Bacillus subtilis: Difference between revisions

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{{short description|Catalase-positive bacterium}}

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'''''Bacillus subtilis''''', known also as the '''hay bacillus''' or '''grass bacillus''', is a [[gram-positive]], [[catalase]]-positive [[bacterium]], found in soil and the [[gastrointestinal tract]] of [[ruminant]]s, humans and marine sponges. As a member of the [[genus]] ''[[Bacillus]]'', ''B. subtilis'' is rod-shaped, and can form a tough, protective [[endospore]], allowing it to tolerate extreme environmental conditions. ''B. subtilis'' has historically been classified as an [[obligate aerobe]], though evidence exists that it is a [[facultative anaerobe]]. ''B. subtilis'' is considered the best studied Gram-positive bacterium and a [[model organism]] to study bacterial chromosome replication and cell differentiation. It is one of the bacterial champions in secreted [[enzyme]] production and used on an industrial scale by biotechnology companies.

==Description==

''Bacillus subtilis'' is a [[Gram-positive]] bacterium, [[rod-shaped]] and [[catalase]]-positive. It was originally named ''Vibrio subtilis'' by [[Christian Gottfried Ehrenberg]], and renamed ''Bacillus subtilis'' by [[Ferdinand Cohn]] in 1872 (subtilis being the Latin for "fine, thin, slender"). ''B. subtilis'' cells are typically rod-shaped, and are about 4–10 micrometers (μm) long and 0.25–1.0 μm in diameter, with a cell volume of about 4.6 fL at stationary phase.

As with other members of the [[genus]] ''[[Bacillus]]'', it can form an [[endospore]], to survive  extreme environmental conditions of temperature and desiccation. ''B. subtilis'' is a [[facultative anaerobe]] and had been considered as an [[obligate aerobe]] until 1998. ''B. subtilis'' is heavily [[flagellate]]d, which gives it the ability to move quickly in liquids.

''B. subtilis'' has proven highly amenable to [[genetic manipulation]], and has become widely adopted as a [[model organism]] for laboratory studies, especially of [[sporulation]], which is a simplified example of [[cellular differentiation]]. In terms of popularity as a laboratory model organism, ''B. subtilis'' is often considered as the [[Gram-positive]] equivalent of ''[[Escherichia coli]]'', an extensively studied [[Gram-negative]] bacterium.

==Characteristics==

Colony, morphological, physiological, and biochemical characteristics of ''Bacillus subtilis'' are shown in the Table below.

Note: + = Positive, – =Negative

==Habitat==

This species is commonly found in the upper layers of the soil and ''B. subtilis'' is thought to be a [[Gut flora|normal gut commensal]] in humans. A 2009 study compared the density of spores found in soil (about 10⁶ spores per gram) to that found in human feces (about 10⁴ spores per gram). The number of spores found in the human gut was too high to be attributed solely to consumption through food contamination. In some bee habitats, ''B. subtilis'' appears in the gut flora of [[honey bee]]s. ''B. subtilis'' can also be found in marine environments.

There is evidence that ''B. subtilis'' is saprophytic in nature. Studies have shown that the bacterium exhibits vegetative growth in soil rich in organic matter, and that spores were formed when nutrients were depleted. Additionally, ''B. subtilis'' has been shown to form [[biofilm]]s on plant roots, which might explain why it is commonly found in gut microbiomes. Perhaps animals eating plants with ''B. subtilis'' biofilms can foster growth of the bacterium in their gastrointestinal tract. It has been shown that the entire lifecycle of ''B. subtilis'' can be completed in the gastrointestinal tract, which provides credence to the idea that the bacterium enters the gut via plant consumption and stays present as a result of its ability to grow in the gut.

==Reproduction==

{{Multiple image|direction=vertical|width=200|align=right|image1=Bacillus subtilis Spore.jpg|image2=Bacillus subtilis endospore stain.png|caption1=Sporulating ''B. subtilis''.|caption2=Another endospore stain of ''B. subtilis''.}}

''Bacillus subtilis'' can divide symmetrically to make two [[daughter cell]]s (binary fission), or asymmetrically, producing a single [[endospore]] that can remain viable for decades and is resistant to unfavourable environmental conditions such as [[drought]], [[salinity]], extreme [[pH]], [[radiation]], and [[solvent]]s. The endospore is formed at times of nutritional stress and through the use of hydrolysis, allowing the organism to persist in the environment until conditions become favourable. Prior to the process of sporulation the cells might become [[Motility|motile]] by producing [[flagella]], take up DNA from the environment, or produce [[antibiotic]]s. These responses are viewed as attempts to seek out nutrients by seeking a more favourable environment, enabling the cell to make use of new beneficial genetic material or simply by killing off competition.

Under stressful conditions, such as nutrient deprivation, ''B. subtilis'' undergoes the process of [[Sporulation in Bacillus subtilis|sporulation]]. This process has been very well studied and has served as a model organism for studying sporulation.

===Sporulation===

{{main|Sporulation in Bacillus subtilis}}

{{excerpt|Sporulation in Bacillus subtilis|Nature of regulation|hat=no}}

''Bacillus subtilis'' is a [[model organism]] used to study bacterial chromosome replication. Replication of the single [[circular chromosome]] initiates at a single locus, the origin (''[[Origin of replication|oriC]]''). Replication proceeds bidirectionally and two [[replication fork]]s progress in clockwise and counterclockwise directions along the chromosome. Chromosome replication is completed when the forks reach the terminus region, which is positioned opposite to the origin on the [[chromosome map]]. The terminus region contains several short DNA sequences (''Ter'' sites) that promote replication arrest. Specific proteins mediate all the steps in DNA replication. Comparison between the proteins involved in chromosomal DNA replication in ''B. subtilis'' and in ''[[Escherichia coli]]'' reveals similarities and differences. Although the basic components promoting initiation, elongation, and termination of replication are well-[[conserved sequence|conserved]], some important differences can be found (such as one bacterium missing proteins essential in the other). These differences underline the diversity in the mechanisms and strategies that various bacterial species have adopted to carry out the duplication of their genomes.

''Bacillus subtilis'' has about 4,100 genes. Of these, only 192 were shown to be indispensable; another 79 were predicted to be essential, as well. A vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related to cell energetics.

The complete genome sequence of ''B. subtilis'' sub-strain QB928 has 4,146,839 DNA base pairs and 4,292 genes. The QB928 strain is widely used in genetic studies due to the presence of various markers [aroI(aroK)906 purE1 dal(alrA)1 trpC2].

Several noncoding RNAs have been characterized in the ''B. subtilis'' genome in 2009, including [[Bacillus subtilis BSR sRNAs|Bsr RNAs]].

Microarray-based comparative genomic analyses have revealed that ''B. subtilis'' members show considerable genomic diversity.

FsrA is a [[small RNA]] found in ''Bacillus subtilis''. It is an [[Effector (biology)|effector]] of the iron sparing response, and acts to down-regulate iron-containing proteins in times of poor iron bioavailability.

A promising fish probiotic, ''Bacillus subtilis'' strain WS1A, that possesses antimicrobial activity against ''Aeromonas veronii'' and suppressed motile ''Aeromonas'' septicemia in ''Labeo rohita''. The de novo assembly resulted in an estimated chromosome size of 4,148,460 bp, with 4,288 open reading frames. ''B. subtilis'' strain WS1A genome contains many potential genes, such as those encoding proteins involved in the biosynthesis of [[riboflavin]], [[vitamin B6]], and [[amino acid]]s (''[https://www.uniprot.org/uniprot/P51785 ilvD]'') and in carbon utilization (''[https://www.uniprot.org/uniprot/P39646 pta]'').

==Transformation==

[[Transformation (genetics)|Natural bacterial transformation]] involves the transfer of DNA from one bacterium to another through the surrounding medium. In ''B. subtilis'' the length of transferred DNA is greater than 1,271 kb (more than 1 million bases). The transferred DNA is likely double-stranded DNA and is often more than a third of the total chromosome length of 4,215 kb. It appears that about 7–9% of the recipient cells take up an entire chromosome.

In order for a recipient bacterium to bind, take up exogenous DNA from another bacterium of the same species and recombine it into its chromosome, it must enter a special physiological state called [[Competence (biology)|competence]].

Competence in ''B. subtilis'' is induced toward the end of logarithmic growth, especially under conditions of amino-acid limitation. Under these stressful conditions of semistarvation, cells typically have just one copy of their chromosome and likely have increased DNA damage. To test whether transformation is an adaptive function for ''B. subtilis'' to repair its DNA damage, experiments were conducted using UV light as the damaging agent. These experiments led to the conclusion that competence, with uptake of DNA, is specifically induced by DNA-damaging conditions, and that transformation functions as a process for recombinational repair of DNA damage.

While the natural competent state is common within laboratory ''B. subtilis'' and field isolates, some industrially relevant strains, e.g. ''B. subtilis'' (natto), are reluctant to DNA uptake due to the presence of restriction modification systems that degrade exogenous DNA. ''B. subtilis'' (natto) mutants, which are defective in a type I restriction modification system endonuclease, are able to act as recipients of conjugative plasmids in mating experiments, paving the way for further genetic engineering of this particular ''B. subtilis'' strain.

By adopting Green Chemistry in the use of less hazardous materials, while saving cost, researchers have been mimicking nature's methods of synthesizing chemicals that can be useful for the food and drug industry, by "piggybacking molecules on shorts strands of DNA" before they are zipped together during their complementary base pairing between the two strands.  Each strand will carry a particular molecule of interest that will undergo a specific chemical reaction simultaneously when the two corresponding strands of DNA pairs hold together like a zipper, allowing another molecule of interest, to react with one another in controlled and isolated reaction between those molecules being carried into these DNA complementary attachments.  By using this method with certain bacterias that naturally  follow a process replication in a multi-step fashion, the researchers can simultaneously carry on the interactions of these added molecules to interact with enzymes and other molecules used for a secondary reaction by treating it like a capsule, which is similar to how the bacteria performs its own DNA replication processes.

===20th century===

[[Image:Bacillus subtilis Gram.jpg|thumb|right|Gram-stained ''B. subtilis'']]

Cultures of ''B.&nbsp;subtilis'' were popular worldwide, before the introduction of [[antibiotics]], as an immunostimulatory agent to aid treatment of [[gastrointestinal]] and [[urinary tract]] diseases. It was used throughout the 1950s as an [[alternative medicine]], which upon digestion has been found to significantly stimulate [[Broad-spectrum therapeutic|broad-spectrum immune activity]] including activation of secretion of specific [[antibodies]] [[IgM]], [[Immunoglobulin G|IgG]] and [[IgA]] and release of [[CpG dinucleotide]]s inducing [[interferon]] [[IFN-α]]/[[IFNγ]] producing activity of [[leukocytes]] and [[cytokines]] important in the development of [[cytotoxicity]] towards [[tumor cells]]. It was marketed throughout America and Europe from 1946 as an immunostimulatory aid in the treatment of gut and urinary tract diseases such as [[Rotavirus]] and [[Shigellosis]]. In 1966, the U.S. Army dumped ''bacillus subtilis'' onto the grates of New York City subway stations for five days in order to observe people's reactions when coated by a strange dust. Due to its ability to survive, it is thought to still be present there.

The antibiotic [[bacitracin]] was first isolated from a variety of ''[[Bacillus licheniformis]]'' named "Tracy I" in 1945, then considered part of the ''B. subtilis'' species. It is still commercially manufactured by growing the variety in a container of liquid [[growth medium]]. Over time, the bacteria synthesizes bacitracin and secretes the antibiotic into the medium. The bacitracin is then extracted from the medium using chemical processes.

Since the 1960s ''B. subtilis'' has had a history as a test species in spaceflight experimentation. Its [[endospore]]s can survive up to 6 years in space if coated by dust particles protecting it from solar UV rays. It has been used as an [[extremophile]] survival indicator in [[outer space]] such as [[Exobiology Radiation Assembly]], [[EXOSTACK]], and [[EXPOSE]] orbital missions.

Wild-type natural isolates of ''B. subtilis'' are difficult to work with compared to laboratory strains that have undergone domestication processes of [[mutagenesis]] and selection. These strains often have improved capabilities of transformation (uptake and integration of environmental DNA), growth, and loss of abilities needed "in the wild".  And, while dozens of different strains fitting this description exist, the strain designated '168' is the most widely used. Strain 168 is a [[tryptophan]] [[auxotroph]] isolated after X-ray mutagenesis of ''B. subtilis'' Marburg strain and is widely used in research due to its high transformation efficiency.

[[Image:Bacillus subtilis colonies.jpg|thumb|right|200px|Colonies of ''B. subtilis'' grown on a [[culture dish]] in a [[molecular biology]] [[laboratory]].]]

''Bacillus globigii'', a closely related but [[phylogenetic]]ally distinct species now known as ''[[Bacillus atrophaeus]]'' was used as a biowarfare [[Wiktionary:simulant|simulant]] during [[Project SHAD]] (aka ''Project 112''). Subsequent genomic analysis showed that the strains used in those studies were products of deliberate enrichment for strains that exhibited abnormally high rates of [[sporulation]].

A strain of ''B. subtilis'' formerly known as ''Bacillus natto'' is used in the commercial production of the Japanese food ''[[nattō]]'', as well as the similar Korean food ''[[cheonggukjang]]''.

===21st century===

*As a model organism, ''B. subtilis'' is commonly used in laboratory studies directed at discovering the fundamental properties and characteristics of Gram-positive spore-forming bacteria.  In particular, the basic principles and mechanisms underlying formation of the durable endospore have been deduced from studies of spore formation in ''B. subtilis''.

*Both metabolically active and non-metabolically active ''B. subtilis'' cells have been shown to reduce gold (III) to gold (I) and gold (0) when oxygen is present. This biotic reduction plays a role in gold cycling in geological systems and could potentially be used to recover solid gold from said systems.

===Novel and artificial substrains===

* Novel strains of ''B. subtilis'' that could use 4-fluorotryptophan (4FTrp) but not canonical tryptophan (Trp) for propagation were isolated. As [[Trp operon|Trp]] is only coded by a single codon, there is evidence that Trp can be displaced by 4FTrp in the genetic code. The experiments showed that the canonical genetic code can be mutable.

*A new strain has been modified to  convert nectar into [[honey]] by secreting enzymes.

===In other animals===

''Bacillus subtilis'' was reviewed by the US FDA [[Center for Veterinary Medicine]] and found to present no safety concerns when used in direct-fed microbial products, so the [[Association of American Feed Control Officials]] has listed it approved for use as an [[animal feed]] ingredient under Section 36.14 "Direct-fed Microorganisms".

On the other hand, several feed additives containing viable spores of ''B. subtilis'' have been positively evaluated by the [[European Food Safety Authority]], regarding their safe use for weight gaining in animal production.

===In humans===

''Bacillus subtilis'' spores can survive the extreme heat generated during cooking. Some ''B. subtilis'' strains are responsible for causing ropiness or rope spoilage&nbsp;– a sticky, stringy consistency caused by bacterial production of long-chain [[polysaccharide]]s&nbsp;– in spoiled bread dough and baked goods. For a long time, bread ropiness was associated uniquely with ''B. subtilis'' species by biochemical tests.  Molecular assays (randomly amplified polymorphic DNA PCR assay, [[denaturing gradient gel electrophoresis]] analysis, and sequencing of the V3 region of [[16S ribosomal DNA]]) revealed greater ''Bacillus'' species variety in ropy breads, which all seems to have a positive amylase activity and high heat resistance.

''B. subtilis'' CU1 (2 × 10⁹ spores per day) was evaluated in a 16-week study (10 days administration of probiotic, followed by 18 days wash-out period per each month; repeated same procedure for total 4 months) to healthy subjects. ''B. subtilis'' CU1 was found to be safe and well tolerated in the subjects without any side effects.

''Bacillus subtilis'' and substances derived from it have been evaluated by different authoritative bodies for their safe and beneficial use in food. In the United States, an opinion letter issued in the early 1960s by the [[Food and Drug Administration]] (FDA) designated some substances derived from microorganisms as [[generally recognized as safe]] (GRAS), including [[carbohydrase]] and protease enzymes from ''B. subtilis''. The opinions were predicated on the use of nonpathogenic and nontoxicogenic strains of the respective organisms and on the use of current good manufacturing practices. The FDA stated that the enzymes derived from the ''B. subtilis'' strain were in common use in food prior to January 1, 1958, and that nontoxigenic and nonpathogenic strains of ''B. subtilis'' are widely available and have been safely used in a variety of food applications. This includes consumption of Japanese fermented soy bean, in the form of ''[[Natto]]'', which is commonly consumed in Japan, and contains as many as 10⁸ viable cells per gram. The fermented beans are recognized for their contribution to a healthy gut flora and [[vitamin K2|vitamin K₂]] intake; during this long history of widespread use, ''natto'' has not been implicated in adverse events potentially attributable to the presence of ''B. subtilis''. The natto product and the ''B. subtilis'' natto as its principal component are FOSHU (Foods for Specified Health Use) approved by the Japanese [[Ministry of Health, Labour, and Welfare]] as effective for preservation of health.

''Bacillus subtilis'' has been granted "Qualified Presumption of Safety" status by the [[European Food Safety Authority]].

==See also==

* [[Adenylosuccinate lyase deficiency]]

* [[YlbH leader]]

==External links==

* {{Commons category-inline}}

* [http://bacdive.dsmz.de/index.php?search=1172&submit=Search Type strain of ''Bacillus subtilis'' at Bac''Dive'' - the Bacterial Diversity Metadatabase]

{{Extremophile}}

{{Taxonbar|from=Q22065}}

{{二次利用|date=10 April 2024}}

[[Category:Bacillus|subtilis]]