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Spore-Based Probiotics

What Are They?

Spore-based probiotics are soil-based microorganisms that form spores, typically found in dirt and vegetation.1  This encapsulation allows them to survive harsh conditions such as extreme temperatures, high pressure, radiation from the sun, and acidity.2,3  Advantages of spore-based probiotics, the most common being Bacillus species, include their ability to withstand stomach acid and tolerate bile salts, allowing them to reach the small intestine fully intact where they can grow and provide digestive benefits.2-4  

What Benefits Do They Have?

In clinical trials, spore-based probiotics including Bacillus indicus, Bacillus subtilis, Bacillus coagulans, Bacillus licheniformis, and Bacillus clausii were shown to reduce post-prandial triglycerides and endotoxins, and decrease inflammatory markers.5,6 In addition, these probiotics have shown to be beneficial for gastrointestinal function including reduced diarrhea, constipation relief, and support of Small Intestinal Bacterial Overgrowth (SIBO).7-12

Triglyceride Lowering

Triglycerides get stored as fat that the body can later use for energy. Although the body needs some fat to function properly, high triglyceride levels are associated with obesity, diabetes, and heart disease. In one study, participants who took two capsules of a spore-based Bacillus probiotic blend for 30 days had a 24% reduction in triglyceride levels at 3­ hours post-prandial compared to a 5% reduction in placebo at the same time point.5In another study of patients with triglyceride levels >150 mg/dl, comparison of the two treatment groups (placebo vs. soil-based probiotic) showed probiotic treatment decreased the mean triglyceride level by 37.3 mg/dl at six weeks and 64.9 mg/dl at twelve weeks.

Reduced Endotoxins

Postprandial endotoxins are substances released in the gut after eating a meal, typically one that is high in fat and calories. These endotoxins cause systemic inflammation which is linked to many chronic disease states. In the previous study showing triglyceride lowering, participants taking the spore-based probiotic also showed a statistically significant 42% reduction in serum endotoxin.These findings are consistent with an in-vitro replication of the human gut that showed the probiotic blend increased production of butyrate, a short-chain fatty acid produced by gut microbes that has several beneficial functions including reducing endotoxins.1

Decreased Inflammatory Markers

Study participants taking daily spore-based probiotics had a reduction in both IL-12p70 and IL-1B, markers of inflammation in the body.5 In the in-vitro simulation, the probiotic blend promoted the growth of Faecalibacterium prausnitzii, an important gut bacteria that has anti-inflammatory effects.

Gastrointestinal Benefits

SIBO is caused by an excess of bad bacteria in the small intestine and data shows Bacillus clausii to be effective.7  In addition, Bacillus clausii has shown to decrease diarrhea in children, reduce hospitalizations associated with diarrhea, and decrease the duration of a diarrhea episode.8,9 Supplementation with Bacillus coagulans and Bacillus subtilis were also found to decrease the severity of constipation in both healthy patients and patients with irritable bowel disease.8,10,11,12  


Spore-based probiotics have multiple benefits that you may not see with traditional probiotic supplements sold at the grocery store. Cholesterol-lowering, reduced after-meal endotoxins, reduced inflammation, and increased intestinal benefits are just some of the advantages this unique product can provide to support a healthy gut.  

Written by MeiLing Montross, PharmD Candidate Class of 2021, Cedarville University School of Pharmacy

Some of our preferred spore-based probiotics include Ortho Spore by Ortho Molecular Products and MegaSporeBiotic by Microbiome Labs.

If you are interested in learning more about gut restoration, our team of functional medicine pharmacists at PharmToTable are here for you.  We developed a short questionnaire that can help determine if gut testing and gut restoration may be appropriate for you. Also, we’d love for you to join one of our discovery classes or book an appointment to work with us!


  1. Duysburgh C, Van den Abbeele P, Krishnan K, et al.  A synbiotic concept containing spore-forming Bacillus strains and a prebiotic T fiber blend consistently enhanced metabolic activity by modulation of the gut microbiome in vitro.  Int. J. Pharm. 2019;7(1):1-10. doi:10.1016/j.ijpx.2019.100021. 
  2. Bader J, Albin A, Stahl U, et al.  Spore-forming bacteria and their utilisation as probiotics.  Benef.  2012;3(1):67-75.  doi: 10.3920/BM2011.0039.    
  3. Elisashvili V, Kachlishvili E & Chikindas M. Recent advances in the physiology of spore formation for bacillus probiotic production.  Probiotics Antimicrob Proteins.  2018;11:731-749.  doi: 10.1007/s12602-018-9492-x.     
  4. Adibpour N, Hosseininezhad M, Pahlevanlo A, et al. A review on bacillus coagulans as a spore-forming probiotic.  Appl Food Biotechnol.  2019;6(2):91-100.  doi: 10.22037/afb.v6i2.23958.  
  5. McFarlin B, Henning A, Bowman E, et al. 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;8(3):117-126.  doi: 10.4291/wjgp.v8.i3.117. 
  6. Campbell A, Sinatra D, Zhang Z, et al. Efficacy of spore forming bacilli supplementation in patients with mild to moderate elevation of triglycerides: a 12 week, randomized, double-Blind, placebo controlled trial.  J. Integr. Med. 2020;4(19):18-23. PMID: 33041703.  
  7. Gabrielli M, Lauritano E, Scarpellini E, et al.  Bacillus clausii as a treatment of small intestinal bacterial overgrowth.  Am J Gastroenterol.  2009;104(5):1327-8. doi: 10.1038/ajg.2009.91.
  8. Guilliams T & Drake L.  The role of probiotics as effective therapies for dysbiosis and gi dysfunctions.  Point Institute. 2020;16(1):1-20.  
  9. Ianiro G, Rizzatti G, Plomer M, et al. Bacillus clausii for the treatment of acute diarrhea in children: a systematic review and meta-analysis of randomized controlled trials. Nutrients. 2018;10(8):1074.  doi: 10.3390/nu10081074.   
  10. Sudha MR, Jayanthi N, Aasin M, et al. Efficacy of bacillus coagulans unique is2 in treatment of irritable bowel syndrome in children: a double blind, randomised placebo controlled study. Benef.2018;9(4):563-572.  doi: 10.3920/BM2017.0129. 
  11. Catinean A, Neag A, Nita A, et al. Bacillus spp. spores-a promising treatment option for patients with irritable bowel syndrome. Nutrients. 2019;11(9).  doi: 10.3390/nu11091968.  
  12. Madempudi R, Neelamraju J, Ahire J, et al. Bacillus coagulans unique is2 in constipation: a double-blind, placebo-controlled study. Probiotics Antimicrob Proteins. 2020;12(2):335-342. doi: 10.1007/s12602-019-09542-9.
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