The answer might surprise you…
Confused by the difference between soil-based and spore-based probiotics?
A lot of companies use these terms interchangeably, but they’re not the same.
Understanding the distinctions will help you make the best choices for your ongoing health.
Soil-Based Microbes Live in the Dirt
The ground is full of a huge, diverse population of microbes, particularly bacteria. Some live and reproduce there. Others just happen to be there temporarily.
True soil-based bacteria, whether they’re probiotic or pathogenic, need to be in dirt to survive and multiply. While they live, they take part in the ecosystem around them, each with a specific job such as:
- Breaking down dead matter
- Converting nitrogen into a form that plants can easily use
- Producing essential nutrients for plants
- Contributing to soil structure and stability
The main identifier here is that true soil-based probiotics live only in soil.
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Spore-Based Probiotics Go Beyond the Soil
Spore-based probiotic bacteria can be found in soil, but it’s not where they really live. Rather, their natural home is the gut microbiome. That’s where they thrive, colonize, and multiply.
Scientists previously thought spore probiotics were just another form of soil-based bacteria. But research shows the most important strains, the Bacillus genus, are naturally at home in animals’ and humans’ intestinal tracts.[1] The numbers found in the gut are much too high to be accidental, just tagging along with food.
That means these Bacillus spore probiotics belong in the gut microbiome, supporting wellness and healthy longevity.

How Spore Probiotics Used to Travel From the Soil to the Gut
Although spore-based probiotics have been classified as “soil organisms,” newer research shows they’re actually gut organisms that simply use soil as a vehicle to transfer from host to host, and they have been doing this for thousands—and based on some strong evidence—for even millions of years.
Back in the day, humans and animals would naturally consume these spores through food grown in soil. Once inside the gut, the spores “wake up.” They shed their protective outer shell and become active, living bacteria.
These spore probiotics are what scientists call commensal (they benefit us without harming us) and transient (they don’t stay in the gut permanently). After they arrive in the gut, they spend 3 to 4 weeks traveling through the digestive tract, clearing out harmful bacteria and helping to rebalance the gut microbiome. Then, just before exiting the body, they re-form their protective shell and (in nature) return to the soil, continuing the cycle.
Unfortunately, most people today no longer eat freshly foraged foods, and modern farming has stripped the soil of these beneficial microbes. That’s why it’s nearly impossible to get spore probiotics naturally anymore — unless you supplement.
The Spore Advantage
When a probiotic bacteria is spore-based, that means it has the ability to protect itself from harsh conditions by creating and retreating into an endospore shell. This lets the probiotic survive whatever gets thrown at it: extreme heat, extreme cold, salt, high or low pressure, even acid. When the danger disappears, the spore shell is shed, and the probiotic bacteria springs back to life.
This tactical advantage makes spore probiotics more resilient than their counterparts. Especially when it comes to digestion.[2]
The digestive process is full of deadly hazards for most bacteria. It’s specifically designed that way to help avoid pathogenic infections. Probiotic bacteria must survive body heat, the body’s pH level, digestive enzymes, and stomach acid to make it to the gut microbiome.[3] And only spore probiotics with their protective armor have the distinct advantage that gets them there.[4]
Once they arrive in the gut, the spore shells are shed and the probiotics activate. After all, that environment is their preferred home. They reawaken and begin to create a safe space for themselves and other probiotic bacteria. Then they go to work providing dozens of health benefits that let them claim probiotic status.

The Unmatched Health Benefits of Spore-Based Probiotics
Unlike other probiotics, spore probiotics arrive in the gut microbiome (home to trillions of bacteria) 100% alive and ready to work. They establish colonies and encourage diverse populations of other beneficial probiotic species to do the same. A 2021 study showed that over a 3 week period, spore probiotics increased bacterial diversity as well as keystone species including Akkermansia muciniphila and Bifidobacteria spp.[5]
And if creating a healthy, well-balanced microbiome was all they did, spore probiotics would be the go-to for gut health. But spore probiotics offer so much more.
They’re so effective that spore probiotics have been used as medicine for decades around the world. For example, Bacillus clausii has been prescribed in Italy since 1958 to treat intestinal disorders.[6]
Four highly studied, proven, effective spore probiotics tend to dominate the research… and for good reason. Both individually and in combination, these four Bacillus species deliver distinct health benefits: Bacillus subtilis, Bacillus indicus, Bacillus coagulans, and Bacillus clausii.
- One study found that two specific strains, Bacillus subtilis HU58™ and Bacillus coagulans SC-208, helped address antibiotic-induced dysbiosis. The pair also supported a healthy inflammatory response and protected the mucosal gut barrier.[7]
- Bacillus indicus HU36™ produces at least 15 distinct carotenoid antioxidants including lycopene, lutein, beta-carotene, and astaxanthin.[8] Because Bacillus indicus HU36™ produces these powerful antioxidants right in the gut where they can be directly absorbed, they’re more stable and effective than food-based options.[9]
- Bacillus clausii, particularly a strain known as SC-109, has been widely used to improve many aspects of gut health including supporting optimal gut barrier function, producing vitamins, promoting health inflammatory responses, and inhibiting pathogens in the gut.[10]
- A combination of B. subtilis HU58™, B. indicus HU36™, B. coagulans SC-208, and B. clausii SC-109 was shown to help people manage triglyceride levels, a critical component of cardiovascular and metabolic health.[11]
- Another clinical trial testing the same four-spore combination found that these probiotics helped reduce signs of leaky gut syndrome.[12]
This is just a sampling of how these spore probiotics can deliver substantial health benefits. It highlights their superior ability to support a well-balanced gut microbiome. Something that most other probiotics (soil-based or otherwise) can’t do.
How can you be sure you’re getting spore-based probiotics? Just check the supplement facts for the word "Bacillus" (and specifically you’ll want to look out for the specific strains mentioned above).
Get the Spore-Based Probiotic Advantage with Just Thrive
Spore-based probiotics have a distinct edge over all other forms of probiotics. Their protective spore shell allows them to always arrive in your gut microbiome where they promote bacterial balance and diversity and total body wellness.
Just Thrive Probiotic & Antioxidant contains four clinically studied spore probiotics:
- Bacillus indicus HU36™
- Bacillus subtilis HU58™
- Bacillus coagulans (SC-208)
- Bacillus clausii (SC-109)
>> Take your gut health to the next level today with Just Thrive Probiotic.
Just Thrive Probiotic is available in two convenient forms: classic capsules and tasty fruit-flavored gummies. Both forms contain the same four clinically-proven strains. And you’ll enjoy the same effectiveness no matter which you choose.
But if you’re not quite sure about trying Just Thrive Probiotic, we can help with that.
EVERY Just Thrive purchase is covered by our Bottom of the Bottle, 100% money back guarantee.
That means you can try it to see how well it works for you… and we’re betting that you’ll notice a positive difference.
But if for any reason you don’t feel a difference, you can ask for a full product refund at any time. Even if it’s 3 months or 3 years later. Even if the bottle is empty!
Sources
- Hong HA, et al. Defining the natural habitat of Bacillus spore-formers. Research in Microbiology
Volume 160, Issue 6, July–August 2009, Pages 375-379 - Elshaghabee FMF, Rokana N, Gulhane RD, Sharma C, Panwar H. Bacillus As Potential Probiotics: Status, Concerns, and Future Perspectives. Front Microbiol. 2017 Aug 10;8:1490.
- Yossef S, Clark F, Bubeck SS, Abernethy J, Bayne T, Krishnan K, Young A. An Oral Formulation of the Probiotic, Bacillus subtilis HU58, Was Safe and Well Tolerated in a Pilot Study of Patients with Hepatic Encephalopathy. Evid Based Complement Alternat Med. 2020 Jun 30;2020:1463108.
- Payne J, Bellmer D, Jadeja R, Muriana P. The Potential of Bacillus Species as Probiotics in the Food Industry: A Review. Foods. 2024 Aug 2;13(15):2444.
- Marzorati M, Van den Abbeele P, Bubeck S, Bayne T, Krishnan K, Young A. Treatment with a spore-based probiotic containing five strains of Bacillus induced changes in the metabolic activity and community composition of the gut microbiota in a SHIME® model of the human gastrointestinal system. Food Res Int. 2021 Nov;149:110676.
- Cutting S. Bacillus Probiotics. Food Microbiology. Volume 28, Issue 2, April 2011, Pages 214-220.
- Marzorati M, Abbeele PVD, Bubeck SS, Bayne T, Krishnan K, Young A, Mehta D, DeSouza A. Bacillus subtilis HU58 and Bacillus coagulans SC208 Probiotics Reduced the Effects of Antibiotic-Induced Gut Microbiome Dysbiosis in An M-SHIME® Model. Microorganisms. 2020 Jul 11;8(7):1028.
- Sy C, Dangles O, Borel P, Caris-Veyrat C. Interactions between Carotenoids from Marine Bacteria and Other Micronutrients: Impact on Stability and Antioxidant Activity. Mar Drugs. 2015 Nov 19;13(11):7020-39.
- Sy C, Dangles O, Borel P, Caris-Veyrat C. Stability of bacterial carotenoids in the presence of iron in a model of the gastric compartment - comparison with dietary reference carotenoids. Arch Biochem Biophys. 2015 Apr 15;572:89-100.
- Ghelardi E, Abreu Y Abreu AT, Marzet CB, Álvarez Calatayud G, Perez M 3rd, Moschione Castro AP. Current Progress and Future Perspectives on the Use of Bacillus clausii. Microorganisms. 2022 Jun 17;10(6):1246.
- Campbell AW, Sinatra D, Zhang Z, Sinatra ST. Efficacy of Spore Forming Bacilli Supplementation in Patients with Mild to Moderate Elevation of Triglycerides: A 12 week, Randomized, Double-Blind, Placebo Controlled Trial. Integr Med (Encinitas). 2020 Apr;19(2):22-27. PMID: 33041703; PMCID: PMC7482325.
- McFarlin BK, Henning AL, Bowman EM, Gary MA, Carbajal KM. Oral spore-based probiotic supplementation was associated with reduced incidence of post-prandial dietary endotoxin, triglycerides, and disease risk biomarkers. World J Gastrointest Pathophysiol. 2017 Aug 15;8(3):117-126.