics. Please let me know your thoughts

    1. Rachel,
      I wish I had a functional medicine degree! I know I’ve heard people say, “Start slowly,” with probiotics, so it definitely could be too much/too fast. SIBO is a very special case you’ll want to research specifically — what strains are helpful for that condition?

      I think you’d do so well having some functional testing done, because you can spend a LOT of money (and time) on supplements for the wrong thing if you don’t know for sure what’s going on, you know? I thought functional testing was fascinating and I learned SO much about my health and can finally start approaching it intelligently because I know what’s actually there.

      SteadyMD has a functional doc, Lauren Jefferis, whom I would go to in a sec if I wasn’t already working with someone.

      I hope that helps!!
      🙂 Katie

    2. For SIBO, look up Dr. Zach Bush and try his version “Restore” avail on Amazon. He’s triple board certified and was one of the first folks to heal patients with SBOs that weren’t responding to improved diet and dairy probiotics.

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