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The Science Behind Bacillus Spore-Based Probiotics

Most of us are at least peripherally aware of the benefits of probiotics. But the probiotic puzzle can be a little tricky to piece together with so much conflicting information and every brand and probiotic strain claiming to be the “best”. But as they say, the proof is in the pudding, and there’s a specific subset of probiotics that have the scientific proof to back up their claims of being the “best”. 

What is this subset of probiotics? A unique group of probiotics known as spore-based probiotics. And more specifically a class of spore-based probiotics that fall under the species bacillus.

In this post, we’re going to explore exactly what bacillus spore-based probiotics are, the science behind their remarkable health-promoting effects, and how you can reap the benefits of these powerful probiotics.

What are Spore-Based Probiotics?

Probiotics is an umbrella term that encompasses a wide range of microbes that are considered beneficial to health. Spore-based probiotics are a subset of probiotics that got their name thanks to their ability to envelope themselves in a protective outer layer known as an endospore. This protective outer layer is designed to protect the bacteria – shielding it from potential harm from the external environment.

You see, spore-based probiotics are also referred to as soil-based probiotics because they are naturally found in soil – making it especially important for them to have protective mechanisms to shield them from the harsh outdoor environment. These unique strains of bacteria have evolved alongside us, making their way into our digestive tract alongside the food we eat since the beginning of time.

Some of the most common (and most potent) strains of spore-based probiotics fall under a class of bacteria known as bacillus and include:1,2

  • Bacillus subtilis HU58
  • Bacillus clausii SC-109
  • Bacillus coagulans SC-208
  • Bacillus indicus HU36
  • Bacillus licheniformis SL-307

Bacillus spores’ ability to encase themselves in their protective endospore makes them especially capable of surviving the perilous journey through our digestive tract – allowing them to arrive unharmed into our intestines. From there, these mighty microbes set up camp and begin colonizing. Once they settle in and get comfy in our gut, that’s when the real magic of spore based-probiotics really kicks in.

Spore-Based Probiotics Research

While “probiotics” have become quite the buzzword in the health world, the truth is, many probiotics available on the market simply aren’t effective. Many strains can’t survive the harsh gastric juices and the treacherous journey it takes to get to the intestines. And others still can actually exacerbate digestive problems, contributing to bacterial overgrowth and imbalance.

But researchers are finding time and time again that spore-based probiotics can actually back up their health-promoting claims. Just a handful of conditions spore-based probiotics have been scientifically proven to help with include:

  • Improving gut microbiome diversity
  • Healing leaky gut syndrome and reversing symptoms of digestive conditions (like IBS, SIBO, and inflammatory bowel disorders)
  • Increasing nutrient absorption and production of digestive enzymes
  • Enhancing immune system function
  • Improving cardiac and metabolic health
  • Protecting against cognitive decline and neurodegenerative diseases

Because your gut health dictates so much of our overall health, these benefits are just scratching the surface. But let’s dive into a few of these a little deeper.

Importance of Microbiome Diversity

One of the most profound impacts of spore-based probiotics is their ability to transform the gut microbiome. You see each unique strain of microbe that resides in your gut excels at certain tasks. So having a diverse assortment of beneficial microbes means your entire gut ecosystem is able to function properly – with each strain of probiotic able to focus on doing their job and doing it well.

Having a diverse microbiome is one of the most important indicators of overall gut health. And spore-based probiotics are particularly adept at increasing microbiome diversity thanks to their ability to:3,4,5

  • Populate the gut: Once spore-based probiotics make their way to your intestines, they ditch their protective endospore and set up camp – replicating and colonizing your gut.
  • Shift the PH of your gut: As these spore-based probiotics replicate and crowd out unwanted strains of bacteria, the entire PH (or how acidic your gut is) begins to shift and create a safer, more welcoming environment for other strains of beneficial probiotics.
  • Boost SCFA production: SCFA stands for short-chain fatty acids. SCFAs are the favorite food source of the cells that line your intestine. More SCFAs equates to a happier, healthier, and stronger gut barrier – which in turn translates to a more supportive environment for a diverse and thriving microbiome.

This ability to supercharge your gut health and enhance the diversity of your microbiome is what makes spore-based probiotics especially adept at addressing a host of gut disorders. Bacillus spore-based probiotics have been scientifically proven to effectively treat digestive disorders such as:6,7,8,9

  • Irritable bowel syndrome (IBS)
  • Small intestinal bacterial overgrowth (SIBO)
  • Inflammatory bowel conditions like ulcerative colitis
  • Leaky gut syndrome

But spore-based probiotics’ impressive health-boosting effects extend much further than your gut.

Natural Antimicrobial Agents Produced by Microorganisms

Certain strains of spore-forming probiotics are able to produce natural antimicrobial agents. For example, the probiotic strain Bacillus subtilis has been found to produce an antimicrobial compound known as levan.10

Levan is a polymer compound produced by plants as a way to protect themselves and in humans, is a powerful antiviral agent and immune system booster. Levan has been used in the pharmaceutical industry as a potent:11

  • Antidiabetic
  • Anti-inflammatory
  • Antitumor
  • Antioxidant 
  • Anticarcinogenic

While we still have more to learn about spore-based probiotics’ remarkable antimicrobial capabilities, this discovery of naturally-occurring antimicrobials could have valuable and far-reaching implications in the health industry. But the ability to produce antimicrobial compounds isn’t the only way spore-based probiotics can boost your immunity.

The Gut-Immune System Connection

The gut-immune connection is an intricately linked system. If your gut health is out of whack, you can all but guarantee your immune system is out of whack too. Just a handful of the ways gut health and immune system health are linked include:12,13

  • Housing immune tissue and cells: Approximately 70-80 percent of your immune cells can be found in special immune-gut tissues known as gut-associated lymphoid tissue.
  • Creating a barrier and trapping bacteria: The lining of your intestines forms a tight barrier that’s loaded with a protective layer of compounds known as mucins and glycoproteins that trap harmful microbes so they can be neutralized and eliminated.
  • Triggering the immune response: If any invaders make it past your intestinal barrier, the immune cells that line your gut are able to directly communicate with your microbiome via your gut-immune axis. If there’s an imbalance or invasion, your gut can immediately sound the alarm – signaling your immune system to launch an attack to neutralize the invaders.
  • Crowding out harmful bacteria and producing crucial metabolic compounds: A rich and diverse population of beneficial probiotics crowds out potentially harmful microbes. And as an added bonus, these friendly probiotics produce a plethora of metabolic by-products (like short-chain fatty acids and vitamins) that help keep your immune system firing on all cylinders.

By supporting and promoting a thriving and diverse microbiome, you naturally enhance your own immune system and natural defense mechanisms. This ability to mitigate inflammation and heal the gut also makes bacillus spore-based probiotics a powerful weapon against another serious health condition –cognitive decline.

Bacillus Spore-Based Probiotics and Cognitive Function

Leaky gut syndrome occurs when the lining of your gut develops gaps that allow harmful substances to “leak” into your bloodstream. This can create a condition known as metabolic endotoxemia in which harmful compounds known as endotoxins from your gut leach into your tissues and begin wreaking havoc. 

Studies have found that leaky gut syndrome and subsequent metabolic endotoxemia can directly lead to significant damage to the nervous system and brain. Exposure to these harmful endotoxins can lead to a host of neurodegenerative and cognitive disorders ranging from dementia to autoimmunity.14,15

But research has also found that supplementing with spore-based probiotics can completely reverse leaky gut syndrome and restore gut health – potentially halting cognitive decline and even reversing neurological damage in some cases. To learn more about how bacillus spore-based probiotics can heal leaky gut syndrome and metabolic endotoxemia, head over and check out our blog post Endotoxemia, Leaky Gut, and Lipopolysaccharides.

Bacillus Spore Probiotics from Microbiome Labs

These studies are just scratching the surface of the multitude of ways bacillus spore-based probiotics can be used to address underlying imbalances, heal chronic conditions, and optimize overall health. If you want to dive deeper into additional studies and research that proves just how powerful these spore-based probiotics are, you can check out the following resources:

Microbiome Labs is at the forefront of the science behind spore-based probiotics. Their unique, 100% spore-based megaspore probiotic blend combines five of the most potent bacillus bacteria strains – creating the most powerful and effective probiotic supplement available on the market. Their one-of-a-kind MegaSporeBiotic probiotic blend is backed by extensive scientific studies (with more studies on the way).

Megasporebiotic Spore-Based Probiotics

Megasporebiotic by Microbiome Labs utilizes a unique blend of 5 particularly potent strains of spore-based, broad-spectrum probiotics that work to not just repopulate your gut but to entirely recondition it. Megaspore probiotic’s blend includes:

  • Bacillus subtilis HU58
  • Bacillus clausii SC-109
  • Bacillus coagulans SC-208
  • Bacillus indicus HU36
  • Bacillus licheniformis SL-307

To dive deeper into the extensive health benefits that have been linked to these specific strains of spore-based probiotics, you can check out these blog posts:

Or if you really want the low down on Megaspore probiotics, head over and check out our webinar replay with Kiran Krishnan, the Chief Science Officer at Microbiome Labs.

While MegaSporeBiotic probiotic supplements have been clinically proven to have extensive health benefits, they’ve been found to be especially powerful when it comes to lowering triglycerides. Just take a look at the following study.

Curious if Bacillus Spore-Based Probiotics Are Right for You? 

Just about everyone can benefit from bacillus spore-based probiotics. Our ancestors’ digestive tracts evolved with and alongside these mighty microbes – making our microbiomes biologically wired to have a healthy and thriving ecosystem of bacillus-based probiotics. 

If you’re interested in experiencing the power of spore-based probiotics for yourself, you can grab your own bottle of MegaSporeBiotic by clicking right here. These powerful probiotics are available on our online store along with a plethora of other products to help you heal and optimize the health of your gut.

And because we never recommend products or strategies without also giving you the science behind why we recommend them, we’ve got tons of educational resources available to you as well. To dive deeper into a subject you can head over and check out the blog, the podcast, and the Wellness Vault. And keep an eye out for future posts – we’re always delivering brand-new cutting-edge content to help you cut through the noise and create abundant health.


  1. Use of bacterial spore formers as probiotics | FEMS Microbiology Reviews | Oxford Academic (
  2. Frontiers | Presence and Germination of the Probiotic Bacillus subtilis DE111® in the Human Small Intestinal Tract: A Randomized, Crossover, Double-Blind, and Placebo-Controlled Study | Microbiology (
  3. Measurement of gastrointestinal pH profiles in normal ambulant human subjects. | Gut (
  4. Bacillus Probiotics: Spore Germination in the Gastrointestinal Tract | Applied and Environmental Microbiology (
  5. 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 – PubMed (
  6. Oral spore-based probiotic supplementation was associated with reduced incidence of post-prandial dietary endotoxin, triglycerides, and disease risk biomarkers – PubMed (
  7. Bacillus spp. Spores—A Promising Treatment Option for Patients with Irritable Bowel Syndrome – PMC (
  8. Probiotic Bacillus Spores Together with Amino Acids and Immunoglobulins Exert Protective Effects on a Rat Model of Ulcerative Colitis – PMC (
  9. Bacillus spp. Spores—A Promising Treatment Option for Patients with Irritable Bowel Syndrome – PMC (
  10. Enhancement of antioxidant activity of levan through the formation of nanoparticle systems with metal ions (
  11. Bacillus in the guts of honey bees (Apis mellifera; Hymenoptera: Apidae) mediate changes in amylase values (
  12. Immunity in the Gut | British Society for Immunology
  13. Allergy and the gastrointestinal system – PMC (
  14. Leaky Gut, Leaky Brain? – PMC (
  15. Metabolic Endotoxemia: A Potential Underlying Mechanism of the Relationship between Dietary Fat Intake and Risk for Cognitive Impairments in Humans? – PubMed (

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