Small intestinal bacterial overgrowth (SIBO) is a rising area of focus in functional medicine. As microorganism levels in the small intestine increase, so does microbial activity, like fermentation. With these type of patients in practice, you may have seen that even healthy diets can cause gas, bloating, and intolerance to certain foods and probiotics. Such gastrointestinal complaints have been attributed to sensitivity, but the reason may be microbial imbalance in the small intestinal environment. As you know, the health of the gut relies on a balanced microbiota. Spore-forming probiotics can contribute to that balance by having a positive influence specifically in the small intestine, promoting organism diversity and immune protection.

Key Takeaways About Spore-Forming Probiotics

Within its protective shell, spore-forming probiotics are dormant when ingested. Why does this matter? This factor is a benefit because it enhances its survivability against the digestive process and causes less uncomfortable symptoms in GI sensitive individuals. When spore-forming probiotics reach the favorable, nutrient-rich environment in the small intestine, they come out of its endospore shell and become active on target. In its active form, they have a long-lifecycle and slowly colonize the GI tract.Also, these types of probiotics are not commensal to the gut. This is ideal for SIBO applications because they leave the small intestine when they are done doing their job as a probiotic and are less likely to contribute to any bacterial overgrowth that may be occurring.

When activated, spore-forming probiotics do things that most probiotics do. For example, activated spore-forming probiotics use quorum sensing to group together, communicate, and produce enzymes and other active compounds that deter unwanted organisms. This action gently pushes non-resident and potentially pathogenic bacteria out of the small intestine, helping to restore proper microbial diversity and balance.2 Also like most probiotics, they produce necessary nutrients like short-chain fatty acids, vitamins, antioxidants, and other compounds necessary for nurturing the gut lining and re-establishing the gut terrain.3

However, in your practice, there are two key advantages you should know that spore forming probiotics have over traditional probiotics like Lactobacillus and Bifidobacterium. First, spore-forming probiotics have a longer transient time in the gut, which means it has a longer life of activity. Spore-forming probiotics have a transient time of about three to four weeks, while traditional probiotics normally have a transient time of four to seven days.1 This allows spore-forming probiotics to have a more sustained probiotic effect in the gut and allows this probiotic to be taken in smaller doses over time. Secondly, spore-forming probiotics are shown to have better outcomes, specifically for SIBO-type patients, compared to traditional probiotics like Lactobacillus. They are also superior to a low-FODMAP diet alone in relieving SIBO-like symptoms, according to recent research.4

An Important Piece of the Puzzle

While each case is unique, spore-forming probiotics can be combined with other key products within a comprehensive SIBO protocol, to provide the multi-faceted support these patients need.

  • Serum-derived bovine immunoglobulins (SBI) bind to and sweep away the resulting bacterial components and toxins from the small intestinal environment.
  • A broad-spectrum, herbal antimicrobial is important for eliminating unwanted bacteria, and even unwanted fungus that may be present in individuals with SIBO.
  • A variety of polyphenols, including pomegranate and citrus fruits, are non-fiber prebiotics shown to induce positive changes in the microbiota and nourish the gut lining with short chain fatty acid production; ideal for SIBO individuals because it helps strengthen and recondition the gut lining, while not producing any gas or bloating.
  • Natural herbal-based prokinetic agents, like ginger and artichoke leaf extract, are shown to be effective in stimulating motility in the stomach and small intestine and relieving temporary GI discomfort associated with SIBO and helping prevent relapse.


More information on protocols, case studies and clinical testing for SIBO can be found in the Pillars of GI Health In-Practice Guide, which is part of the Pillars of GI Health Program. To dig into the latest research and assessment of SIBO, download a free monograph.


Although spore forming probiotics are becoming more popular in the functional medicine community, they are not the “one size fits all” solution. Instead, spore-forming probiotics hold their place alongside traditional probiotics in a complete spectrum of probiotics you may offer in your practice. However, for several reasons, spore-forming probiotics can be helpful specifically for individuals with SIBO. In your practice, it is essential that spore-forming probiotics are combined with other key nutritional supplements for a complete and comprehensive SIBO protocol, giving you more “tools” at your disposal to fight this common condition.




Dr. Joseph Ornelas is the Pillars of GI Health Brand Manager at Lifestyle Matrix Resource Center. He holds a PhD from University of Illinois with concentration in Health Economics, an MA degree in Public Policy from the Harris School at the University of Chicago, an MS degree in Health Systems Management from Rush University, and a DC degree from National University of Health Sciences. As a licensed provider and health economist, Dr. Ornelas has published numerous evidence-based clinical practice guidelines, helping to improve quality standards of care and provide value for health care practitioners across several specialty areas.


  1. Bernardeau M, Lehtinen MJ, Forssten SD, Nurminen P. Importance of the gastrointestinal life cycle of Bacillus for probiotic functionality. J Food Sci Technol. 2017;54(8):2570-2584. doi:10.1007/s13197-017-2688-3
  2. Dong YH, Wang LH, Xu JL, Zhang HB, Zhang XF, Zhang LH. Quenching quorum-sensing-dependent bacterial infection by an N-acyl homoserine lactonase. Nature. 2001 Jun 14;411(6839):813-7. doi: 10.1038/35081101. PMID: 11459062.
  3. Elshaghabee FMF, Rokana N, Gulhane RD, Sharma C, Panwar H. Bacillus As Potential Probiotics: Status, Concerns, and Future Perspectives. Front Microbiol. 2017;8:1490. Published 2017 Aug 10. doi:10.3389/fmicb.2017.01490
  4. Catinean A, Neag AM, Nita A, Buzea M, Buzoianu AD. Bacillus spp. Spores-A Promising Treatment Option for Patients with Irritable Bowel Syndrome. Nutrients. 2019 Aug 21;11(9):1968. doi: 10.3390/nu11091968. PMID: 31438618; PMCID: PMC6770835.