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Bacillota
Bacillus subtilis, Gram-stained
Scientific classification Edit this classification
Domain: Bacteria
Kingdom: Bacillati
Phylum: Bacillota
Gibbons and Murray 2021[1]
Classes and incertae sedis[2]
Synonyms
  • "Bacillaeota" Oren et al. 2015
  • "Bacillota" Whitman et al. 2018
  • "Desulfotomaculota" Watanabe et al. 2019
  • "Endobacteria" (Cavalier-Smith 1998) Cavalier-Smith 2020
  • "Endobacteria" Cavalier-Smith 1998
  • "Endospora" Margulis and Schwartz 1998
  • "Firmacutes" Gibbons and Murray 1978 (Approved Lists 1980)
  • "Firmicutes" (Gibbons & Murray 1978) Garrity & Holt 2001
  • "Posibacteria" Cavalier-Smith 2002

The Bacillota (synonym "Firmicutes") are a phylum of bacteria, most of which have Gram-positive cell wall structure.[3] They have round cells, called cocci (singular coccus), or rod-like forms (bacillus).[citation needed] A few Bacillota, such as Megasphaera, Pectinatus, Selenomonas, and Zymophilus from the class Negativicutes, have a porous pseudo-outer membrane that causes them to stain Gram-negative.[citation needed] Many Bacillota produce endospores, which are resistant to desiccation and can survive extreme conditions.[citation needed] They are found in various environments, and the group includes some notable pathogens.[citation needed] Those in one family, the Heliobacteria, produce energy through anoxygenic photosynthesis.[citation needed] Bacillota play an important role in beer, wine, and cider spoilage.[citation needed]

Taxonomy

[edit]

The renaming of phyla such as Firmicutes in 2021 remains controversial among microbiologists, many of whom continue to use the earlier names of long standing in the literature.[4] The name "Firmicutes" was derived from the Latin words for 'tough skin', referring to the thick cell wall typical of bacteria in this phylum. Scientists once classified the Firmicutes to include all Gram-positive bacteria, but have recently defined them to be of a core group of related forms called the low-G+C group, in contrast to the Actinomycetota.[citation needed]

The group is typically divided into the Clostridia, which are anaerobic, and the Bacilli, which are obligate or optional aerobes.[citation needed] On phylogenetic trees, the first two groups show up as paraphyletic or polyphyletic, as do their main genera, Clostridium and Bacillus.[5] However, Bacillota as a whole is generally believed to be monophyletic, or paraphyletic with the exclusion of Mollicutes.[6]

Evolution

[edit]

The Bacillota are thought by some [7] to be the source of the archaea, by models where the archaea branched relatively late from bacteria, rather than forming an independently originating early lineage (domain of life) from the last universal common ancestor of cellular life (LUCA).[citation needed]

Phylogeny

[edit]

The currently accepted taxonomy based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[8] and the National Center for Biotechnology Information (NCBI).[9]

16S rRNA based LTP_01_2022[10][11][12] GTDB 08-RS214 by Genome Taxonomy Database[13][14][15]
"Clostridiia"
{Bacillota_A} ♦
"Bacillia"
{Bacillota} ♦

♦ Paraphyletic Firmicutes

Mycoplasmatota

Mollicutes [incl. Erysipelotrichia]

Bacillota G
Bacillota s.s.

"Bacillia" [incl. Alicyclobacillia; Desulfuribacillia; Culicoidibacteria]

Genera

[edit]

More than 274 genera were considered as of 2016 to be within the Bacillota phylum,[citation needed] notable genera of Bacillota include:

Bacilli, order Bacillales

Bacilli, order Lactobacillales

Clostridia

Erysipelotrichia

Clinical significance

[edit]
See also: Infectobesity

Bacillota can make up between 11% to 95% of the human gut microbiome.[16] The phylum Bacillota as part of the gut microbiota has been shown to be involved in energy resorption, and potentially related to the development of diabetes and obesity.[17][18][19][20] Within the gut of healthy human adults, the most abundant bacterium: Faecalibacterium prausnitzii (F. prausnitzii), which makes up 5% of the total gut microbiome, is a member of the Bacillota phylum. This species is directly associated with reduced low-grade inflammation in obesity.[21] F. prausnitzii has been found in higher levels within the guts of obese children than in non-obese children.

In multiple studies a higher abundance of Bacillota has been found in obese individuals than in lean controls. A higher level of Lactobacillus (of the Bacillota phylum) has been found in obese patients and in one study, obese patients put on weight loss diets showed a reduced amount of Bacillota within their guts.[22]

Diet changes in mice have also been shown to promote changes in Bacillota abundance. A higher relative abundance of Bacillota was seen in mice fed a western diet (high fat/high sugar) than in mice fed a standard low fat/ high polysaccharide diet. The higher amount of Bacillota was also linked to more adiposity and body weight within mice.[23] Specifically, within obese mice, the class Mollicutes (within the Bacillota phylum) was the most common. When the microbiota of obese mice with this higher Bacillota abundance was transplanted into the guts of germ-free mice, the germ-free mice gained a significant amount of fat as compared to those transplanted with the microbiota of lean mice with lower Bacillota abundance.[24]

The presence of Christensenella (Bacillota, in class Clostridia), isolated from human faeces, has been found to correlate with lower body mass index.[25]

See also

[edit]

References

[edit]
[edit]
Revisions and contributorsEdit on WikipediaRead on Wikipedia

Bacillota

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Bacillota is a phylum of bacteria within the domain Bacteria, primarily characterized by Gram-positive cell walls, low mol% G+C content in their DNA, and diverse morphologies including spheres (cocci), rods (bacilli), and filaments (branching or nonbranching). Formerly known as Firmicutes, the name Bacillota was formally adopted in 2021, derived from the type genus Bacillus and the neuter plural suffix -ota for phyla, reflecting its taxonomic position under the subphylum Bacillati. Members reproduce mainly by binary fission, exhibit varied motility (some flagellated, most nonmotile), and display metabolic versatility as aerobes, anaerobes, or facultative anaerobes; many form resilient endospores or spores on hyphae or in sporangia to withstand harsh conditions. Bacillota encompasses a vast array of ecological roles and habitats, being ubiquitous across environments such as soils, aquatic systems (freshwater and marine), rhizospheres and stems, and microbiomes (including the gut, , and oral cavity), and even extreme settings like geothermal sites. In these niches, they contribute significantly to nutrient cycling through decomposition, , and biogeochemical processes like . Within host-associated communities, particularly the intestinal , Bacillota often dominate (sometimes comprising over 50% of the bacterial population) and influence energy harvest, immune modulation, and disease susceptibility, with their prevalence linked to evolutionary adaptations in humans and animals. The is taxonomically diverse, divided into at least nine classes with valid names, including (aerobic or facultatively anaerobic, e.g., endospore-forming rods), (mostly strict anaerobes involved in ), Erysipelotrichia, Negativicutes (Gram-negative staining but Gram-positive ancestry), Tissierellia, and others like Limnochordia and Thermolithobacteria. It includes more than 274 genera, with prominent examples such as (soil-dwelling spore-formers used in ), (anaerobic gut fermenters and pathogens like C. difficile), (lactic acid producers in and food ), (common commensals and opportunistic pathogens on skin), and (foodborne pathogens). This diversity underscores Bacillota's dual significance in ecology and human health, where beneficial strains support applications and production, while pathogenic ones cause infections ranging from food poisoning to severe tissue damage.

Overview

General Characteristics

Bacillota, formerly known as Firmicutes, are primarily characterized by a thick layer in their , which provides structural rigidity and contributes to their retention of stain during Gram staining. This monoderm cell envelope typically lacks an outer membrane, distinguishing them from , although some lineages exhibit variations such as a thin or diderm-like structures in certain classes like Negativicutes. The DNA of Bacillota generally features a low G+C content, ranging from 30% to 50%, which influences their genomic stability and evolutionary dynamics. Morphologically, Bacillota display diverse forms, predominantly rod-shaped (bacilli) or spherical (cocci), with cell sizes varying from 0.5 to 5 μm in length depending on the species. Many members, particularly in classes such as Bacilli and Clostridia, possess the ability to form endospores, which are dormant, resistant structures enabling survival under extreme conditions like heat, desiccation, and radiation; this trait is mediated by a conserved set of approximately 60 sporulation genes. Cell wall variations include the presence of S-layers—crystalline protein arrays that serve as protective exoskeletons, aiding in adhesion, enzyme display, and environmental resistance—in genera like Bacillus and Clostridium. Metabolically, Bacillota exhibit versatility, encompassing aerobic, anaerobic, and facultative anaerobes, with energy derivation from diverse substrates including sugars, , and inorganic compounds; some lineages are even capable of or chemolithoautotrophy. This metabolic flexibility supports their roles in , , and environmental . Genomically, Bacillota typically have compact genomes ranging from 1 to 5 Mb in size, with high coding densities often exceeding 85% and an abundance of such as plasmids and transposons that facilitate and adaptation.

Habitat and Distribution

Bacillota exhibit a ubiquitous presence across a wide array of environmental niches, including soils, freshwater bodies, marine ecosystems, hot springs, and extreme conditions such as acidic mine drainages and hypersaline salt marshes. In terrestrial soils, they form a significant component of the microbial , contributing to nutrient cycling and decomposition. Aquatic environments, including freshwater s and marine waters, harbor Bacillota at varying abundances, often comprising around 1% of the total microbial , with distributions influenced by factors like type and anthropogenic inputs. These are also prominently associated with and microbiomes, colonizing sites such as the gut, , and oral cavities, where they play roles in host health and microbial balance. For instance, genera like and are prevalent in the gastrointestinal tract, while others inhabit digestive systems and surfaces. Thermophilic Bacillota species, such as those in the genera and Geobacillus, thrive in geothermal sites, including hot springs with temperatures exceeding 70°C, demonstrating their adaptability to high-heat conditions. The distribution of Bacillota is facilitated by their ability to form endospores, which enable long-term and resistance to harsh conditions, allowing during unfavorable periods and dispersal through mechanisms like , currents, or attachment to host organisms. This spore-forming capability enhances their ecological versatility, permitting colonization of transient or isolated habitats. Bacillota encompass numerous genera, reflecting substantial , with greater observed in terrestrial soils compared to aquatic systems, where diversity is more constrained by physicochemical factors. This disparity underscores their preferential adaptation to soil-based niches over water columns or sediments.

Taxonomy and Classification

Historical Classification

In the early , bacteria now classified within Bacillota were grouped among Gram-positive organisms based on cell wall staining properties first described by in 1884, with significant contributions from microbiologists like Sigurd Orla-Jensen, who in proposed a classification of into genera such as Betabacterium, Thermobacterium, and Streptobacterium, emphasizing their morphological and physiological traits within the broader Gram-positive category. This early phenomenological approach laid the foundation for recognizing endospore-forming rods like and as key representatives of robust, Gram-positive forms capable of surviving harsh conditions. The formal recognition of Firmicutes as a distinct emerged in 1978, when N.E. Gibbons and R.G.E. Murray proposed it as a division encompassing all prokaryotes with Gram-positive-type cell walls, including low G+C content , to distinguish them from other bacterial groups like Gracilicutes (Gram-negatives). This nomenclature was validated in the Approved Lists of Bacterial Names in 1980 and further solidified in the first edition of (Volume 2, 1986), which detailed Firmicutes as including classes of endospore-formers such as (aerobes) and (anaerobes), alongside non-spore-formers, based primarily on phenotypic and limited molecular criteria. By the late 20th and early 21st centuries, molecular data from 16S rRNA sequencing began revealing the polyphyletic nature of Firmicutes, as deep phylogenetic branches separated groups like Actinobacteria into a distinct , while inconsistencies arose from the inclusion of morphologically divergent members, such as Gram-negative-walled Negativicutes. In , Boone et al. proposed as a core class within Firmicutes, centering the taxonomy around anaerobic, spore-forming lineages to better reflect phylogenetic coherence. Genomic studies in the , including whole-genome phylogenies, further exposed these inconsistencies by identifying paraphyletic assemblages and novel deep branches, prompting revisions to achieve . Culminating these efforts, and Garrity in 2021 reclassified the phylum as Bacillota in the List of Prokaryotic Names with Standing in , adopting the standardized -ota ending and emphasizing its monophyletic composition based on integrated molecular and genomic evidence.

Current Taxonomic Framework

In 2021, the Bacillota was formally established through the List of Prokaryotic Names with Standing in (LPSN) as a replacement for the polyphyletic Firmicutes, encompassing most of its former members while excluding the family Thermodesulfobiaceae (reclassified into the separate Thermodesulfobacteriota). This reorganization aimed to align prokaryotic with phylogenetic , drawing from comprehensive analyses of 16S rRNA sequences and emerging genomic to define boundaries, though the exact remains a subject of some debate in the literature. The current hierarchy under Bacillota includes numerous classes, such as , , Erysipelotrichia, Negativicutes, Tissierellia, Limnochordia, and Thermolithobacteria, with delineation primarily based on phylogenetic clustering from 16S rRNA genes (typically <82.5% identity for class-level separation), supplemented by whole-genome comparisons such as average amino acid identity (AAI) and relative evolutionary divergence (RED) metrics from genome taxonomy databases. For finer resolution within classes and orders, average nucleotide identity (ANI >95-96%) and digital DNA-DNA hybridization (dDDH >70%) are applied to ensure and exclude divergent groups. The is Bacillus, with emendations to the phylum description emphasizing Gram-positive cell walls and formation in core lineages while accommodating atypical members. Ongoing taxonomic updates from 2023 to 2025, driven by metagenomic assemblies, have expanded the framework with new orders in anaerobic clades, such as additions to and Tissierellia from uncultured gut and soil microbiomes. These incorporate high-throughput sequencing to refine boundaries, addressing remnants through iterative phylogenetic validation.

Phylogeny and Evolution

Phylogenetic Relationships

Phylogenetic analyses of Bacillota have traditionally relied on 16S rRNA sequences for initial classifications, but more robust trees are now constructed using multi-locus sequence typing and phylogenomics based on concatenated alignments of conserved proteins, such as the 120 universal bacterial marker genes employed by the Genome Taxonomy Database (GTDB). These approaches provide higher resolution for resolving deep divergences within the compared to single- methods, enabling the inference of evolutionary relationships across thousands of genomes. Within the bacterial domain, Bacillota forms part of the Terrabacteria superphylum, where it branches closely to , supported by analyses of ribosomal proteins and shared genomic signatures like insertion sequences in conserved loci. This positioning is reinforced by phylogenomic trees showing Terrabacteria as a monophyletic group adapted to terrestrial environments, distinct from the Gracilicutes superphylum that includes . Key internal branching reveals a deep split between the predominantly spore-forming classes and , which encode complete sporulation gene sets, and non-spore-forming lineages such as Erysipelotrichia, where sporulation genes are absent or incomplete. Post-2021 taxonomic revisions addressed previous in the (then Firmicutes) by excluding Mollicutes-related lineages, now classified as the separate , based on phylogenomic from conserved protein alignments. Phylogenetic trees are typically inferred using maximum-likelihood software like RAxML or IQ-TREE, with bootstrap supports exceeding 90% for major nodes, ensuring statistical robustness. Recent 2024 metagenomic studies have further illuminated deep-branching Bacillota lineages, revealing atypical Gram-staining patterns in basal groups without outer membrane genes, consistent with ancestral monoderm configurations.

Evolutionary Origins and Diversification

The Bacillota phylum traces its evolutionary origins to the eon, with molecular clock analyses indicating that its diversified between 3.6 and 3.0 billion years ago, contemporaneous with the onset of oxygenic photosynthesis by ancient . This timing links the early Bacillota to nascent oxygenic environments, where rising atmospheric oxygen levels began to reshape microbial ecosystems. Fossil evidence from cherts, such as the 1.88 billion-year-old Gunflint Chert in , preserves a diverse including filament-like and spherical structures potentially attributable to spore-forming . A pivotal innovation in Bacillota was the emergence of formation around 2 billion years ago, serving as a protective mechanism against the of the (approximately 2.4 billion years ago). enabled survival in fluctuating redox conditions, allowing Bacillota to persist and radiate in increasingly aerobic settings. Complementing this, (HGT) facilitated metabolic versatility, enabling adaptations such as novel fermentative and respiratory pathways through the acquisition of genes from distantly related . These mechanisms collectively underpinned the phylum's resilience and expansion. Genomic reconstructions of the ancestral reveal a predominantly fermentative metabolic base, consistent with an anaerobic lifestyle in conditions, with subsequent aerobic adaptations layered atop this foundation.

Diversity

Major Clades and Orders

The phylum encompasses several major classes, each characterized by distinct morphological, physiological, and ecological traits that reflect their evolutionary diversification. The class represents aerobic, endospore-forming predominantly found in terrestrial environments. This class includes two primary orders: , which comprises soil-dwelling taxa adapted to aerobic conditions and capable of surviving harsh environments through sporulation, and Lactobacillales, consisting of fermentative, often lactic acid-producing commonly associated with nutrient-rich, anaerobic niches such as fermented foods and animal mucosa. The class forms the largest and most diverse group within Bacillota, accounting for approximately half of the phylum's overall and encompassing a wide array of anaerobic, spore-forming . Key orders include , which features many pathogenic and fermentative lineages prevalent in anaerobic sediments and host-associated environments, and Halanaerobiales, specialized halophilic anaerobes thriving in high-salt, anoxic conditions such as salt lakes and hypersaline soils. Clostridia includes hundreds of families, highlighting its extensive taxonomic depth derived from both cultured and uncultured lineages. Additional classes contribute to Bacillota's , often with specialized adaptations. The class Erysipelotrichia is notable for its gut-associated members, which play roles in host-microbe interactions within mammalian intestinal microbiomes. Thermoanaerobacteria comprises thermophilic anaerobes adapted to high-temperature environments like hot springs and geothermal soils, featuring thin layers that support their extremophily. Tissierellia includes opportunistic anaerobes frequently linked to clinical infections, such as abscesses and polymicrobial diseases. Furthermore, the class Negativicutes, which exhibits Gram-negative staining despite its phylogenetic placement in Bacillota, incorporates transferred orders like Selenomonadales, comprising anaerobic, curved-rod from guts and oral cavities. Other classes include Limnochordia and Thermolithobacteria, further expanding the phylum's taxonomic diversity. Recent taxonomic emendations from 2023 to 2025, based on metagenomic analyses of uncultured lineages, have expanded order-level classifications within these classes, revealing previously unrecognized diversity in environmental and host-associated niches.

Notable Genera and Species

Bacillota encompasses more than 274 genera, showcasing remarkable diversity in morphology, , and ecological roles, with many belonging to the classes and . The Bacillus represents prominent spore-forming aerobes or facultative anaerobes, often rod-shaped and ubiquitous in soil, water, and plant-associated environments. Bacillus subtilis stands out as a foundational for bacterial and , owing to its natural transformability, robust genetic tools, and fully sequenced , enabling extensive studies on sporulation, competence, and formation. Other key species include Bacillus anthracis, the etiological agent of with its plasmid-encoded toxins, and Bacillus thuringiensis, valued for producing insecticidal crystal proteins used in biopesticides, thus contributing to the phylum's biotechnological significance. The genus comprises strictly anaerobic, spore-forming rods prevalent in anaerobic sediments, soil, and animal guts, highlighting the phylum's adaptation to oxygen-free niches. is notorious for producing botulinum neurotoxin, the most potent known toxin, which causes —a paralytic illness from contaminated food—demonstrating the genus's role in challenges. Clostridium difficile drives antibiotic-associated and by overgrowing in disrupted gut microbiomes, producing toxins that damage and leading to severe healthcare-associated infections. Certain species, such as Clostridium pasteurianum, perform biological under anaerobic conditions, utilizing enzymes to convert atmospheric N₂ into , thereby aiding and exemplifying the phylum's metabolic versatility. Non-spore-forming genera further illustrate Bacillota's breadth. includes Gram-positive, acid-tolerant rods that ferment sugars to , thriving in fermented foods and host-associated sites like the human vagina and gut. is a cornerstone strain, promoting gut barrier integrity, modulating immune responses, and alleviating through to epithelial cells and production. In contrast, features clustering cocci that colonize skin and mucous membranes as commensals. , particularly methicillin-resistant strains (MRSA), exemplifies opportunistic pathogenicity, causing skin abscesses, pneumonia, and bloodstream infections via virulence factors like and enterotoxins, underscoring the genus's dual commensal-pathogen nature. Additional notable genera expand the phylum's atypical diversity. consists of motile, Gram-positive rods adapted for intracellular survival in hosts. is a leading foodborne , invading the intestinal barrier and spreading systemically to cause , which poses high risks of or in vulnerable populations. Within the class Negativicutes, represents Gram-negative-staining (despite phylogenetic Gram-positive ancestry) anaerobic cocci that utilize lactate produced by other microbes in oral and gut biofilms, fostering interspecies interactions and contributing to community stability in polymicrobial environments. These genera collectively highlight Bacillota's evolutionary innovations, from spore resilience to specialized symbioses.

Ecology and Physiology

Metabolic Capabilities

Bacillota exhibit a predominance of fermentative , particularly among anaerobic members, enabling energy generation in oxygen-limited environments. In genera such as , homolactic fermentation predominates, where glucose is converted to through the Embden-Meyerhof-Parnas glycolytic pathway, yielding a net gain of two ATP molecules per glucose molecule. This process can be represented as: C6H12O6+2ADP+2Pi→2CH3CH(OH)COOH+2ATP+2H2O\text{C}_6\text{H}_{12}\text{O}_6 + 2 \text{ADP} + 2 \text{P}_i \rightarrow 2 \text{CH}_3\text{CH(OH)COOH} + 2 \text{ATP} + 2 \text{H}_2\text{O} Such fermentation supports rapid growth in carbohydrate-rich niches like fermented foods and the animal gut. In contrast, many clostridia employ mixed-acid fermentation, diversifying end products to include acetate, butyrate, propionate, and ethanol alongside lactate and gases like CO₂ and H₂, which allows for more flexible redox balancing under varying substrate conditions. This pathway, initiated via glycolysis to pyruvate, branches into multiple routes such as the acetyl-CoA and butyryl-CoA pathways, optimizing ATP yield to approximately 2.5-4 per glucose depending on products formed. Respiratory metabolism occurs in aerobic or facultatively anaerobic Bacillota, exemplified by species, which utilize branched electron transport chains involving menaquinones, , and terminal oxidases like cytochrome aa₃ or bd to transfer electrons from NADH or quinol to oxygen, generating a proton motive force for ATP synthesis via . This aerobic respiration yields up to 28-38 ATP per glucose, far exceeding , and supports resistance through management. Certain capable of use alternative electron acceptors, such as reduced to via respiratory , coupling this to and enhancing growth yields over pure . reduction, though less common in strict , occurs in some sulfate-reducing Bacillota relatives, where serves as the terminal acceptor, producing and facilitating anaerobic carbon oxidation. Bacillota demonstrate versatile biosynthetic capabilities, including de novo synthesis of essential amino acids like branched-chain types (valine, leucine, isoleucine) via pathways shared across firmicutes, which are crucial for protein assembly in nutrient-poor habitats. Vitamin production is prominent, particularly cobalamin (B₁₂) in anaerobic genera such as Clostridium and Lactobacillus reuteri, involving a complex aerobic or anaerobic pathway from uroporphyrinogen III to the corrin ring, enabling methylmalonyl-CoA mutase activity for propionate metabolism. During sporulation, a hallmark of many Bacillota, metabolism shifts to accumulate dipicolinic acid (DPA), comprising up to 10% of spore dry weight, which complexes with calcium to dehydrate the core and confer resistance to heat, radiation, and chemicals by stabilizing DNA and proteins. DPA biosynthesis, mediated by the SpoVF enzyme, occurs late in sporulation and is essential for viability upon germination. Metabolic adaptations enhance survival in extreme conditions; lactobacilli exhibit acid tolerance down to 3-4 through mechanisms like proton pumps (F₁F₀-ATPase), reactions generating counterions, and changes in membrane composition to maintain internal . In thermophilic lineages like Thermoanaerobacter, heat-stable enzymes such as glucokinases and alcohol dehydrogenases, stabilized by ionic interactions and reduced hydrophobic exposure, sustain at temperatures up to 70°C, supporting applications.

Environmental Roles

Bacillota members, particularly within the class, play essential roles in the decomposition of matter in anaerobic environments such as soils and sediments. Cellulolytic species like produce carbohydrate-active enzymes (CAZymes), including endoglucanases from families GH5, GH9, and GH48, which target and in lignocellulose complexes. This degradation process converts complex polymers into simpler compounds like volatile fatty acids (e.g., , butyrate), facilitating carbon cycling and contributing significantly to breakdown. In ruminant gut ecosystems, Bacillota such as Ruminococcus flavefaciens and Ruminococcus albus form mutualistic symbioses by degrading , producing volatile fatty acids that supply up to 70% of the host's energy needs through . Similarly, certain strains in rhizospheres perform biological , as evidenced by acetylene reduction assays showing enhanced activity under microaerobic conditions, thereby increasing nitrogen availability for growth and supporting . In biogeochemical cycles, Desulfotomaculum species, gram-positive endospore-forming reducers, drive reduction in anoxic sediments, converting to using organic electron donors and influencing and carbon dynamics in subsurface environments like marine deposits and aquifers. These thrive in oligotrophic and thermophilic settings, contributing to the global where dissimilatory reduction accounts for substantial organic matter mineralization. Bacillota also exhibit potential in hydrocarbon-contaminated sites; for instance, genera like Geobacillus, Brevibacillus, and degrade n-s and polycyclic aromatic hydrocarbons via enzymes such as alkane hydroxylases (alkB, ladA), and produce biosurfactants like surfactin to enhance cleanup in polluted soils and waters. Within microbial communities, Bacillota often function as keystone taxa, stabilizing dynamics through strong biotic interactions and metabolic versatility, as seen in gut microbiomes where species like Ruminococcus bromii facilitate polysaccharide breakdown and influence co-occurring taxa via substrate provision. Recent research (as of 2025) has identified specific metabolic pathways, including those for and , that contribute to the and of Bacillota in host gut microbiomes, underscoring their ecological significance in energy harvest and host adaptation. exacerbates these roles by altering dispersal and community assembly; increased temperatures and thawing promote endospore , potentially accelerating carbon release from frozen soils. Recent studies on thaw highlight Bacillota enrichment during aerobic incubation, where they respond consistently to warming, driving organic carbon decomposition and contributing to feedbacks in ecosystems. A 2025 study on Alaskan soils further confirms consistent increases in Bacillota taxa, such as , during aerobic thaw, attributed to and enhancing microbial activity and carbon flux.

Human and Industrial Relevance

Pathogenic Aspects

Certain members of the Bacillota phylum are significant human pathogens, capable of causing a spectrum of diseases ranging from gastrointestinal infections to severe systemic illnesses. (formerly Clostridium difficile) is a primary cause of antibiotic-associated , responsible for nearly 500,000 infections annually in the United States, often leading to severe , pseudomembranous , and high mortality in vulnerable populations. is a leading etiologic agent of skin and soft tissue infections, bacteremia, , and , contributing to substantial morbidity worldwide as a common nosocomial and community-acquired pathogen. causes , a zoonotic that manifests in cutaneous, gastrointestinal, or inhalational forms, with untreated inhalational cases carrying fatality rates exceeding 80%. These pathogens exploit the phylum's spore-forming capabilities and metabolic versatility to persist in diverse environments and invade host tissues. Virulence in Bacillota pathogens is driven by an array of factors, including potent exotoxins, formation, and mechanisms of antibiotic resistance. Clostridium botulinum produces botulinum , the most lethal known toxin, which inhibits release and causes in , with a human lethal dose as low as 1 ng/kg body weight. Similarly, Clostridium tetani secretes tetanospasmin, a that blocks inhibitory in the , resulting in spastic paralysis characteristic of . S. aureus employs —structured communities embedded in an —to shield against host immunity and antimicrobials, enhancing persistence in chronic infections such as and device-related . Antibiotic resistance is frequently conferred by , including plasmids; for instance, methicillin-resistant S. aureus (MRSA) harbors the mecA gene, which encodes a penicillin-binding protein (PBP2a) with low affinity for β-lactam antibiotics, enabling resistance to and related drugs. Transmission of these pathogens often involves environmental persistence, particularly via resilient endospores. C. difficile spores can survive on surfaces for months, facilitating nosocomial spread and contributing to outbreaks in the , such as hypervirulent ribotype 027 strains that surged in North American and European healthcare facilities, exacerbating incidence. B. anthracis spores remain viable in for decades, enabling zoonotic transmission through contaminated animal products or intentional release, as seen in concerns. Epidemiologically, these traits amplify burdens, with S. aureus bloodstream infections showing an incidence rate of approximately 37 per 100,000 person-years in the United States (as of 2017). Control strategies emphasize prevention and targeted interventions. Anthrax vaccination using adsorbed (AVA), administered as a series of intramuscular doses, provides protective immunity for at-risk individuals, such as laboratory workers or . For C. difficile-associated , like Saccharomyces boulardii have shown efficacy in reducing recurrence rates by restoring balance, though clinical guidelines recommend them adjunctively with like . Post-COVID-19 trends, as of 2025, reveal accelerated in Bacillota due to heightened antibiotic overuse during the , with studies documenting increased conjugation of resistance plasmids in clinical and environmental isolates, underscoring the need for programs.

Beneficial Applications

Bacillota, encompassing diverse genera such as , , and , exhibit significant beneficial applications across human health, industry, , and environmental management due to their metabolic versatility, spore-forming resilience, and GRAS () status for many species. These bacteria contribute to for gut health modulation, production for biotechnological processes, generation, in , and pollutant degradation in efforts. In human and animal health, Bacillota species serve as to support gastrointestinal function and immune responses. For instance, Bacillus subtilis spores enhance nutrient absorption, inhibit pathogenic bacteria like through , and alleviate antibiotic-associated diarrhea, with clinical trials demonstrating reduced cholesterol levels and improved cardiovascular risk factors. Similarly, species, such as L. acidophilus and L. rhamnosus, modulate the by producing , which lowers to suppress pathogens, and promote anti-inflammatory effects via pathway regulation, aiding in the prevention of , eczema, and recurrent urinary tract infections. also acts as a , producing like butyrate to strengthen the intestinal barrier and mitigate symptoms. These applications extend to and , where B. licheniformis improves feed efficiency and reduces disease incidence in . Industrially, Bacillota are pivotal in enzyme production and processes. Bacillus species, particularly B. subtilis and B. licheniformis, are engineered as cell factories for thermostable enzymes like α-amylase, proteases, and β-lactamases, which are essential in (e.g., for syrups), detergents (for protein stain removal), and pharmaceuticals (for synthesis). Bacillus species contribute approximately 50% of the industrial enzyme market. Lactobacillus strains facilitate dairy and vegetable fermentations, enhancing flavor and shelf life in products like and while producing vitamins such as . In biofuel production, anaerobic Clostridium species, including C. acetobutylicum, perform ABE (acetone-butanol-ethanol) fermentation from , yielding up to 20 g/L in optimized co-culture systems, offering a sustainable alternative to fossil fuels. Thermophilic genera like Geobacillus thermoglucosidasius further support high-yield production from renewable substrates. Agriculturally, Bacillota promote plant growth and biocontrol. produces Cry toxins that target pests like lepidopteran larvae, reducing losses by over 50% in transgenic and serving as a in . and Lysinibacillus species fix atmospheric nitrogen and secrete to stimulate root development, enhancing yields in . These microbes also suppress soil-borne pathogens, minimizing the need for chemical fertilizers. In environmental applications, Bacillota aid by degrading pollutants. Bacillus strains break down hydrocarbons and pesticides in contaminated soils, while metabolizes persistent organics like . Anaerobic species such as Anaerobacillus reduce toxic oxyanions like selenate and , and Amphibacillus detoxifies in industrial effluents. These capabilities underscore the phylum's role in restoring ecosystems, with field studies showing up to 90% reduction in heavy metal bioavailability.
Application CategoryKey Genera/SpeciesRepresentative BenefitsExample Impact
Probiotics, , Gut barrier enhancement, inhibition, immune modulationSignificant reduction in the risk of antibiotic-associated (up to 51% in meta-analyses of )
Industrial Enzymes, Geobacillus spp.Thermostable amylases, proteases for processingBacillus species contribute approximately 50% of the industrial enzyme market
Biofuels, Geobacillus thermoglucosidasiusABE fermentation, ethanol from biomassButanol yields of 15-20 g/L in bioreactors
Agriculture, polymyxa, Reported yield increases of up to 30% in various crops
Bioremediation, Anaerobacillus alkalilacustrePollutant degradation, metal reductionUp to 88% removal in lab studies

References

  1. https://link.springer.com/article/10.1007/s00248-024-02482-0
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