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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 ruminants and humans. 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 aerobe . _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.

CONTENTS

* 1 Description * 2 Habitat * 3 Reproduction * 4 Chromosomal replication * 5 Genome * 6 Transformation

* 7 Uses

* 7.1 1900s * 7.2 2000s

* 8 Safety

* 8.1 In animals * 8.2 In humans

* 9 Identification * 10 See also * 11 References * 12 External links

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'). _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 flagellated , 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.

HABITAT

This species is commonly found in the upper layers of the soil, and evidence exists that _B. subtilis_ is a 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.

REPRODUCTION

_ Sporulating B. subtilis_. _ Another endospore stain of B. subtilis_.

_B. subtilis_ can divide symmetrically to make two daughter cells (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 solvents . The endospore is formed at times of nutritional stress, allowing the organism to persist in the environment until conditions become favourable. Prior to the process of sporulation the cells might become motile by producing flagella , take up DNA from the environment, or produce antibiotics . 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 of competition.

Under stressful conditions, such as nutrient deprivation, _B. subtilis_ undergoes the process of sporulation . This process has been very well studied and has served as a model organism for studying sporulation.

CHROMOSOMAL REPLICATION

_B. subtilis_ is a model organism used to study bacterial chromosome replication. Replication of the single circular chromosome initiates at a single locus, the origin (_oriC _). Replication proceeds bidirectionally and two replication forks 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 , 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.

GENOME

_B. 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 .

Several noncoding RNAs have been characterized in the _B. subtilis_ genome in 2009, including Bsr RNAs . Microarray-based comparative genomic analyses have revealed that _B. subtilis_ members show considerable genomic diversity.

TRANSFORMATION

Natural bacterial transformation involves the transfer of DNA from one bacterium to another through the surrounding medium. In _B. subtilis_, length of transferred DNA is greater than 1271 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 4215 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 . 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.

USES

1900S

_ Gram-stained B. subtilis_

Cultures of _B. 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 immune activity including activation of secretion of specific antibodies IgM , IgG and IgA and release of CpG dinucleotides inducing INF A/Y 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 .

Since the 1960s _B. subtilis_ has had a history as a test species in spaceflight experimentation. Its endospores 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
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. _ Colonies of B. subtilis_ grown on a culture dish in a molecular biology laboratory

_B. globigii,_ a closely related but phylogenetically distinct species now known as _ Bacillus atrophaeus _ was used as a biowarfare 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 _.

2000S

* 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_. * Its surface-binding properties play a role in safe radionuclide waste disposal. * Recombinant strains pBE2C1 and pBE2C1AB were used in production of polyhydroxyalkanoates (PHA), and malt waste can be used as their carbon source for lower-cost PHA production. * Due to its excellent fermentation properties, with high product yields (20 to 25 gram per litre) it is used to produce various enzymes, such as amylase and proteases. * Other enzymes produced by _B. subtilis_ and _B. licheniformis _ are widely used as additives in laundry detergents . * It is used to produce hyaluronic acid , which is used in the joint-care sector in healthcare and cosmetics. * _B. subtilis_ is used as a soil inoculant in horticulture and agriculture . * It may provide some benefit to saffron growers by speeding corm growth and increasing stigma biomass yield. * Monsanto has isolated a gene from _B. subtilis_ that expresses cold shock protein B and spliced it into their drought-tolerant corn hybrid MON 87460, which was approved for sale in the US in November 2011. * It is used as an "indicator organism" during gas sterilization procedures, to ensure a sterilization cycle has completed successfully. This is due to the difficulty in sterilizing endospores. * Novel strains of _B. subtilis_ that could use 4-fluorotryptophan (4FTrp) but not canonical tryptophan (Trp) for propagation were isolated. As 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.

SAFETY

IN ANIMALS

_B. 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". The Canadian Food Inspection Agency Animal Health and Production Feed Section has classified _Bacillus_ culture dehydrated approved feed ingredients as a silage additive under Schedule IV-Part 2-Class 8.6 and assigned the International Feed Ingredient number IFN 8-19-119.

IN HUMANS

_B. subtilis_ spores can survive the extreme heat during cooking. Some _B. subtilis_ strains are responsible for causing ropiness — a sticky, stringy consistency caused by bacterial production of long-chain polysaccharides — in spoiled bread dough. 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) evaluated in 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.

_B. subtilis_ and substances derived from it has 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) recognized 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 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 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.

_B. subtilis_ has been granted "Qualified Presumption of Safety" status by the European Food Safety Authority .

IDENTIFICATION

Below is a table that helps identify _B. subtilis_ through certain identification tests.

TEST RESULT

Acid from Glucose +

Acid from Lactose -

Acid from Sucrose +

Acid from Mannitol +

Catalase +

Citrate (Simmons) +

Endospore +

Gas from Glucose -

Gelatin Hydrolysis +

Gram Stain +

Hydrogen Sulfide Production -

Indole Production -

Motility +

Nitrate Reduction +

Oxidase +

Phenylalanine Deaminase -

Shape Rod

Urea Hydrolysis -

Voges-Proskaeur-Proskaeur +

SEE ALSO

* Adenylosuccinate lyase deficiency * Extremophile * Guthrie test

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EXTERNAL LINKS

_ Media related to Bacillus subtilis at Wikimedia Commons

* Subti_Wiki "up-to-date information for all genes