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Bacillus

Bacillus is a genus of Gram-positive, rod-shaped bacteria renowned for their ability to form endospores, which confer resistance to extreme environmental conditions such as heat, desiccation, and radiation. The genus name Bacillus derives from the Latin bacillus (diminutive of baculum, meaning "stick" or "rod"), reflecting the rod-shaped morphology of its members.^[1] These aerobic or facultatively anaerobic microbes are ubiquitous in nature, commonly found in soil, freshwater and marine environments, air, and the gastrointestinal tracts of humans and other animals.^[2] The genus comprises a heterogeneous collection of over 400 species, exhibiting diverse metabolic capabilities and ecological roles, from free-living saprophytes to opportunistic pathogens.^[3] Members of the Bacillus genus play significant roles in various fields due to their physiological versatility and spore-forming nature. Industrially, species like Bacillus subtilis serve as model organisms for genetic studies and are extensively utilized as cell factories for producing enzymes, antibiotics, and biofuels, owing to their rapid growth, protein secretion efficiency, and genetic tractability.^[4] In agriculture, certain Bacillus strains act as plant growth-promoting rhizobacteria, enhancing nutrient uptake and providing biocontrol against pathogens through antimicrobial compound production.^[5] However, some species pose health risks; Bacillus anthracis is the etiologic agent of anthrax, a potentially lethal zoonotic disease, while Bacillus cereus is implicated in food poisoning via toxin production.^[2]^[6] The taxonomy of Bacillus has evolved with advances in molecular phylogenetics, leading to reclassification of some species into related genera like Paenibacillus and Lysinibacillus, yet the core group remains defined by endospore formation and Gram-positive staining.^[3] Ongoing research highlights their biotechnological potential, including probiotic applications for gut health and environmental remediation, underscoring Bacillus as a cornerstone in microbiology.^[3]

Introduction

Overview

Bacillus is a genus of Gram-positive, rod-shaped bacteria that are capable of forming endospores, belonging to the phylum Bacillota. These organisms are typically aerobic or facultatively anaerobic, exhibiting versatile metabolic capabilities that contribute to their ecological adaptability.^[2]^[1] Members of the genus Bacillus are ubiquitous environmental microbes, commonly isolated from diverse habitats such as soil, freshwater and marine environments, air, and even the gastrointestinal tracts of animals. Their widespread distribution underscores their role in nutrient cycling and decomposition processes in natural ecosystems.^[7] The genus was established in 1872 by the German botanist Ferdinand Cohn, who formalized the classification based on morphological observations of spore-forming rods, marking a foundational contribution to early bacteriology. As of 2025, the genus comprises 115 validly described species, reflecting ongoing taxonomic refinements.^[8]^[1] Their endospore-forming ability enables survival under extreme conditions like heat, desiccation, and radiation. Notable species include B. subtilis, widely used as a model for genetic and cellular studies, and B. anthracis, a pathogen responsible for anthrax.^[2]^[9]

Etymology

The genus name Bacillus is derived from the Late Latin bacillus, a diminutive form of baculum meaning "stick," "staff," or "walking stick," which alludes to the characteristic rod-shaped morphology of the bacteria it describes.^[10] This linguistic root emphasizes the visual resemblance of the bacterial cells to small rods or staffs, a feature central to early microscopic observations in microbiology.^[11] The name was formally coined for the genus by German botanist and microbiologist Ferdinand Cohn in 1872, during his foundational studies on bacterial classification published in Beiträge zur Biologie der Pflanzen.^[8] Cohn, a pioneer in bacteriology, established Bacillus as a distinct genus by reclassifying earlier descriptions, such as Christian Gottfried Ehrenberg's 1835 Vibrio subtilis, into a new taxonomic framework based on morphology, spore formation, and physiological traits.^[12] Subsequent developments in microbial nomenclature have refined the broader classification of Bacillus, including a 2021 shift in the phylum name from Firmicutes to Bacillota, reflecting updated phylogenetic analyses and efforts to standardize prokaryotic taxonomy across databases like NCBI.^[13] This change, proposed by Whitman et al., maintains the genus name while aligning higher-level groupings with genomic evidence.^[14]

Taxonomy and Phylogeny

Phylogenetic Classification

The genus Bacillus is placed within the phylum Bacillota, class Bacilli, order Bacillales, and family Bacillaceae, encompassing aerobic, endospore-forming, rod-shaped bacteria primarily characterized by their Gram-positive cell wall composition.^[15] This taxonomic hierarchy reflects the evolutionary grouping of low G+C-content Gram-positive bacteria, with Bacillus serving as the type genus for the family.^[16] Historically, the genus underwent significant taxonomic revisions, notably in 2021 when the phylum Firmicutes was restructured based on phylogenetic analyses, renaming it Bacillota to better align with monophyletic clades derived from conserved protein sequences and 16S rRNA data.^[16] A major overhaul of the genus itself occurred around 2020–2021, driven by phylogenomic studies that revealed its polyphyletic nature; over 200 species previously assigned to Bacillus were transferred to more than 40 new genera to resolve inconsistencies in evolutionary relationships. These changes were prompted by the limitations of traditional markers like 16S rRNA gene sequences, which often failed to delineate clear boundaries due to horizontal gene transfer and sequence similarities exceeding 97% among distantly related strains, leading to reliance on whole-genome analyses such as average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH).^[17] Ongoing refinements as of 2024–2025 continue to incorporate high-throughput genomic sequencing, further adjusting classifications based on core genome phylogenies and pan-genome comparisons to ensure monophyly. Since the 2020 emendation, additional species have been described within the defined clades, increasing the total to approximately 115 as of November 2025.^[1]^[3] Phylogenetic studies using 16S rRNA sequences have historically shown Bacillus as a diverse assemblage branching within the Bacillaceae, but whole-genome approaches have confirmed its polyphyly, with core operational genes revealing multiple deep-branching clades not supported by single-gene trees. For instance, the B. subtilis and B. cereus clades remain central to the emended Bacillus sensu stricto, comprising the current approximately 115 species, while others form distinct lineages.^[17] This polyphyletic structure necessitated transfers, such as the thermophilic species to Geobacillus (established in 2001 and affirmed in recent phylogenomics) and the B. megaterium group to Priestia in 2020, highlighting closer evolutionary ties to environmental adaptations like thermophily or alkaliphily in these relatives.^[3]

Species Diversity

The genus Bacillus encompasses approximately 115 validly published species as recognized by the List of Prokaryotic names with Standing in Nomenclature (LPSN) as of 2025, a significant reduction from over 200 species prior to major taxonomic revisions. This contraction stems primarily from the 2020 emendation by Gupta et al., which restricted the genus to two main operational clades—the B. subtilis clade (Bacillus sensu stricto) and the B. cereus clade—based on phylogenomic analyses, relocating numerous polyphyletic species to over 40 new genera such as Priestia, Cytobacillus, and Peribacillus to better reflect monophyletic groupings. These core clades represent the foundational diversity within the modern circumscription of Bacillus, with the B. subtilis clade comprising aerobic, spore-forming rods often associated with soil and plant environments, and the B. cereus clade including species with varying pathogenic potentials. Prominent species in the B. subtilis clade include Bacillus subtilis, a saprophytic, Gram-positive bacterium ubiquitous in soil and widely utilized as a model organism for studying Gram-positive bacterial physiology, genetics, and sporulation due to its well-characterized genome and genetic tractability. In contrast, the B. cereus clade features Bacillus anthracis, the etiological agent of anthrax, distinguished by its virulence factors such as protective antigen and lethal toxin, enabling pathogenesis in mammals including humans. Bacillus cereus is another key member, notorious for causing foodborne gastroenteritis through production of emetic and diarrheal toxins, with outbreaks linked to contaminated rice and dairy products. Bacillus thuringiensis, closely related within the same clade, is renowned for its insecticidal crystal proteins (Cry toxins) that target lepidopteran larvae, making it a cornerstone of biological pest control in agriculture. Species delineation within Bacillus relies on integrated genomic and phenotypic criteria, including average nucleotide identity (ANI) values exceeding 95–96% for conspecific strains, digital DNA-DNA hybridization (dDDH) above 70%, and 16S rRNA gene sequence similarities greater than 98.7%. Additionally, DNA G+C content serves as a supporting metric, typically ranging from 35 to 50 mol% across the genus, with the B. cereus clade often at the lower end (around 35 mol%) and the B. subtilis clade higher (42–46 mol%). Recent taxonomic refinements, such as those proposed in 2024 reviews addressing polyphyly and genomospecies boundaries, continue to refine these thresholds using whole-genome sequencing to resolve ambiguous affiliations.

Morphology and Structure

Cell Morphology

Bacillus species are defined by their rod-shaped (bacillary) morphology, with vegetative cells typically measuring 0.5–2.5 µm in diameter and 1.2–10 µm in length.^[3]^[18] This elongated form distinguishes them from spherical or spiral bacteria and supports their classification within the genus. Cells of Bacillus commonly appear as single rods or in pairs (diplobacilli), though they may also form chains (streptobacilli) under certain growth conditions, such as during exponential or stationary phases where cell division may be asynchronous.^[19]^[20] The majority of Bacillus species are motile, facilitated by peritrichous flagella that surround the cell body and enable swimming in liquid environments, though exceptions exist in non-motile species like Bacillus anthracis.^[3] While most exhibit straight rods, some environmental isolates show slight curvature, contributing to morphological diversity within the genus.^[19]

Cell Wall and Envelope

Bacillus species are Gram-positive bacteria distinguished by a robust cell wall featuring a thick peptidoglycan layer, typically measuring 20-80 nm in thickness, which imparts mechanical strength and rigidity to the cell. This peptidoglycan matrix consists of alternating N-acetylglucosamine and N-acetylmuramic acid units cross-linked by short peptide chains, forming a mesh-like structure that envelops the protoplast.^[21] Embedded within this layer are teichoic acids, which are anionic glycerol- or ribitol-based phosphate polymers covalently linked to the peptidoglycan, contributing to cell wall expansion, ion homeostasis, and interactions with the environment.^[22] Additionally, lipoteichoic acids, amphipathic molecules anchored to the cytoplasmic membrane via lipid moieties and extending through the peptidoglycan, further stabilize the envelope and modulate surface charge.^[23] Many Bacillus species assemble S-layer proteins on the outermost surface of the cell wall, forming a paracrystalline monolayer that enhances structural integrity against osmotic and mechanical stresses. These proteins, often glycosylated or organized into lattice arrays with lattice constants of 10-20 nm, also promote adhesion to host tissues or environmental substrates, playing a key role in colonization and pathogenicity.^[24] In certain species, such as B. anthracis, the S-layer interacts with secondary cell wall polymers to anchor the structure securely to the peptidoglycan.^[25] Pathogenic members of the genus, exemplified by Bacillus anthracis, produce an extracellular capsule composed of poly-γ-D-glutamic acid, a homopolymer of D-glutamate residues linked via γ-carboxyl groups, which surrounds the cell wall and shields it from host immune defenses. This capsule, synthesized by plasmid-encoded enzymes, is antiphagocytic and non-immunogenic, allowing evasion of opsonization.^[26] The capsule's negative charge repels antimicrobial peptides and complements the underlying S-layer for comprehensive envelope protection.^[27] In Gram staining, Bacillus cells generally appear purple due to the retention of crystal violet-iodine complexes within the thick peptidoglycan layer, confirming their Gram-positive status. However, staining can be variable in older cultures or those with prominent endospores, where decolorization may occur unevenly, leading to mixed purple and pink appearances.^[28]

Endospore Formation

Endospore formation, known as sporulation, in Bacillus species is a tightly regulated developmental response to adverse environmental conditions, primarily nutrient limitation such as starvation for carbon, nitrogen, or phosphorus. This process ensures survival by producing dormant, highly resistant endospores within a sacrificial mother cell. Sporulation proceeds through seven morphologically defined stages (I–VII), beginning with the activation of the Spo0A transcription factor in response to stress signals detected via kinases like KinA. In stage II, the cell undergoes asymmetric division, generating a smaller forespore compartment and a larger mother cell separated by an intermembrane peptidoglycan layer. The mother cell then engulfs the forespore (stage III), surrounding it with two membranes, after which the cortex—a layer of modified peptidoglycan—forms (stage IV) to maintain the forespore's dehydrated state. Subsequent stages involve coat assembly (stage V), spore maturation with dehydration and pigment accumulation (stage VI), and finally lysis of the mother cell (stage VII) to release the mature endospore. This entire process, lasting 6–8 hours in Bacillus subtilis under optimal conditions, requires coordinated gene expression between the two compartments via sigma factors σ^F and σ^E in the forespore and mother cell, respectively.^[29] The mature endospore features a multilayered structure that underpins its resilience. At the core lies a dehydrated cytoplasm with low water activity (approximately 25–50% of vegetative cell levels), containing the genome protected by small acid-soluble proteins (SASPs), ribosomes, and high concentrations of dipicolinic acid (DPA) complexed with Ca^{2+} ions, which facilitates dehydration and stabilizes macromolecules against damage. Surrounding the core is the germ cell wall, followed by the cortex of loosely cross-linked peptidoglycan that prevents premature hydration while being susceptible to lytic enzymes during germination. The coat, comprising over 70 proteins organized into inner, outer, and crust layers, forms a rigid barrier impermeable to many chemicals and enzymes. In certain species like Bacillus anthracis and Bacillus cereus, an additional exosporium—a glycoprotein-rich, balloon-like envelope—encases the coat, potentially aiding in host interactions and further shielding against environmental threats.^[30]^[31]^[32] These structural features endow Bacillus endospores with exceptional resistance, allowing survival under conditions lethal to vegetative cells. They tolerate wet heat up to 120°C for minutes (e.g., Bacillus stearothermophilus spores survive autoclaving at 121°C for 10–15 minutes), dry heat exceeding 150°C, ionizing radiation doses 5–50 times higher than those killing vegetative bacteria, UV radiation through DNA photoproduct repair by SASPs, desiccation for decades (with viable Bacillus spores recovered from ancient samples), and chemical stresses including oxidizing agents, aldehydes, and acids. Resistance mechanisms include the core's low water content minimizing chemical reactions, the coat's exclusion of large toxic molecules, and the cortex's role in stabilizing dormancy; for instance, B. subtilis spores can remain viable for over 50 years in dry soil.^[31] Germination reverses sporulation, transforming the dormant endospore into a metabolically active vegetative cell when conditions improve. Nutrient germinants, such as L-alanine or inosine binding to Ger receptors in the inner membrane, initiate the process by triggering rapid ion release (Ca-DPA), cortex hydrolysis by lytic enzymes like CwlJ, and water influx, completing within minutes. Alternatively, heat activation (e.g., 5–10 minutes at 80–95°C) sensitizes spores to nutrients by damaging inhibitory factors, enhancing germination efficiency. This tightly controlled activation ensures spores germinate only in hospitable environments, minimizing energy waste.^[33]

Physiological Characteristics

Growth and Metabolism

Bacillus species display a range of oxygen tolerances, with most being strict aerobes that rely on aerobic respiration via cytochrome-based electron transport systems for energy generation. However, facultative anaerobes like Bacillus subtilis can adapt to oxygen limitation by performing anaerobic respiration using nitrate or nitrite as terminal electron acceptors, or by shifting to fermentation pathways that produce mixed acids such as acetate, lactate, and ethanol when external acceptors are unavailable.^[34]^[35] These bacteria are predominantly heterotrophic, exhibiting nutritional versatility by metabolizing diverse carbon sources including simple sugars via glycolysis, complex carbohydrates like starches through extracellular amylases, and proteins via proteases. This enzymatic capability enables efficient breakdown of polymeric substrates in nutrient-poor environments. Additionally, certain species, such as Bacillus megaterium and Paenibacillus polymyxa (formerly Bacillus polymyxa), can fix atmospheric nitrogen, supporting growth in nitrogen-deficient conditions through symbiotic or free-living associations.^[19]^[36] Growth optima vary by species, with mesophilic Bacillus typically thriving at temperatures between 20°C and 40°C, often peaking around 30–37°C for model organisms like B. subtilis. Thermophilic members, such as Geobacillus stearothermophilus (formerly Bacillus stearothermophilus), exhibit higher optima up to 55–65°C, reflecting adaptations in membrane lipids and enzymes for thermal stability. Regarding pH, most species tolerate a broad range of 5 to 9, with neutrophilic growth favored near pH 7, maintained by robust cytoplasmic buffering systems that preserve internal pH homeostasis during external fluctuations. The production of degradative enzymes like α-amylases and subtilisin proteases not only aids nutrient acquisition but also underpins their industrial utility in processes requiring starch hydrolysis and protein degradation.^[37]^[3]^[38]^[39]

Environmental Adaptations

Bacillus species exhibit remarkable adaptability to diverse environmental stresses through the formation of biofilms, which provide protection and facilitate colonization in both soil and aquatic habitats. In soil environments, Bacillus subtilis forms complex biofilms that enhance community diversity and resilience against desiccation and nutrient scarcity by embedding cells in an extracellular matrix of polysaccharides and proteins, promoting interactions with clay minerals for stability. Similarly, in aquatic settings, marine Bacillus strains increase biofilm production under warmer conditions, utilizing amyloid fibers to bolster ecological fitness and resistance to hydrodynamic forces and predation. These biofilms not only shield against abiotic stressors like UV radiation and fluctuating pH but also enable surface attachment, allowing Bacillus to exploit micro-niches in dynamic ecosystems. To compete for limited resources, Bacillus species produce antimicrobial compounds and iron-chelating siderophores, which confer selective advantages in nutrient-poor environments. For instance, Bacillus licheniformis synthesizes bacitracin, a peptide antibiotic that inhibits competing Gram-positive bacteria, thereby reducing microbial competition in soil and rhizosphere settings. Complementing this, species such as Bacillus subtilis generate siderophores like bacillibactin, which sequester iron from the surroundings, limiting its availability to rivals and supporting Bacillus growth in iron-restricted habitats like alkaline soils or aquatic sediments. These secondary metabolites are regulated by environmental cues, such as iron limitation or population density, ensuring efficient resource acquisition and community dominance. Certain Bacillus species have evolved as extremophiles, thriving in conditions lethal to most mesophiles and showcasing specialized physiological adaptations. Alkaliphilic variants, including Alkalihalobacillus pseudofirmus (formerly Bacillus pseudofirmus) and Alkalihalobacillus alcalophilus (formerly Bacillus alcalophilus), maintain optimal growth at pH 9–11 through mechanisms like high intracellular proton concentrations and modified cell wall compositions that prevent alkali-induced lysis in soda lake sediments. Moderately halophilic species, such as Bacillus coahuilensis isolated from hypersaline lagoons, accumulate compatible solutes like ectoine to stabilize proteins and membranes under salt concentrations up to 15% NaCl, enabling persistence in evaporative environments like solar salterns. Psychrophilic Bacillus strains, exemplified by Bacillus psychrophilus isolated from cold marine sediments and polar soils, produce cold-active enzymes and antifreeze proteins that facilitate metabolism at temperatures near 0°C, with optimal growth around 15–20°C, allowing colonization of permafrost and deep-sea habitats.^[40] Genetic plasticity further enhances Bacillus adaptability via horizontal gene transfer (HGT), which introduces beneficial traits for surviving variable conditions. In Bacillus subtilis, HGT occurs readily during swarm interactions at colony boundaries, mediated by competence genes and stress responses, allowing acquisition of antibiotic resistance or metabolic genes from neighboring cells in biofilms or soil consortia. Experimental evolution studies demonstrate that HGT integrates foreign DNA fragments, often from mobile elements, to rapidly expand the pangenome and confer advantages like enhanced nutrient scavenging in fluctuating environments, underscoring its role in long-term ecological persistence.

Isolation and Identification

Laboratory Isolation Methods

Laboratory isolation of Bacillus species typically begins with the collection of environmental samples such as soil or water, followed by serial dilution in sterile saline or phosphate buffer to reduce competing microorganisms.^[41] A key step involves heat shock treatment, where the diluted sample is heated at 60–80°C for 10–20 minutes to eliminate vegetative bacterial cells while activating and enriching heat-resistant endospores characteristic of Bacillus.^[42] This method, often referred to as thermal activation or pasteurization, selectively favors spore-formers by inactivating non-spore-forming competitors, with temperatures around 80°C for 10 minutes commonly used for soil suspensions.^[41] Post-treatment, the sample is cooled rapidly and plated onto non-selective media like nutrient agar for initial colony development, or selective media such as mannitol-egg yolk-polymyxin (MYP) agar, which inhibits many non-Bacillus species through polymyxin sulfate while allowing lecithinase-positive colonies (e.g., Bacillus cereus group) to appear as distinctive turquoise-blue zones.^[43] For targeted isolation of specific Bacillus subgroups, enrichment cultures exploit their physiological adaptations prior to plating. Alkaliphilic strains are enriched in broth media adjusted to pH 9–10, often supplemented with peptone, glucose, or yeast extract, incubated at 30–37°C for 24–48 hours to promote growth of alkali-tolerant spore-formers from alkaline soil or sediment samples.^[44] Similarly, halophilic Bacillus species are isolated using high-salt enrichment in media containing 5–15% NaCl, such as nutrient broth amended with sodium chloride, to select for salt-tolerant variants from saline environments like solar salterns or hypersaline waters.^[45] These enrichment steps, combined with heat shock, yield pure cultures upon streaking onto solid media, following standard aseptic techniques outlined in contemporary microbiological protocols as of 2024.^[46] Incubation occurs aerobically at 25–37°C for 24–72 hours, with colonies exhibiting typical Bacillus morphology—large, irregular, and opaque—subsequently subcultured for further processing.^[47]

Identification Techniques

Identification of Bacillus species begins with classical microbiological techniques that confirm key morphological and physiological traits. Gram staining reveals these bacteria as Gram-positive, rod-shaped cells, often appearing as chains or singles, which distinguishes them from Gram-negative counterparts.^[48] Spore staining, typically using malachite green, highlights the characteristic endospores, which are central or terminal and resistant to heat and chemicals, a hallmark feature for presumptive identification.^[49] Motility tests, such as the hanging drop or wet mount method, demonstrate peritrichous flagella in most species, confirming their aerobic, motile nature.^[20] Additionally, the catalase test yields a positive reaction, producing bubbles upon addition of hydrogen peroxide, aiding differentiation from catalase-negative genera like Clostridium.^[50] Biochemical assays provide further differentiation by assessing metabolic capabilities. The API 50CHB system, a commercial strip containing 50 substrates, evaluates carbohydrate fermentation patterns, such as acid production from glucose, arabinose, and mannitol, which vary among species and enable species-level profiling with high accuracy when combined with reference databases.^[51] Oxidase testing shows variability, with most Bacillus species oxidase-negative, though exceptions like B. pumilus may test positive, helping to narrow identifications within the genus.^[52] Molecular tools offer precise, culture-independent confirmation, particularly for taxonomically complex groups. 16S rRNA gene sequencing targets conserved and variable regions of this housekeeping gene, achieving >90% genus-level accuracy and 65-83% species-level resolution by comparing sequences to databases like SILVA or NCBI, though intragenus similarity can limit fine-scale discrimination.^[53] MALDI-TOF mass spectrometry analyzes whole-cell protein profiles via matrix-assisted laser desorption/ionization, providing rapid species identification (e.g., distinguishing B. cereus group members) with >95% accuracy after database matching, surpassing traditional methods in speed and cost for clinical isolates.^[54] For pathogenic species, PCR assays detect toxin genes, such as ces for emetic B. cereus or pagA in B. anthracis, enabling virulence assessment and outbreak tracing with high specificity.^[55] As of 2025, advances in whole-genome sequencing (WGS) address taxonomic flux in Bacillus by employing average nucleotide identity (ANI) calculations, where values ≥95-96% delineate species boundaries, revealing novel rearrangements and improving delineation amid the genus's polyphyletic nature.^[56] This approach, integrated with phylogenomics, outperforms 16S rRNA for resolving cryptic species, as demonstrated in analyses of over 10,000 genomes.

Ecology

Natural Habitats

Bacillus species are ubiquitous in terrestrial and aquatic environments, with soil serving as their primary natural habitat. In soil, these bacteria are highly abundant, often reaching concentrations of up to 10^6 spores per gram, owing to their ability to form resilient endospores that persist in diverse conditions.^[57] They are also commonly found in freshwater systems and sediments, where they constitute approximately 1% of the microbial community on average, though their relative abundance can vary significantly across sites.^[58] Additionally, Bacillus thrives in plant rhizospheres, colonizing the root zones of various crops and wild plants, where they interact with root exudates to establish dense populations.^[59] Beyond temperate and standard soils, Bacillus species inhabit extreme niches that highlight their environmental versatility. Thermophilic strains, such as those in the genus Bacillus, are isolated from hot springs with temperatures ranging from 50°C to 95°C, enabling survival in geothermal environments.^[60] Halophilic variants occur in hypersaline lakes and brine sediments, including deep-sea anoxic basins like those in the Eastern Mediterranean, where they tolerate high salinity levels.^[61] Psychrophilic Bacillus are present in arctic and polar soils, adapting to subzero temperatures and contributing to cold permafrost microbiomes.^[2] Globally, Bacillus exhibits a wide distribution across continents, with higher species diversity observed in tropical soils compared to temperate or polar regions, reflecting climatic influences on microbial richness.^[62] Their dispersal is facilitated by airborne mechanisms, particularly via dust storms that carry viable spores over long distances, promoting colonization of distant habitats.^[63] The abundance of Bacillus in these habitats is influenced by edaphic factors, including the decomposition of organic matter, which provides carbon sources for growth, and variations in soil pH, which can selectively favor certain species.^[64]^[65] These elements drive population dynamics, with neutral to slightly alkaline pH often correlating with higher densities in fertile soils.^[66]

Microbial Interactions

Bacillus species exhibit antagonistic interactions with other microbes through the production of antimicrobial compounds, including bacteriocins and antibiotics, which inhibit competitors such as fungi and bacteria in soil environments. For instance, Bacillus licheniformis produces bacteriocins like lichenicidin and lichenin that target Gram-positive and Gram-negative bacteria, as well as fungal pathogens, by disrupting cell envelopes and metabolic processes. Similarly, Bacillus subtilis synthesizes antibiotics such as bacillaene and surfactin, which suppress fungal growth, including Fusarium species, by interfering with hyphal development and spore germination, thereby reducing competition for resources in the rhizosphere. These mechanisms contribute to disease suppression in plant-associated microbial communities, with studies showing up to 80% inhibition of phytopathogenic fungi by Bacillus-derived compounds.^[67]^[68]^[69] In symbiotic associations, certain Bacillus strains, particularly Bacillus amyloliquefaciens, function as plant growth-promoting rhizobacteria (PGPR) by colonizing plant roots and enhancing host fitness through mutualistic interactions. B. amyloliquefaciens promotes plant growth by solubilizing phosphates, fixing nitrogen, and producing indole-3-acetic acid (IAA), which stimulates root elongation and nutrient uptake, leading to improved seedling vigor in crops like maize and tomato. These symbiotic relationships also involve induced systemic resistance (ISR) against pathogens, where bacterial elicitors trigger plant defense pathways without direct antagonism. Field trials have demonstrated 20-30% increases in plant biomass attributed to such PGPR traits in B. amyloliquefaciens.^[70]^[71]^[72] Bacillus species engage in quorum sensing (QS) to coordinate behaviors within biofilm communities in soil microbiomes, facilitating collective responses to population density. In Bacillus subtilis, the ComX pheromone acts as a QS signal to regulate competence and biofilm matrix production, enabling cells to form structured communities that enhance adhesion to surfaces and resistance to environmental stresses. These QS-mediated biofilms integrate with diverse soil microbes, modulating community structure by promoting cooperative gene expression for exopolysaccharide synthesis and sporulation. Interactions with fungi, such as Setophoma sp., can select for QS mutants in B. subtilis, altering biofilm dynamics and microbial diversity in the rhizosphere.^[73]^[74]^[75] Predatory interactions involving Bacillus contribute to soil microbial dynamics, where species like B. subtilis defend against predators such as Myxococcus xanthus through antimicrobial production and sporulation. B. subtilis resists predation by secreting bacillaene, which inhibits M. xanthus motility and fruiting body formation, achieving up to 68% survival rates for ancestral strains compared to less than 1% for sensitive lab strains. Additionally, Bacillus plays a key role in nutrient cycling via decomposition, breaking down organic matter through enzyme secretion like cellulases and proteases, which releases carbon and nitrogen for other soil organisms. This decomposer activity supports ecosystem nutrient turnover, with Bacillus communities enhancing soil fertility by recycling up to 40% of plant residues in agricultural soils.^[76]^[77]^[78]

Significance

Pathogenic and Clinical Roles

Bacillus anthracis is the primary pathogenic species within the genus, responsible for anthrax, a zoonotic disease that manifests in three main forms depending on the route of infection: cutaneous, inhalational, and gastrointestinal. Cutaneous anthrax, the most common form, occurs when spores enter through skin abrasions and typically presents as a painless black eschar surrounded by edema, with a mortality rate of less than 1% when treated promptly. Inhalational anthrax results from spore inhalation into the lungs, leading to severe systemic infection with symptoms including fever, chest pain, and hemorrhagic mediastinitis, and has a high mortality rate of up to 45% with treatment (90% untreated).^[79] Gastrointestinal anthrax arises from ingestion of contaminated meat, causing abdominal pain, bloody diarrhea, and systemic toxemia, with mortality rates up to 60% in untreated cases. The virulence of B. anthracis is primarily driven by two plasmid-encoded components: the poly-γ-D-glutamic acid capsule, encoded by pXO2, which inhibits phagocytosis, and the tripartite toxin complex on pXO1, consisting of protective antigen (PA), lethal factor (LF), and edema factor (EF). The lethal toxin (PA + LF) disrupts immune cell signaling and induces macrophage lysis, while the edema toxin (PA + EF) elevates intracellular cAMP, impairing neutrophil function and promoting edema. These factors enable rapid bacterial dissemination and host death, facilitating spore release into the environment. Epidemiologically, anthrax is sporadic in humans, often linked to handling infected animal products in endemic regions like parts of Africa, Asia, and the Americas, with global incidence estimated at 2,000 to 100,000 cases annually, though underreporting is likely.^[80] However, B. anthracis poses a significant bioterrorism risk due to its spore stability and ease of aerosolization, as demonstrated by the 2001 U.S. attacks that caused 22 cases and 5 deaths. Treatment involves prompt administration of antibiotics such as ciprofloxacin or doxycycline, often combined with antitoxins like raxibacumab for severe cases, and supportive care; the anthrax vaccine adsorbed (AVA, BioThrax) provides pre-exposure prophylaxis for at-risk groups and post-exposure protection when paired with antibiotics. Diagnosis relies on culture from clinical specimens and confirmatory real-time PCR targeting toxin genes, enabling rapid identification. Bacillus cereus is another notable pathogen, causing two distinct types of foodborne illness: the emetic syndrome, characterized by rapid-onset nausea and vomiting due to preformed cereulide toxin in contaminated rice or pasta, and the diarrheal syndrome, involving enterotoxins (e.g., hemolysin BL, non-hemolytic enterotoxin) that lead to abdominal cramps and watery diarrhea 8-16 hours post-ingestion. These illnesses are typically self-limiting, lasting 24 hours, but can be severe in vulnerable populations like infants or the immunocompromised. Virulence in B. cereus stems from plasmid- or chromosomally encoded toxins, with cereulide acting as a superantigen-like emetic agent and enterotoxins causing fluid secretion and tissue damage in the gut. Globally, B. cereus accounts for 1.4% to 12% of reported foodborne outbreaks, with an estimated 94% of infections being food poisoning cases and a very low mortality rate of approximately 0.05%, though underreporting is common due to mild symptoms; major concerns involve improper food storage in rice-based dishes, affecting millions annually in temperate climates.^[81]^[82] Treatment for foodborne cases is supportive with hydration, as antibiotics are ineffective against preformed toxins, but severe systemic infections may require vancomycin or clindamycin. Diagnosis involves stool culture and toxin detection assays, though PCR for toxin genes is increasingly used in outbreak investigations.

Industrial and Biotechnological Applications

Bacillus species are extensively utilized in industrial biotechnology due to their robust spore-forming capabilities, high secretion efficiency for extracellular enzymes, and GRAS (Generally Recognized as Safe) status, enabling large-scale production processes.^[83] These Gram-positive bacteria contribute to sectors such as enzyme manufacturing, agriculture, animal nutrition, and environmental remediation, leveraging their metabolic versatility for sustainable applications.^[84] In enzyme production, Bacillus subtilis serves as a primary host for secreting subtilisin, a serine protease widely incorporated into laundry detergents for its alkaline stability and ability to break down protein-based stains at elevated temperatures.^[84] Subtilisin from B. subtilis enhances cleaning efficiency in commercial formulations, with optimized fed-batch fermentation yielding up to several grams per liter, reducing reliance on chemical alternatives.^[85] Similarly, Bacillus licheniformis produces thermostable α-amylase, essential for starch hydrolysis in food processing, textile desizing, and biofuel production, where it operates effectively at 90–100°C to convert starches into fermentable sugars.^[86] This enzyme's high yield in recombinant B. licheniformis strains supports industrial-scale liquefaction, improving energy efficiency in ethanol manufacturing.^[87] Bacillus thuringiensis is a cornerstone of biopesticide development, primarily through its production of Cry toxins—crystal proteins that form pores in the midgut epithelium of target insects, leading to paralysis and death.^[88] These toxins, such as Cry1 and Cry3 families, are applied in spray formulations or genetically engineered into crops like cotton and maize to control lepidopteran and coleopteran pests, reducing chemical pesticide use by up to 50% in integrated pest management systems.^[89] The specificity of Cry toxins minimizes non-target effects, making Bt-based products environmentally safer for agricultural applications worldwide.^[90] As probiotics and feed additives, Bacillus coagulans promotes gut health in both humans and livestock by modulating intestinal microbiota, enhancing nutrient absorption, and boosting immune responses.^[91] In animal husbandry, supplementation with B. coagulans spores improves average daily feed intake and growth performance in piglets and broilers, with studies showing up to 10% better weight gain through better protein digestion and reduced diarrhea incidence.^[92] For human applications, it alleviates symptoms of irritable bowel syndrome and supports metabolic health by producing lactic acid and short-chain fatty acids during sporulation and germination in the gut.^[93] Fermentation processes highlight Bacillus subtilis in the production of nattō, a traditional Japanese food where the bacterium ferments cooked soybeans at 40–42°C for 18–24 hours, yielding a mucilaginous product rich in vitamin K2 and nattokinase.^[94] This process involves B. subtilis subsp. natto initiating polyglutamic acid formation for texture and fibrinolytic enzymes for potential cardiovascular benefits, with industrial optimization ensuring consistent quality and safety.^[95] Additionally, Bacillus species produce biosurfactants like lipopeptides (e.g., surfactin from B. subtilis), which lower surface tension to enhance hydrocarbon emulsification in bioremediation efforts.^[96] These amphiphilic compounds facilitate the degradation of oil spills and heavy metals in contaminated soils and wastewater, with field applications demonstrating up to 70% removal efficiency for crude oil pollutants.^[97]

Use as Model Organisms

Bacillus subtilis stands as the premier model organism for Gram-positive bacteria, enabling in-depth investigations into genetics and sporulation processes. Its complete genome sequence, determined in 1997, spans 4,214,810 base pairs and encodes approximately 4,100 protein-coding genes, providing a foundational resource for genetic studies. This sequencing effort has supported the creation of extensive mutant libraries and high-throughput analyses, accelerating research on cellular differentiation and development. Since the 1990s, B. subtilis has been pivotal in sporulation research, with milestones including the identification of over 300 sporulation-related genes and the delineation of six key stages in the process.^[98]^[99]^[100] In synthetic biology, B. subtilis facilitates CRISPR-mediated genome editing and the design of synthetic gene circuits for optimized protein expression. CRISPR-Cas9 and Cpf1 systems have enabled precise multi-gene manipulations, including deletions and insertions, to fine-tune metabolic pathways and heterologous protein production. For example, engineered circuits based on quorum sensing have achieved high-level recombinant protein secretion, leveraging B. subtilis's natural competence and secretion machinery. Recent innovations include genetic code expansion techniques that incorporate up to 20 non-standard amino acids into proteins, broadening its applications in biotechnology.^[101]^[102]^[103]^[104] B. subtilis has advanced comprehension of quorum sensing, biofilms, and antibiotic resistance through its well-characterized regulatory networks. The ComQXPA quorum sensing system exemplifies how peptide signals coordinate biofilm formation and competence, influencing bacterial social behaviors. Biofilm studies in B. subtilis reveal intricate networks involving over 50 genes for appendages and extracellular matrix production, serving as a paradigm for Gram-positive community dynamics. Furthermore, investigations into B. subtilis biofilms have illuminated antibiotic resistance strategies, such as quorum sensing-mediated persistence and disruption of mature biofilms to enhance susceptibility.^[73]^[105]^[106]^[107] As of 2025, metagenomic analyses of microbial communities have increasingly employed B. subtilis as a chassis for engineering microbiome interactions. In rhizosphere studies, B. subtilis strains like H38 have been shown to reshape microbiome composition, promoting plant growth and stress tolerance through targeted genomic modifications informed by metagenomics. These efforts extend to aquaculture, where B. subtilis-based interventions enhance gut microbiome resilience and disease resistance in species like shrimp, integrating metagenomic data for synthetic chassis design. Such applications underscore B. subtilis's role in translating metagenomic insights into functional microbiome engineering.^[108]^[109]^[110]

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[PDF] Bacillus subtilis, the model Gram-positive bacterium - Hal-CEA
Dec 13, 2023 · genome [more than 300 genes for sporulation, and 51 for appendages, flagella (43) and pili (8), often grouped into islands]. The role of ...
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Milestones in Bacillus subtilis sporulation research - Microbial Cell
Nov 27, 2020 · In this review, we highlight foundational discoveries that shaped the sporulation field, from its origins to the present day, tracing a chronology that spans ...Abstract · B. Subtilis And The Genetic... · The Genetic Basis Of...Missing: paper | Show results with:paper
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CRISPR-assisted multi-dimensional regulation for fine-tuning gene ...
Feb 15, 2019 · A powerful tool kit to regulate the expression of multiple genes multi-directionally and multi-dimensionally in bacteria.
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Fragment Exchange Plasmid Tools for CRISPR/Cas9-Mediated ...
INTRODUCTION. Bacillus subtilis and its relatives have been widely used as bacterial hosts for the recombinant expression of heterologous proteins (1–3).
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Efficient Protein Expression and Biosynthetic Gene Cluster ...
Oct 26, 2023 · Efficient expression of recombinant proteins in Bacillus subtilis using a rewired gene circuit of quorum sensing. Biotechnology Progress ...
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Designing efficient genetic code expansion in Bacillus subtilis to ...
Sep 14, 2021 · Here we report broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins.
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The ComX Quorum Sensing Peptide of Bacillus subtilis Affects ...
We report that ComX signaling peptide deficient mutants form thicker and more robust pellicle biofilms that contain chains of cells.Missing: microbiomes | Show results with:microbiomes
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The Biofilm Regulatory Network from Bacillus subtilis: A Structure ...
Bacillus subtilis is an extensively studied model organism used to understand the process of biofilm formation. A complex network of principal regulatory ...
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Bacillus subtilis-derived peptides disrupt quorum sensing and ...
Aug 20, 2024 · We identify a single strain B. subtilis 6D1, with a potent ability to inhibit biofilm growth, disassemble mature biofilm, and improve antibiotic sensitivity.
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Modulation of the rhizosphere microbiome structure and ... - PubMed
Sep 30, 2025 · The rhizosphere microbiome critically determines plant health and productivity. This study investigated the impact of Bacillus subtilis H38 ...Missing: studies | Show results with:studies
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[PDF] Microbiome engineering to enhance disease resistance in aquaculture
Sep 16, 2025 · This principle is demonstrated in a study where dietary Bacillus subtilis. BSXE-1601 enhanced disease resistance of Penaeus vannamei against.
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[PDF] 1 Bacillus subtilis reprograms host transcriptome and rhizosphere ...
Oct 5, 2025 · Genomic insights into Bacillus subtilis MBB3B9 mediated aluminium stress mitigation for. 726 enhanced rice growth. Scientific Reports, 13(1) ...