Other Names
B. pumilusBacillus aminoglucosidicusBacillus pumilus Meyer and Gottheil 1901
Bacillus pumilus is a Gram-positive, aerobic, spore-forming bacillus commonly found in soil. Its full taxonomic lineage is: cellular organisms β Bacteria β Bacillati β Bacillota β Bacilli β Bacillales β Bacillaceae β Bacillus. Bacillus pumilus is a bacterial species belonging to the Bacillus subtilis group.
Bacillus pumilus group strains have been studied due to their agronomic, biotechnological, and pharmaceutical potential. Classifying strains of this taxonomic group at species level is a challenging procedure since it is composed of seven species that share among them over 99.5% of 16S rRNA gene identity. Bacteria closely related to B. pumilus cannot be distinguished from such other species as B. safensis, B. stratosphericus, B. altitudinis, and B. aerophilus simply by 16S rRNA gene sequence.
B. pumilus has one circular chromosome with a varying length from 3.7 to 3.8 Mbp; strains SAFR-031 and ATCC 7061 are 3,704,465 and 3,833,998 base pairs, respectively. It is a Gram-positive, rod-shaped, spore-forming bacterium found in soil, water, and a variety of other habitats. Like most Gram-positive bacteria, teichoic and lipoteichoic acids cover the outermost layer of the peptidoglycan cross-links. They play a role in adhesion to host cells and other surfaces found in the environment, as well as being major surface antigens. These acids are composed of polyglycosyl phosphates (i.e., glycerol-P or ribitol-P) with mono- and disaccharides in the repeating units.
Bacillus pumilus is a spore-forming bacterium that is rod-shaped, Gram-positive, and aerobic. It resides in soils, and some strains colonize the root area of plants, where B. pumilus exhibits antibacterial and antifungal activity. B. pumilus and B. subtilis were among the most abundant Bacillus spp. associated with marine sponges, ascidians, soft corals, and seawater. B. pumilus has been found in extreme environments such as the interior of Sonoran desert basalt and the Mars Odyssey spacecraft.
Bacillus pumilus spores β with the exception of mutant strain ATCC 7061 β generally show high resistance to environmental stresses, including UV light exposure, desiccation, and the presence of oxidizers such as hydrogen peroxide. Environmental microbial sampling of the ultraclean Spacecraft Assembly Facility at NASA's Jet Propulsion Laboratory identified spores of Bacillus pumilus as major culturable bacterial contaminants found on and around spacecraft. As part of an effort to assess the efficacy of various spacecraft sterilants, purified spores of 10 JPL-SAF B. pumilus isolates were subjected to 254-nm UV; spores of six of the 10 isolates were significantly more resistant to UV than the B. subtilis biodosimetry strain. The Bacillus pumilus SAFR-032 strain, originally isolated from the Jet Propulsion Lab Spacecraft Assembly Facility, exhibits unusually high resistance to UV radiation and peroxide treatment compared to other Bacillus species; spores of B. pumilus SAFR-032 exhibited at least six-fold more resistance to UV irradiation than others.
Bacillus pumilus is a spore-forming, non-pathogenic bacterium that has garnered attention as a probiotic ingredient in nutritional and functional food products. Historically, members of the Bacillus genus have been utilized for their stability, safety, and potential health-promoting effects. B. pumilus itself has shown remarkable resistance to extreme environmental conditions, making it an appealing candidate for use in food and dietary supplements where shelf-stability is critical.
When formulated as a dietary supplement or animal feed additive, B. pumilus is almost invariably delivered in its spore form. Bacillus spp. probiotics are suitable feed additives due to their ability to form spores that enable them to endure harsh environmental conditions and to germinate in the gut of animals when exposed to adequate nutrients. Based on its abilities in producing vanillin, keratinase, xylanase, alkaline serine protease, and several other bioactive substances, B. pumilus is widely used in industrial processes, such as the production of several traditional fermented foods, the treatment of wastewater, and the degradation of environmental pollutants.
Bacillus pumilus does not have a well-documented history of deliberate therapeutic or dietary use by a named cultural tradition in the way that herbs or fermented foods are described in classical texts. Rather, its historical significance is inseparable from the broader microbial ecology of traditional fermented foods and soils.
Of note, Bacillus subtilis, Bacillus licheniformis, and Bacillus pumilus were recurrently isolated from fermented fish-based products. Since the aquatic environment does not represent the ideal habitat for the growth of Bacillus spp., their frequent isolation from fermented fish-based products was ascribable to contamination of the raw materials throughout production or to their ability to survive adverse environments. The establishment of favorable conditions during the early stages of the fermentative process allowed the proliferation of several Bacillus species able to use amino acids and organic acids as carbon or energy sources.
Bacteria from the genus Bacillus occur widely within the environment and are frequently detected both in raw materials used in the food industry and in food products at the point of sale. The species' presence in traditional fermented foods reflects passive colonization and environmental ubiquity rather than deliberate addition, as intentional use of defined B. pumilus strains as probiotics is a modern development that emerged alongside advances in microbiology during the twentieth century.
More recently, B. pumilus found in healthy plant tissue was reported with properties in promoting plant growth by enhancing the uptake of nutrients, nitrogen fixation, interaction with symbiotic microorganisms, and producing antimicrobial agents against pathogenic bacteria and fungi, as well as by reducing metal toxicity. The organism's agricultural associations are extensive and predate formal probiotic science; it would have been a natural constituent of soil-applied organic matter used in traditional farming across many cultures. Several B. pumilus strains are also used as probiotics for animals.
Members of the surfactin family include surfactin, produced by strains of B. subtilis and B. amyloliquefaciens; lichenysin, produced by strains of B. licheniformis; and pumilacidin, produced by strains of B. pumilus. A mass spectrometry analysis of the size-fractionated supernatant of a marine B. pumilus isolate identified the small anti-Staphylococcus molecule as a pumilacidin, a nonribosomally synthesized biosurfactant composed of a mixture of cyclic heptapeptides linked to fatty acids of variable length.
A novel circular bacteriocin, pumilarin X (7,045 Da), was produced during early growth phase and identified as an anti-Listeria metabolite. Genome analysis revealed the biosynthetic gene clusters of pumilarin X and pumilacidins (molecular masses of 1,058, 1,072, 1,086, and 1,100 Da). Purified pumilacidins exhibited specific activity against L. lactis HP but were inactive against Listeria and Staphylococcus. This study offers valuable insights into the target specificity of Bacillus pumilus metabolites, identifying the traits of pumilarin X and pumilacidins as narrow-spectrum agents.
B. pumilus, like other members of the Bacillus subtilis complex, ubiquitously produces surfactins or related lipopeptides such as pumilacidins, as well as the siderophore bacillibactin. Plantazolicin is formed by B. subtilis, B. velezensis, and B. pumilus. Iturin compounds (iturins A and C; bacillomycins D, F, and L; mycosubtilins) were produced specifically by B. atrophaeus, B. amyloliquefaciens, and B. velezensis, but not by B. subtilis, B. licheniformis, and B. pumilus. Fengycin, an antifungal lipotridecapeptide and efficient biocontrol agent against filamentous fungi, was found for B. subtilis, B. atrophaeus, B. amyloliquefaciens, and B. velezensis, but not for B. licheniformis and B. pumilus.
B. pumilus produces a variety of enzymes such as lichenase, lyase, cellulase, and serine proteases. The cellulases and hemicellulases are responsible for partial hydrolysis of lignocellulosic materials, dehulling of cereal grains, and hydrolysis of Ξ²-glucans.
Bacillus cyclic lipopeptides (CLP), part of the three main families β surfactins, iturins, and fengycins β are secondary metabolites with a unique chemical structure that includes both peptide and lipid components. Being amphiphilic compounds, CLPs exhibit antimicrobial activity in vitro by damaging the membranes of microorganisms. However, the concentrations of CLPs used in vitro are difficult to achieve in natural conditions. Therefore, in a natural environment, alternative mechanisms of antimicrobial action by CLPs are more likely, such as inducing apoptosis in fungal cells, preventing microbial adhesion to the substrate, and promoting the death of phytopathogens by stimulating plant immune responses.
Pore-formation metabolites act in a concentration-dependent manner, forming ion-like channels that release vital ions from the cell, leading to cell death. At low concentrations, these metabolites form unilamellar vesicles on the outer lipid membrane, distorting the shape of the cell, and eventually lead to apoptosis. At higher concentrations, these metabolites aggregate to form pores at the plasma membrane, causing the leakage of nucleic acids, essential ions, and ATP from the cell to cause necrosis. Bacillus metabolites that typically utilize this mechanism include the class of compounds known as lipopeptides.
Spores of B. pumilus and of a laboratory strain of B. subtilis were found to induce the proinflammatory cytokine interleukin-6 in a cultured macrophage cell line; and in vivo, spores of B. pumilus and B. subtilis induced the proinflammatory cytokine tumor necrosis factor alpha and the Th1 cytokine gamma interferon. The B. pumilus strain was found to produce a bacteriocin-like activity against other Bacillus species.
Chemical examination of the octocoral-associated Bacillus sp. DT001 led to the isolation of pumilacidins A and C. Investigation of the effect of these compounds on the viability of Plasmodium falciparum and the mechanism of pumilacidin-induced death showed that inhibitors of protein kinase C (PKC) and phosphoinositide 3-kinase (PI3K) were able to prevent the effects of pumilacidins A and C. The results indicated that pumilacidins inhibit parasite growth via mitochondrial dysfunction and decreased cytosolic CaΒ²βΊ. This is a purely preclinical, in vitro finding.
Animal (Preclinical) Evidence:
A 2025 study published in Frontiers in Microbiology investigated gut microbiota dysbiosis, which significantly impacts ulcerative colitis (UC) progression and exacerbation, against which probiotics show promise in UC management. The study evaluated the effects of different doses of Bacillus pumilus LV149, an aquatic-derived probiotic, on gut injury repair in male C57BL/6 mice with dextran sulfate sodium (DSS)-induced ulcerative colitis (UC) and investigated the underlying mechanisms. Ulcerative colitis was induced by allowing mice free access to a 3% DSS solution for 7 days, with concurrent daily oral gavage of either a low (LV149-L, 1 Γ 10βΈ CFU/day/mouse) or high (LV149-H, 1 Γ 10βΉ CFU/day/mouse) dose of LV149. The study demonstrated that LV149, particularly at the higher dose, effectively mitigated DSS-induced colonic injury by modulating gut microbiota, enhancing gut barrier integrity, and reducing inflammation. The dose-dependent effects underscored LV149-H's potential as a therapeutic agent for UC due to its stronger anti-inflammatory properties and gut-protective effects.
Inflammatory cytokines such as IL-1Ξ², IL-6, and TNF-Ξ± are key mediators of UC pathology; in DSS-induced UC, these cytokines are abnormally upregulated, promoting inflammation and further tissue damage. In the LV149 study, LV149 significantly reduced the expression of these pro-inflammatory cytokines, particularly at the higher dosage (LV149-H), while the lower dosage (LV149-L) showed a trend toward improvement. This dose-dependent effect suggests that LV149 modulates the inflammatory response by reducing the production of key inflammatory cytokines.
In animal models, B. pumilus supplementation has been associated with improved gut barrier function and increased populations of beneficial bacteria. Evidence strength note: Given these properties, Bacillus pumilus LV149 may hold potential as a probiotic for human gastrointestinal health; however, to date, no studies have explored its role in gut injury repair in humans.
In vitro and Animal Evidence:
Evidence of colonization, immunostimulation, and antimicrobial activity support the hypothesis that the organisms have a potential probiotic effect. Spores of B. pumilus were found to induce the proinflammatory cytokine interleukin-6 in a cultured macrophage cell line, and in vivo, spores of B. pumilus induced the proinflammatory cytokine tumor necrosis factor alpha and the Th1 cytokine gamma interferon.
Multiple animal studies, primarily in poultry, have examined immunomodulatory effects. B. pumilus improves the growth performance of broilers, the feed conversion rate, and composition of intestinal flora; stimulates the immune system; produces antibacterial compounds; protects the body from pathogens; and increases the survival rate of chicks, according to previous research.
A 2024 study (PMC11082403) evaluated B. pumilus TS2, isolated from yaks, for its impact on growth performance, gut microbial community, antioxidant activity, and cytokines related to immunity and inflammation in broilers. A separate 2024 study on B. pumilus TS1 examined anti-inflammatory properties in a lipopolysaccharide (LPS) challenge model in broilers, investigating whether Bacillus pumilus TS1 improves growth performance and alleviates inflammatory damage. The study divided 240 one-day-old AA308 white-feathered broilers into five groups (con, LPS, TS1L + LPS, TS1M + LPS, and TS1H + LPS).
Additionally, a study investigating B. pumilus TS1 in the context of Salmonella Enteritidis-induced intestinal injury divided 120 6-day-old white-feathered broilers into four groups (con, TS1, SE, TS1 + SE). TS1 and TS1 + SE group chickens were fed with 1.4 Γ 10β· colony-forming units per mL of TS1 for 15 days and intraperitoneally injected with SE to establish the oxidative stress model.
Evidence strength: All immune-modulation evidence for B. pumilus in the context of human or companion-animal dietary use comes from in vitro systems and experimental animal models. Scientific validation for B. pumilus primarily stems from in vitro studies and animal models. No peer-reviewed, randomized controlled trials in human subjects examining immune outcomes with B. pumilus as a dietary supplement have been identified in the available literature.
A marine-isolated strain of Bacillus pumilus (SF214) produces at least two different molecules with antibacterial activity: a molecule smaller than 3 kDa active against Staphylococcus aureus and a molecule larger than 10 kDa active against Listeria monocytogenes. The anti-Staphylococcus molecule showed activity at a wide range of pH conditions, with its secretion dependent on the growth phase, medium, and temperature.
Results showed that B. pumilus APC 4184 exhibits a broad inhibitory spectrum, mainly against gram-positive bacteria. The novel circular bacteriocin pumilarin X (7,045 Da) was produced during early growth phase and identified as the anti-Listeria metabolite.
A strain of B. pumilus isolated from black tiger shrimp (Penaeus monodon) was found to have high salt tolerance and to inhibit the growth of marine pathogens, including Vibrio alginolyticus, when cultured together.
Evidence strength: Antimicrobial activity of B. pumilus metabolites is well-documented in vitro. These findings establish mechanistic plausibility but have not been translated into human clinical trials demonstrating therapeutic efficacy against infectious pathogens.
The largest body of controlled experimental evidence for B. pumilus pertains to its use as a feed additive in livestock and aquaculture, rather than human supplementation.
Weaned Pigs β Human Study Analogue (Controlled Animal Trial): Forty-eight individually housed pigs (8.7 Β± 0.26 kg) weaned at 28 Β± 1 day of age were used in a 22-day study to evaluate the effect of oral administration of a Bacillus pumilus spore suspension on growth performance and health indicators. Treatments were: (1) non-medicated diet; (2) medicated diet with apramycin (200 mg/kg) and pharmacological levels of zinc oxide (2,500 mg zinc/kg); and (3) B. pumilus diet (non-medicated diet + 10ΒΉβ° spores/day B. pumilus). Final body weight and average daily gain tended to be lower and feed conversion ratio was worsened for the medicated treatment compared to the B. pumilus treatment. Ileal E. coli counts were lower for the B. pumilus and medicated treatments compared to the non-medicated treatment, perhaps as a result of increased ileal propionic acid concentrations.
Weaned Pigs β Disease Challenge Model (PMC7491085): An experiment investigated the effects of two Bacillus spp. strains β Bacillus subtilis DSM 32540 and Bacillus pumilus DSM 32539 β on growth performance, diarrhea, intestinal health, microbiome, and systemic immunity of weaned pigs experimentally infected with an enterotoxigenic Escherichia coli (ETEC).
Pigs β Lawsonia intracellularis Challenge: A study compared the effect of Bacillus amyloliquefaciens, Bacillus licheniformis, and Bacillus pumilus on L. intracellularis infection. The results were directly compared to those obtained with a commercial live L. intracellularis vaccine. At three weeks of age, pigs were either vaccinated, supplied feed supplemented with one of the three probiotics, or remained non-treated.
Poultry (SA388 Strain): Bacillus pumilus SA388 was isolated from chicken feces and confirmed to be a probiotic. The selected strain was tested for its antimutagenic and antioxidant capabilities before being employed as a probiotic food supplement and antibiotic alternative. The effect of B. pumilus SA388 on broiler chickens' growth performance, gut microbiome, blood biochemical markers, immunological response, and meat quality was also studied.
Aquaculture: Bacillus pumilus is a host-associated probiotic of recent interest in aquaculture. Use of B. pumilus as a known nitrogen removal bacterium together with periphytic algae in a biofloc system reduced total ammonia and nitrite. A strain of Bacillus pumilus LV149 was previously isolated from the gut mucosa of healthy Litopenaeus vannamei and shown to exhibit significant extracellular protease, lipase, and amylase activities, while effectively inhibiting Vibrio parahaemolyticus infection without causing hemolysis.
Evidence strength: Feed-additive studies in livestock are controlled but conducted in non-human species. They demonstrate proof-of-concept for probiotic mechanisms but cannot be directly extrapolated to human health outcomes or supplementation.
Though not a direct human dietary supplement application, B. pumilus's role in agriculture is scientifically well-characterized and directly relevant to understanding its ecological niche. Research based on growing plants on Murashige and Skoog liquid medium proved that the strain B. pumilus LZP02 is able to promote rice growth by increasing root length, root surface area, number of nodes, root tips, forks, and chlorophyll content. The application also caused an increase in nitrogen, phosphorus, calcium, and magnesium contents in rice roots. B. pumilus TUAT1 significantly enhanced growth, root development, and nutrient absorption in 21-day-old rice seedlings compared to the control.
Human clinical studies remain limited, and thus definitive claims regarding the probiotic efficacy of B. pumilus cannot yet be made. Some studies have explored its role in modulating the gut microbiome, supporting digestive health, and enhancing immune responses, although these effects are mainly documented in preclinical settings. As of the available literature, no published randomized controlled trials in humans specifically using B. pumilus as a defined single-strain or primary ingredient dietary supplement with human health outcomes have been identified. The existing preclinical body of work provides mechanistic rationale but does not constitute clinical evidence.
B. pumilus is principally administered in its spore form. Dosages reported in the scientific literature vary widely by application, species, and strain:
For healthy individuals, Bacillus pumilus is generally considered non-pathogenic, meaning it does not typically cause disease. Its long-standing use in fermented foods, along with its GRAS (Generally Recognized As Safe) status in certain applications, supports its safety profile.
The European Food Safety Authority (EFSA) maintains a Qualified Presumption of Safety (QPS) process for microorganisms intended for use in food and feed. Two papers confirmed the need for the qualification of the absence of toxigenic potential and the antimicrobial resistance genes for Bacillus pumilus. This indicates that B. pumilus does not currently hold unconditional QPS status from EFSA; rather, per-strain demonstration of absence of toxigenicity and absence of clinically relevant antimicrobial resistance genes is required for approval. EFSA considers the QPS approach to safety assessment to require the identity of the strain to be conclusively established, evidence that the strain is not toxigenic, and that it does not show resistance to antibiotics of human and veterinary importance.
Bacillus pumilus is a ubiquitous spore-forming bacterium that has rarely been implicated in extraintestinal infections, mostly in immunocompromised hosts. Of the non-anthrax Bacillus species, B. cereus, B. licheniformis, and B. pumilus may be more pathogenic in immunosuppressed hosts than other common Bacillus species (B. subtilis or B. megaterium). However, Bacillus pumilus has rarely been reported as a human pathogen.
There have been rare instances of B. pumilus causing active infections, with symptoms of postprandial epigastric pain and diarrhea, with dizziness, headaches, back pain, and chills that can persist for several days. B. pumilus has also been associated with a case of septic arthritis, cutaneous infections similar to anthrax lesions, central venous catheter infections, and sepsis in newborns and immunocompromised individuals.
A case report published in 2024 documented B. pumilus cellulitis with bacteremia in a person who injects drugs living with HIV-HCV co-infection.
Toxin-producing B. pumilus has been detected in guinea pigs with experimentally induced enterocolitis, and components produced by B. pumilus have shown toxicity against mice and eukaryotic cells. A published case report documented a case of a B. pumilus-caused food poisoning in an adult male; a 51-year-old Japanese man complained of severe abdominal cramps, fever with chills, diarrhea, dizziness, and loss of appetite after eating reheated rice with stewed minced meat. Bacillus pumilus was isolated from blood culture and was identified using a biochemical test and 16S rRNA gene sequencing analysis. The patient was treated with probiotics and ciprofloxacin and recovered after 3 days.
A literature reference cited in a case report notes food poisoning associated with pumilacidin-producing Bacillus pumilus in rice (From, Hormazabal, and Granum, 2007, Int J Food Microbiol 115:319β324). Several species of Bacillus are well-known pathogens for gastrointestinal disease; however, little is known about the pathogenicity of Bacillus pumilus. Due to its ubiquitous nature, B. pumilus is a gram-variable rod that is a common contaminant in clinical microbial studies.
Bacillus species are common contaminants of blood cultures, but clinically significant infection is rare. Risk factors for Bacillus bacteremia include intravenous drug use, hemodialysis, and leukemia. Intravascular catheters, pacemaker wires, skin or wound infections have all been reported as potential portals of entry for bacteremia with Bacillus.
B. pumilus has been reported to be sensitive to vancomycin and erythromycin in at least one case report, though susceptibility profiles are strain-dependent and systematic clinical antibiogram data are limited.
At least one article had a methodological problem identifying the causing agent of an endophthalmitis as B. pumilus or B. safensis. Given that B. pumilus and closely related species share >99.5% 16S rRNA gene identity, misidentification at the species level remains a real clinical and research concern.
Papers have confirmed the need for the qualification of the absence of toxigenic potential and the absence of antimicrobial resistance genes for Bacillus pumilus before regulatory approval for use in food or feed. This represents an active area of per-strain safety screening rather than a confirmed systemic risk.
The scientific evidence base for Bacillus pumilus as a human dietary supplement ingredient is at an early stage. Mechanistic evidence from in vitro systems and animal models is substantial, supporting plausible roles in gut health, immunomodulation, and antimicrobial defense. Controlled trials in livestock species β particularly weaned pigs and poultry β provide proof-of-concept for probiotic mechanisms, but these cannot be directly extrapolated to human efficacy. Scientific validation for B. pumilus primarily stems from in vitro studies and animal models. The complete absence of published human randomized controlled trials specifically using B. pumilus means that all health claims for this organism in human supplementation remain preliminary and unvalidated by clinical standards as of the reviewed literature.
Health conditions that Bacillus pumilus may help support.
Body systems that Bacillus pumilus may help support.