What Is Bacillus clausii?

Bacillus clausii is a Gram-positive, rod-shaped, aerobic bacterium that forms heat-resistant endospores. It belongs to the broader Bacillus genus—a group of soil-dwelling organisms that have adapted to survive in some of the most hostile environments on Earth. In scientific literature you may also encounter it referred to as Alkalihalobacillus clausii or Shouchella clausii—the result of ongoing phylogenetic reclassification as genomic analysis has advanced—though the clinical literature overwhelmingly continues to use the Bacillus clausii name.^[7]

As a soil-based organism (SBO), B. clausii is part of a category of probiotics that evolved in the external environment rather than exclusively in the human gut. This distinction matters: SBOs typically produce spores as a survival strategy, giving them resilience characteristics that conventional dairy-derived probiotics simply do not possess. You can read more about why soil-based organism probiotics are increasingly valued in modern gut health protocols.

A Probiotic With a Long Track Record

The clinical use of B. clausii predates most modern probiotic research. Preparations containing this organism were first commercialized in Europe in the mid-twentieth century and have been dispensed in countries like Italy, India, and Vietnam for over sixty years. This longevity has generated a larger-than-average body of real-world safety data and clinical observation. A 2022 narrative literature review covering decades of evidence concluded that B. clausii probiotics have "been efficaciously and safely used in humans for several decades."^[1]

Strain Designations and Multi-Strain Formulas

The most extensively studied B. clausii preparations include four strains designated O/C, N/R, SIN, and T—named partly for their antibiotic resistance profiles. Each carries resistance to different antibiotic classes: O/C is chloramphenicol-resistant, SIN resists neomycin and streptomycin, N/R resists novobiocin and rifampin, and T resists tetracycline.^[3] This multi-strain combination is the formulation behind most clinical trials, and it's the reason B. clausii is uniquely suited for concurrent use with antibiotic therapy—a rare capability among probiotics.

How Bacillus clausii Spores Survive the GI Tract

Most people are surprised to learn that delivering a live probiotic to the colon is far more difficult than supplement labels make it appear. Stomach acid sits between pH 1.5 and 3.5—an environment that kills many Lactobacillus strains outright. Bile salts in the small intestine add another hostile layer. And for anyone taking antibiotics, a broad-spectrum antibiotic course can decimate the very probiotic bacteria they're trying to supplement.

Bacillus clausii sidesteps all three of these obstacles through its spore-forming biology.

The Spore Structure Explained

When environmental conditions become inhospitable, B. clausii cells form endospores—dormant structures encased in multiple protective protein and peptidoglycan layers. Inside this shell, the bacterium's genetic material and essential proteins are preserved in a dehydrated, metabolically inactive state. The spore coat is extraordinarily resistant to heat (surviving temperatures above 75°C), chemical stress, UV radiation, and the low pH of gastric acid.^[8]

Research comparing B. clausii spores against other probiotics found that the spores survived at least 120 minutes in simulated gastric fluid with no detectable loss of viability, while the majority of other probiotics tested experienced measurable reductions after just 30 minutes of acid exposure.^[1] A separate study evaluating the full gastrointestinal journey confirmed that B. clausii UBBC07 spores remained viable throughout both simulated gastric and intestinal phases—and importantly, germinated into active vegetative cells within the intestinal environment, where they can actually exert probiotic activity.^[9]

Germination and Gut Colonization

Survival through the stomach is only the first hurdle. To be useful, a probiotic must also germinate and transiently colonize the intestinal epithelium. Clinical pharmacokinetic data shows that B. clausii spores begin germinating in the human gut as early as day one following ingestion, with detection continuing through day twelve after the final dose—indicating active, sustained colonization during the supplementation window.^[1]

Upon germination, vegetative B. clausii cells have been shown to adhere to intestinal mucous-producing cell lines and upregulate mucin secretion—a finding with direct relevance to gut barrier integrity and protection against enteropathogens.^[2]

Antibiotic Resistance as a Probiotic Asset

Perhaps the most clinically relevant survival advantage of B. clausii is its resistance to commonly prescribed antibiotics. Most probiotic bacteria are eliminated when taken alongside an antibiotic course—which is precisely when gut support is most needed. B. clausii's antibiotic resistance allows it to remain viable and active in the gut during antibiotic therapy.

Crucially, multiple studies have confirmed that this antibiotic resistance is non-transferable—meaning B. clausii cannot pass its resistance genes to other bacteria in the gut microbiome, including pathogens. This non-transferability is a key safety attribute that differentiates B. clausii from antibiotic-resistant organisms that pose public health risks.^[1] If you're recovering from a course of antibiotics or currently on one, understanding probiotics after antibiotics becomes especially relevant to your protocol.

Bacillus clausii Benefits: What the Clinical Evidence Shows

The clinical research on B. clausii is more extensive than most consumers realize. Below is a summary of the key evidence across the major areas where this probiotic has been evaluated.

Acute Diarrhea in Children: Meta-Analytic Evidence

The most robust body of evidence for B. clausii concerns pediatric acute diarrhea, where it has been the subject of multiple randomized controlled trials and at least two independent meta-analyses. A 2018 systematic review and meta-analysis of six randomized controlled trials (1,298 children) found that B. clausii significantly reduced the duration of acute diarrhea by a mean difference of 9.12 hours (95% CI: −16.49 to −1.75, p = 0.015) and reduced the duration of hospitalization by a mean of 0.85 days compared to control.^[3]

A more recent and comprehensive 2025 meta-analysis examining eleven randomized controlled trials and three non-randomized controlled trials reached consistent conclusions: B. clausii significantly shortened diarrhea duration, reduced stool frequency, and shortened hospital stay—with favorable safety profiles across all trials.^[10] A 2024 randomized, double-blind trial specifically evaluating persistent diarrhea (rather than acute diarrhea) found that B. clausii spore probiotics led to a two-day shorter recovery period compared to standard care, with 1.5- to 1.6-fold greater efficacy in reducing key diarrheal symptoms.^[6]

Antibiotic-Associated Diarrhea: A Unique Clinical Role

Antibiotic-associated diarrhea (AAD) affects between 5% and 35% of patients on antibiotic therapy and results from disruption of the gut microbiota. Most probiotics cannot be taken concurrently with antibiotics because they're simply eliminated by the drugs. B. clausii is a notable exception.

A 2024 systematic review evaluating the role of B. clausii (O/C, N/R, SIN, T) in preventing AAD identified that all included randomized controlled trials reported reductions in antibiotic-associated gastrointestinal symptoms—including diarrhea, abdominal pain, nausea, and vomiting—compared to placebo or no probiotic control.^[4] The review noted that B. clausii's ability to survive during antibiotic therapy, combined with its immunomodulatory and antimicrobial properties, positions it as "a promising approach to improving patient outcomes and minimizing the adverse effects of antibiotics on gut health."

Studies in patients receiving Helicobacter pylori eradication therapy—which typically involves triple antibiotic combinations—showed particular benefit, with B. clausii supplementation reducing the rate and severity of gastrointestinal side effects that often cause patients to discontinue the treatment protocol.^[4] This is especially relevant given the growing clinical challenge of H. pylori treatment compliance. You can explore the evidence on evidence-based probiotic strains for gut imbalance in our broader coverage of this topic.

Gut Barrier Support and Microbiota Restoration

Beyond its direct effects on diarrhea outcomes, B. clausii has demonstrated meaningful activity at the gut epithelial level. Preclinical models show that B. clausii vegetative cells upregulate tight junction proteins—the molecular "zippers" that maintain gut barrier integrity—and increase mucin secretion from goblet cells.^[2] Disruption of these same structures is a hallmark of what many practitioners call leaky gut, making this mechanistic evidence clinically relevant.

In a murine model of enteropathogenic E. coli infection, pre-treatment with B. clausii spores reduced intestinal lesions and lymphocytic infiltration, preserved mucus-secreting goblet cell populations, and maintained more intact intestinal mucosa compared to controls.^[1] These findings suggest B. clausii doesn't merely provide temporary symptom relief—it may actively support the structural integrity of the gut lining.

Bacillus clausii and Immune Modulation: Beyond the Gut

One of the more compelling and underappreciated aspects of B. clausii research is its systemic immune activity. While much of the public conversation about probiotics centers on digestion, B. clausii has been specifically studied for its ability to modulate immune responses—both locally in the gut and at remote mucosal sites like the respiratory tract.

Antimicrobial Substance Production

In addition to its probiotic effects, B. clausii actively produces antimicrobial compounds that can directly suppress pathogenic bacteria. A foundational study evaluating the antimicrobial activity of B. clausii probiotic strains found that they release antimicrobial substances during the stationary growth phase—coinciding with sporulation. These substances demonstrated activity against Gram-positive bacteria including Staphylococcus aureus, Enterococcus faecium, and notably, Clostridium difficile.^[5]

Among the antimicrobial compounds B. clausii produces is clausin, a lantibiotic (a class of ribosomally synthesized antimicrobial peptide). More recent research has confirmed that B. clausii also produces human beta-defensin 2 and cathelicidin—antimicrobial peptides that are part of the body's innate immune defense—in human pediatric enterocyte models.^[1] This capacity to stimulate the host's own antimicrobial defenses, rather than simply acting as a competitive organism itself, represents a sophisticated and clinically meaningful immune contribution.

Cytokine Modulation: Shifting Immune Balance

The adaptive immune system operates through a balance of T-helper cell subsets—Th1 cells drive cell-mediated immunity and anti-infection responses, while Th2 cells drive allergic and antibody-mediated responses. Chronic imbalance toward Th2 dominance underlies many allergic and inflammatory conditions. B. clausii has been shown to meaningfully shift this balance.

A clinical pilot study administering B. clausii to allergic children with recurrent respiratory infections found that treatment produced significant changes in cytokine levels measured in nasal lavage fluid: IL-4 (a Th2 cytokine) decreased significantly, while IFN-γ, IL-12, TGF-β, and IL-10 all increased.^[13] In practical terms, this means B. clausii supplementation was associated with a measurable reduction in the allergic inflammatory signaling that contributes to respiratory symptoms, while simultaneously promoting protective Th1 and regulatory T-cell (Treg) immunity.

In vitro research confirmed that B. clausii vegetative cells induce NOS II synthetase activity, IFN-gamma production, and CD4+ T-cell proliferation in murine immune cells—mechanistic evidence that aligns with the cytokine shifts observed in clinical settings.^[5]

Respiratory Health: A Gut-Lung Connection

The gut-lung axis—the bidirectional communication between the gastrointestinal microbiome and pulmonary immune function—has emerged as an active area of probiotic research. B. clausii is one of the few probiotic strains with specific published clinical data on respiratory outcomes.

A randomized pilot study enrolled 80 children with recurrent respiratory infections (RRI) and randomly assigned 40 to three months of B. clausii supplementation while 40 served as untreated controls. Children treated with B. clausii experienced significantly shorter duration of respiratory infections during the treatment phase (mean 11.7 vs. 14.37 days, p=0.037) and during the subsequent three-month follow-up period (mean 6.6 vs. 10.92 days, p=0.049). Importantly, this protective effect persisted even after supplementation ended.^[11]

A more recent double-blind, randomized, placebo-controlled study of B. clausii UBBC-07 in 90 children ages 4–7 with upper respiratory tract infections reported that supplementation significantly decreased the number, duration, and severity of URTIs. Notably, IgE levels were significantly reduced and salivary IgA—a key mucosal defense antibody—was significantly increased in the probiotic group, providing immunological mechanistic support for the clinical findings.^[12]

Antioxidant Activity

Emerging research on B. clausii has identified antioxidant properties as another dimension of its probiotic activity. A 2023 characterization study of B. clausii CSI08 demonstrated that both spores and vegetative cells of this strain attenuated LPS- and Poly I:C-triggered pro-inflammatory cytokine gene expression in intestinal cell lines—a finding with relevance to inflammatory gut conditions—while also exhibiting antioxidant activity in ex vivo models.^[8] This oxidative stress-buffering activity is consistent with findings in other Bacillus species and adds a further dimension to the clinical rationale for including B. clausii in a comprehensive gut health formula.

Choosing a Bacillus clausii Supplement: Safety and What to Look For

As consumer interest in spore-forming probiotics grows, so does the number of products claiming to contain Bacillus clausii. Not all of them deliver what they promise. The quality gap in this space is significant—and understanding it can help you make a more informed purchasing decision.

Safety Profile: What the Clinical Record Shows

The decades-long clinical history of B. clausii formulations provides a reassuringly large safety dataset. A 2024 randomized clinical trial evaluating Alkalihalobacillus clausii AO1125 in human subjects found no pathogenicity, no cytotoxicity, no hemolytic activity, and no clinically meaningful adverse events—mild, transient abdominal gas was the most commonly reported effect.^[7] This finding is consistent across the broader clinical trial literature, where adverse event rates in B. clausii-treated groups have been consistently similar to those in placebo or control groups.^[10]

It is worth noting that a small number of case reports have documented B. clausii bacteremia (bacteria in the bloodstream) in immunocompromised patients following probiotic use. These reports are rare and involve individuals with pre-existing immune deficiencies or underlying medical conditions. For healthy adults and children, the consensus safety record is well-established.

Quality Variability: A Documented Problem

A rigorous quality assessment study evaluated eleven commercially available B. clausii probiotic products on the Indian market. The findings were sobering: with the exception of the reference product (Enterogermina®) and one other preparation, contaminants were found in all products. Two formulations were found to contain Bacillus cereus—a foodborne pathogen—despite labeling only B. clausii.^[14]

This isn't an isolated finding; it reflects a broader challenge in the probiotic industry where label claims and actual contents can diverge significantly. When choosing a probiotic supplement, third-party testing and manufacturing transparency matter enormously—particularly for spore-forming organisms where species identification requires more sophisticated methods than visual inspection.

Multi-Strain Synergy: B. clausii Is Stronger With Company

An important nuance from the clinical literature is that B. clausii is most often studied and clinically used as a multi-strain preparation. The four-strain combination (O/C, N/R, SIN, T) that dominates the research has complementary antibiotic resistance profiles, which means the collective formula maintains activity across a broader range of antibiotic exposures than any single strain alone could achieve.

Similarly, combining B. clausii with conventional Lactobacillus and Bifidobacterium strains creates a complementary ecosystem. Spore-forming Bacillus species can survive and colonize during conditions that eliminate non-spore-formers, while Lactobacillus and Bifidobacterium strains provide important functions—including lactic acid production, competitive exclusion, and direct immune interactions—that Bacillus species handle less efficiently. The evidence on single vs. multi-strain probiotic formulas supports this complementary approach. Our article on the most well-researched probiotic strains covers the broader landscape of clinically supported organisms.

Prebiotics: The Ecosystem Support B. clausii Needs

Like all probiotic organisms, B. clausii functions optimally in a gut environment that supports microbial growth and diversity. Fermentable prebiotics—dietary fibers and polysaccharides that serve as fuel for beneficial bacteria—are a critical part of this support structure. MicroBiome Restore pairs its 26 probiotic strains with nine organic prebiotic sources: Jerusalem artichoke, maitake mushroom, fig fruit, bladderwrack, Norwegian kelp, oarweed, acacia, maltodextrin (included for shelf stability of the live strains), and a prebiotic pullulan capsule. This prebiotic-probiotic pairing is designed to support the establishment and activity of all strains, including B. clausii, once they reach the gut.

What to Look For on a Label

When evaluating any Bacillus clausii supplement, consider the following:

Strain designation: Look for confirmed B. clausii identification, ideally with strain codes (O/C, N/R, SIN, T or equivalent) rather than a generic species claim.

CFU at expiry, not at manufacture: CFU counts should be guaranteed through the expiration date. Spore-based probiotics retain viability better than non-spore-forming strains, but label claims should still reflect end-of-shelf-life potency.

Third-party testing: Given the documented contamination issues in this category, third-party verification of species identity and absence of contaminants is a meaningful quality signal.

Filler-free formulation: Unnecessary excipients like microcrystalline cellulose, magnesium stearate, titanium dioxide, and silicon dioxide add nothing to the probiotic's efficacy and may carry their own concerns. MicroBiome Restore excludes all of these additives. You can read more about the benefits of multi-strain probiotics without microcrystalline cellulose in our ingredient transparency articles.

Frequently Asked Questions