What Is Bacillus subtilis?

Bacillus subtilis is a Gram-positive, rod-shaped bacterium that occurs naturally in soil, fermented foods, and—as research has increasingly confirmed—the human gastrointestinal tract.^[8] It has been studied since the early 19th century and was used medically in Europe as early as the 1940s as an oral intervention for gastrointestinal complaints. Today, it remains one of the best-characterized bacteria in all of microbiology, with one of the most thoroughly sequenced and annotated genomes of any organism.

In the probiotic context, B. subtilis belongs to a class sometimes called "soil-based organisms" (SBOs)—bacteria that evolved in environments with extreme variability in temperature, pH, moisture, and nutrient availability. This evolutionary history produced a resilience that is highly relevant to probiotic efficacy: most conventional probiotic strains from the Lactobacillus and Bifidobacterium families are adapted to stable, anaerobic, nutrient-rich environments and are consequently fragile outside them. Bacillus species are not.

B. subtilis in Traditional Foods

Perhaps the most well-known natural source of Bacillus subtilis is nattō—a traditional Japanese fermented soybean product that has been consumed for over a thousand years and is strongly associated with the health and longevity profiles seen in Japanese populations. B. subtilis natto (the specific strain used in nattō production) produces nattokinase, a fibrinolytic enzyme with studied effects on blood coagulation markers, as well as vitamin K2 (menaquinone-7).^[11] Other fermented foods where B. subtilis is commonly found include doenjang (Korean fermented soybean paste) and various African fermented products.

While dietary sources can contribute to intake, consistent therapeutic levels of Bacillus subtilis require supplementation—and the biological effects documented in clinical trials come from supplemental spore preparations rather than occasional dietary exposure.

The Spore-Forming Advantage: Why B. subtilis Survives Where Others Don't

The central challenge in probiotic supplementation is viability delivery: getting a meaningful number of live, active bacteria to the sites in the gut where they can exert therapeutic effects. For most conventional probiotics, this involves fighting an uphill battle against gastric acid (pH 1.5–3.5), bile salts in the duodenum, pancreatic enzymes, and the mechanical churning of the digestive process. Even refrigerated products can arrive at their targets with substantially diminished viable counts.

Bacillus subtilis sidesteps this problem by existing primarily as a spore during transit. Multiple studies using in vitro simulated gastrointestinal models have confirmed that B. subtilis spores survive exposure to simulated gastric juice (pH 2.0), bile salts at concentrations found in the small intestine, and heat up to 85°C without meaningful loss of viability.^[7] When researchers at Cork Teaching Hospitals gave ileostomy patients a single dose of B. subtilis DE111 spores and then analyzed ileal effluent samples over the following eight hours, they confirmed both the presence and germination of the bacteria in the human small intestinal tract—providing direct in vivo evidence of survival and activation.^[7]

Shelf Stability: What It Means for Supplement Quality

Beyond survival in the gut, the spore structure has a practical implication for supplement quality. Most Lactobacillus and Bifidobacterium strains require refrigeration to maintain viable counts from manufacture through consumption. Even with refrigeration, label claims can be aspirational; some products lose significant potency before the expiration date. B. subtilis spores, by contrast, remain stable at room temperature for extended periods—and critically, the spore count at time of consumption reflects what will actually reach the gut.^[1]

This stability is also why B. subtilis is one of the only probiotic organisms that can be meaningfully incorporated into heat-processed food and beverage products. For supplement formulations, it means that a verified CFU count on the label corresponds more reliably to what you're ingesting compared to fragile strains that may have experienced die-off.

Oxygen Consumption and the Anaerobic Advantage

An often-overlooked property of Bacillus subtilis is that it is a facultative aerobe—it can metabolize both in the presence and absence of oxygen. When vegetative B. subtilis cells establish themselves in the gut, they consume free oxygen in the local environment, creating conditions that favor the growth of strict anaerobes like Bifidobacterium and Lactobacillus. Research has demonstrated that supplementation with B. subtilis can increase the relative abundance of these beneficial anaerobic bacteria as an indirect consequence.^[9] In this sense, B. subtilis functions not only as a probiotic in its own right but as an ecological facilitator for the broader community of gut bacteria.

Bacillus subtilis Gut Health Benefits: What Clinical Research Shows

The gut health evidence for B. subtilis spans multiple well-controlled human trials, with meaningful data on GI symptom relief, intestinal barrier function, microbiome composition, and pathogen inhibition. The picture that emerges is of a probiotic organism with several distinct and complementary mechanisms of action.

Reducing Gastrointestinal Symptoms in Healthy Adults

One of the most rigorous clinical investigations of B. subtilis was a 2022 randomized, double-blind, placebo-controlled trial of 76 healthy adults by Garvey and colleagues.^[1] Participants received either 2 billion CFU of B. subtilis BS50 daily or placebo for six weeks, recording gastrointestinal symptoms daily via a validated multi-symptom questionnaire. The results were clear: compared to the placebo group, the B. subtilis group showed significantly greater improvement in the composite score for bloating, burping, and flatulence (47.4% vs. 22.2% showing improvement), with odds of improvement nearly 3.2-fold higher in the probiotic group (OR 3.2 [95% CI: 1.1, 8.7]; p = 0.024).^[1]

The researchers attributed the improvement to the germination and colonization of BS50 in the small intestine, where vegetative cells secrete digestive enzymes that assist in breaking down dietary proteins, lipids, and carbohydrates—theoretically reducing the fermentable substrate that reaches the large intestine and drives gas production. The strain's secreted proteases and amylases were confirmed in vitro.^[1]

An earlier study using B. subtilis DE111 evaluated stool consistency in healthy adults experiencing occasional constipation and/or diarrhea, finding improvements in normalized stool type—a meaningful quality-of-life outcome for a population dealing with functional GI complaints. For more information on how spore-based probiotics specifically support relief from digestive discomfort, see our review of evidence-based probiotic strains for bloating.

Intestinal Barrier Function and Tight Junctions

The intestinal barrier is the single-cell-thick layer of epithelial cells lining the gut, held together by specialized protein structures called tight junctions. When tight junction integrity is compromised—a state colloquially known as "leaky gut"—bacterial components, lipopolysaccharides, and undigested food particles can cross into systemic circulation, triggering immune activation and low-grade inflammation. Probiotic support for this barrier is an active area of research, and B. subtilis has emerged as one of the more compelling organisms in this context.

Rhayat and colleagues published a detailed investigation of how three B. subtilis strains—including DSM 29784—affected intestinal epithelial integrity using the gold-standard Caco-2 cell model.^[5] The study found that strain DSM 29784 produced a 50% increase in transepithelial electrical resistance (TEER)—a direct measure of barrier integrity—and this improvement was associated with significantly upregulated expression of the tight junction proteins ZO-1, occludin, and claudin-1. Pre-treatment with B. subtilis strains also substantially blunted subsequent IL-8 secretion in response to pro-inflammatory signals including IL-1β and deoxynivalenol, with inhibition of the NF-κB signaling pathway identified as the likely mechanism.^[5]

More recent mechanistic work has identified a novel metabolite produced by B. subtilis—2-hydroxy-4-methylpentanoic acid (HMP)—as playing a direct role in barrier protection through activation of the GADD45A–Wnt/β-catenin pathway, which promotes tight junction protein expression. This represents what researchers describe as a "postbiotic" effect, where the organism's secreted metabolites exert biological activity independent of the bacteria themselves. For those dealing with intestinal permeability concerns, our deep-dive on probiotics for intestinal barrier repair covers the broader clinical evidence on this topic.

Pathogen Inhibition and Microbiome Balance

Bacillus subtilis produces a remarkably diverse array of antimicrobial compounds—bacteriocins, lipopeptides (iturin, fengycin, surfactin), and polyketides—that have inhibitory activity against a wide spectrum of pathogenic organisms including Staphylococcus aureus, Escherichia coli, Salmonella, Clostridium difficile, and Helicobacter pylori.^[7] This is not merely laboratory observation; the production of these compounds appears to occur in the gastrointestinal environment and may explain B. subtilis's documented ability to reduce pathogen colonization in clinical settings.

B. subtilis has also been studied in relation to small intestinal bacterial overgrowth (SIBO), where its antimicrobial and microbiome-normalizing effects may be therapeutically relevant. For a full review of strain-specific evidence in this condition, see our article on evidence-based probiotics for SIBO.

Immune System Support: Evidence from Human Clinical Trials

The relationship between the gut microbiome and immune function is now well established: roughly 70–80% of the body's immune tissue is located in the gut-associated lymphoid tissue (GALT), and the composition of gut bacteria is a primary determinant of how that immune tissue is calibrated. Bacillus subtilis has specific, documented mechanisms for interacting with mucosal immunity—and these have been examined in several human trials.

The CU1 Immune Trials: Elderly Subjects

The most frequently cited human immune data for B. subtilis comes from work by Lefevre and colleagues on the CU1 strain in an elderly population.^[2] In a randomized, double-blind, placebo-controlled parallel-arms study, 100 healthy subjects aged 60–74 received either 2 billion B. subtilis CU1 spores daily (administered in 10-day cycles with 18-day washout periods) or placebo across a four-month winter period. While overall reduction in days with common infectious disease symptoms did not reach statistical significance in the full population, the immunological findings in the biological sample subset (n=44) were striking.

Subjects in the probiotic group showed significantly higher concentrations of fecal secretory IgA (sIgA) after 10 days of consumption compared to the placebo group (2,062 vs. 1,249 μg/ml; p = 0.0038). Elevated sIgA persisted through the end of consumption and 18 days after cessation.^[2] Salivary sIgA also increased significantly in the probiotic group at study end (p = 0.0219). Secretory IgA is the primary antibody of mucosal immunity—the first line of defense against pathogens at mucosal surfaces including the gut, respiratory tract, and oral cavity. Its elevation by B. subtilis supplementation represents a meaningful indicator of enhanced mucosal immune readiness.

A follow-up clinical study on B. subtilis CU1 (published 2024) extended this immune characterization by examining peripheral blood immune markers across three age groups in 88 subjects. The study found positive effects on a consistent set of peripheral immunity markers, with B. subtilis CU1 shown to prime innate immune responses and reduce low-grade inflammation—suggesting effects that extend beyond mucosal immunity into systemic immune regulation.^[10]

Anti-Inflammatory Immune Cell Activity

A 2021 randomized controlled trial by Freedman and colleagues at Colorado State University examined B. subtilis DE111 in healthy adults over four weeks, with a focus on peripheral blood mononuclear cells (PBMCs).^[3] The study found that when PBMCs from the DE111 group were stimulated with bacterial lipopolysaccharide (LPS) ex vivo, anti-inflammatory immune cell populations were increased relative to the placebo group—suggesting a priming effect on the immune response to inflammatory stimuli. In athletes undertaking intense training programs, separate work found that DE111 supplementation reduced circulating TNF-α (a pro-inflammatory cytokine elevated by intense exercise) and increased salivary sIgA, consistent with the mucosal immune findings from the CU1 trials.^[3]

Spore-Based Immune Mechanisms

The immune activity of B. subtilis appears to involve at least two distinct mechanisms. First, oral administration of B. subtilis spores stimulates cytokine production and activates splenic macrophages and natural killer (NK) cells in animal models, with oral treatment increasing activation markers on lymphocytes in a dose-dependent manner in healthy volunteers.^[6] Second, a quorum-sensing pentapeptide produced by B. subtilis—competence and sporulation factor (CSF)—has been shown to activate key cell-survival pathways including p38 MAP kinase and protein kinase B (Akt) in intestinal epithelial cells, providing direct cytoprotective effects alongside immune stimulation.^[6]

Metabolic and Cardiovascular Effects

The connection between gut microbiome composition and systemic metabolic health is one of the most active frontiers in microbiome research. Bacillus subtilis has produced some notable findings in this space—particularly regarding lipid metabolism and cardiovascular risk markers—that go well beyond what most people associate with probiotics.

Cholesterol and Lipid Profiles

Trotter and colleagues at Colorado State University conducted a randomized, double-blind, placebo-controlled four-week intervention in 88 healthy adults, comparing B. subtilis DE111 against B. lactis (with and without bacteriophages) and placebo across four arms.^[4] Neither the B. lactis nor bacteriophage interventions produced significant changes in cardiovascular parameters. The B. subtilis DE111 group, however, showed a statistically significant reduction in total cholesterol from baseline (−8 mg/dl; p = 0.04) and a significant decrease in non-HDL cholesterol (−11 mg/dl; p = 0.01)—with trending improvements in both LDL cholesterol (p = 0.06) and endothelial function as measured by reactive hyperemia index (p = 0.05).^[4]

These effects are notable for occurring in a healthy population with normal baseline lipid levels, over only four weeks—suggesting that more pronounced effects might be observed in populations with dyslipidemia or over longer intervention periods. The authors note that this was the first randomized controlled trial to directly examine B. subtilis supplementation on endothelial function in humans.^[4]

Blood Metabolite Modulation

A 2023 study investigating the effects of B. subtilis on the microbiota-gut-blood system documented significant alterations in circulating metabolite levels following probiotic supplementation, including changes in serine, arginine, adenine, uric acid, and pyridoxal levels.^[9] The metabolisms of amino acids, purines, and vitamin B were identified as primary pathways influenced by B. subtilis. This metabolomic picture aligns with the enzyme-secreting capacity of vegetative B. subtilis cells in the gut—particularly for amino acid metabolism—and suggests that the probiotic's effects extend to systemic metabolic homeostasis beyond the gut itself.

Reducing Post-Meal Endotoxemia

A meaningful contributor to cardiovascular risk that often goes undiscussed is post-prandial dietary endotoxemia—the spike in circulating lipopolysaccharides (LPS) that can occur after meals, particularly those high in dietary fat. LPS triggers TLR-4 receptors on vascular endothelial cells and macrophages, driving acute inflammation. Research on a multi-Bacillus spore preparation including B. subtilis found that 30 days of supplementation was associated with significant reductions in post-prandial endotoxin, triglycerides, and pro-inflammatory cytokines in subjects with dietary endotoxemia—an effect attributed to improved intestinal barrier integrity and reduced translocation of gut-derived LPS into systemic circulation.^[12]

Bacillus subtilis in Multi-Strain Probiotic Formulas: Synergy and Formulation Context

Bacillus subtilis doesn't need to work alone—and in practice, it performs better when it doesn't. The mechanisms described above don't overlap cleanly with those of Lactobacillus and Bifidobacterium species; they tend to complement them. Understanding why B. subtilis belongs in a comprehensive formula (rather than as a standalone product) requires looking at the ecological logic of multi-strain design.

The Ecological Case for Multi-Strain Formulas

The adult human gut microbiome contains hundreds to thousands of bacterial species operating in a complex web of competitive and cooperative relationships. No single probiotic strain can replicate this complexity—but a well-designed multi-strain formula can address multiple niches simultaneously. B. subtilis contributes to this in specific ways: its oxygen scavenging creates conditions favoring anaerobic Lactobacillus and Bifidobacterium species; its antimicrobial compounds suppress potential pathogens that would otherwise compete with probiotic organisms; and its barrier-strengthening effects reduce the inflammatory background that can suppress mucosal immune responses needed for probiotic colonization. In short, B. subtilis helps create conditions in which other beneficial bacteria can thrive.^[9]

For a broader discussion of how single-strain and multi-strain approaches compare in clinical outcomes, our guide on multi-strain probiotics without MCC fillers covers this in detail.

The Other Bacillus Species in MicroBiome Restore

MicroBiome Restore includes four additional Bacillus species alongside B. subtilis: Bacillus coagulans, Bacillus clausii, Bacillus licheniformis, and Bacillus pumilus. Each brings distinct properties to the formula. Bacillus coagulans, for example, produces L+ lactic acid as a metabolic byproduct—a less common feature among spore-formers that contributes to local pH management. Together, these five Bacillus species create a layered spore-based probiotic foundation that no single-species Bacillus supplement can replicate.

Prebiotics That Support B. subtilis Activity

MicroBiome Restore's prebiotic matrix—which includes Jerusalem artichoke, maitake mushroom, fig fruit, bladderwrack, Norwegian kelp, oarweed, and acacia—provides fermentable substrates that support the colonization and metabolic activity of both the Bacillus species and the anaerobic organisms in the formula. Jerusalem artichoke inulin, in particular, preferentially feeds Bifidobacterium species whose growth B. subtilis indirectly promotes. This kind of formulation synergy—where spore-formers and anaerobes are supported by a complementary prebiotic blend—represents what the evidence suggests is the most effective architecture for a comprehensive probiotic supplement.

Pullulan capsules (the encapsulation material used in MicroBiome Restore) provide delayed release that protects both spore and non-spore organisms through the stomach, ensuring that even the more acid-sensitive strains benefit from the same protection mechanism that makes Bacillus so resilient. This stands in contrast to gelatin or HPMC capsule materials that dissolve earlier in the GI tract.

Filler-Free Formulation: Why It Matters Here

B. subtilis in particular benefits from a clean formulation environment. Research has confirmed that titanium dioxide—one of the most common supplement fillers—can reduce the abundance of both Bifidobacterium and Lactobacillus species in the gut.^[5] Introducing a probiotic formula containing organism-harming additives creates an internal contradiction. When you're paying for 26 strains and 15 billion CFU, the inactive ingredients shouldn't be undermining what the active ones are doing. Our full breakdown of common flow agents and fillers in probiotic supplements explains why this matters more than most manufacturers acknowledge. For help identifying these on labels, see our guide on reading probiotic supplement labels for hidden fillers.

Dosage, Safety, and Frequently Asked Questions

Safety Profile and Regulatory Status

Bacillus subtilis has a well-established safety profile supported by decades of use and multiple formal regulatory reviews. The FDA has granted GRAS status to multiple B. subtilis strains including DE111 (GRAS Notice No. 831) and SG188 (GRAS Notice No. 905). The European Food Safety Authority (EFSA) lists B. subtilis on its Qualified Presumption of Safety (QPS) register.^[1] Comprehensive safety assessments of probiotic B. subtilis strains—including genomic analysis for virulence factors, toxin-encoding genes, and antibiotic resistance—have consistently demonstrated absence of safety concerns at therapeutic doses.^[10]

The clinical trials reviewed above used doses ranging from 1 to 2 billion CFU per day, administered for periods of four to sixteen weeks, with no adverse events attributed to B. subtilis supplementation across any of the studies. The strain is considered non-pathogenic in immunocompetent individuals, and no cases of bacteremia attributable to therapeutic probiotic B. subtilis strains have been reported in clinical trial populations.

Dosage Considerations

Most clinical trials have used doses between 1 and 5 billion CFU per day for B. subtilis specifically. MicroBiome Restore delivers 15 billion CFU across 26 strains—with B. subtilis as one component of that total alongside four other Bacillus species and 21 additional Lactobacillus, Bifidobacterium, Lactococcus, Pediococcus, Streptococcus, and Enterococcus strains. This multi-strain distribution is important context: the 15 billion CFU represents the full formula, not a single-strain dose, which is consistent with how comprehensive probiotic products are typically formulated and studied.

For information on optimal timing and how to integrate probiotic supplementation into a daily routine, our guide on the best time to take probiotics covers the clinical evidence on meal timing and absorption. If you've recently completed a course of antibiotics, our guide on probiotics for recovery after antibiotics is particularly relevant—spore-based organisms like B. subtilis are especially well-suited to post-antibiotic recolonization support.

Putting It Together

Bacillus subtilis occupies a specific and defensible niche in the probiotic landscape—not just as one more organism on a label, but as a mechanistically distinct, clinically studied addition that complements the Lactobacillus and Bifidobacterium species that dominate most probiotic formulas. Its spore-based delivery, enzyme-secreting activity, tight junction support, antimicrobial properties, and immune-modulating effects create a profile of benefit that is both broad and well-grounded in peer-reviewed research.

What the clinical data consistently suggests is that B. subtilis works best as part of a diverse probiotic ecosystem—one that includes the anaerobic species it indirectly supports, the prebiotic substrates that sustain the whole community, and a formulation approach that doesn't introduce ingredients working against the organisms it's supposed to deliver. That's precisely the design logic behind MicroBiome Restore—and why it includes B. subtilis not as a marketing checkbox, but as a functional pillar of a comprehensive formula.