bacillus subtilis

Bacillus subtilis is a Gram-positive bacterium, rod-shaped and catalase-positive. It was originally named Vibrio subtilis by Christian Gottfried Ehrenberg,{{cite book | vauthors = Ehrenberg CG |title=Physikalische Abhandlungen der Koeniglichen Akademie der Wissenschaften zu Berlin aus den Jahren 1833–1835 |pages=145–336 |year=1835 |author-link=Christian Gottfried Ehrenberg}} and renamed Bacillus subtilis by Ferdinand Cohn in 1872{{cite book | vauthors = Cohn F |chapter=Untersuchungen über Bacterien |chapter-url=https://books.google.com/books?id=wnyHvEtfRrQC&pg=RA1-PA127 |title=Beiträge zur Biologie der Pflanzen |year=1872 |volume=1 |pages=127–224 |author-link=Ferdinand Cohn}} (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.{{cite journal | vauthors = Yu AC, Loo JF, Yu S, Kong SK, Chan TF | title = Monitoring bacterial growth using tunable resistive pulse sensing with a pore-based technique | journal = Applied Microbiology and Biotechnology | volume = 98 | issue = 2 | pages = 855–62 | date = January 2014 | pmid = 24287933 | doi = 10.1007/s00253-013-5377-9 | s2cid = 2956197 }}

As with other members of the genus Bacillus, it can form an endospore, to survive extreme environmental conditions of temperature and desiccation.{{cite book | veditors = Madigan M, Martinko J | title = Brock Biology of Microorganisms | edition = 11th | publisher = Prentice Hall | year = 2005| isbn=978-0-13-144329-7 }}{{page needed|date=October 2013}} B. subtilis is a facultative anaerobe{{cite journal | vauthors = Nakano MM, Zuber P | title = Anaerobic growth of a "strict aerobe" (Bacillus subtilis) | journal = Annual Review of Microbiology | volume = 52 | issue = 1 | pages = 165–90 | year = 1998 | pmid = 9891797 | doi = 10.1146/annurev.micro.52.1.165 }} 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.{{cite journal | vauthors = Ruiz N, Silhavy TJ | title = How Escherichia coli Became the Flagship Bacterium of Molecular Biology | journal = Journal of Bacteriology | volume = 204 | issue = 9 | pages = e0023022 | date = September 2022 | pmid = 35916528 | pmc = 9487582 | doi = 10.1128/jb.00230-22 | s2cid = 251254431 }}

Colony, morphological, physiological, and biochemical characteristics of Bacillus subtilis are shown in the Table below.{{Cite journal | vauthors = Paul SI, Rahman MM, Salam MA, Khan MA, Islam MT |date=2021-12-15|title=Identification of marine sponge-associated bacteria of the Saint Martin's island of the Bay of Bengal emphasizing on the prevention of motile Aeromonas septicemia in Labeo rohita |journal=Aquaculture |language=en |volume=545 |pages=737156 |doi=10.1016/j.aquaculture.2021.737156 |issn=0044-8486 }}

Note: + = Positive, – = Negative

This species is commonly found in the upper layers of the soil and B. subtilis is thought to be 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.{{cite journal | vauthors = Hong HA, Khaneja R, Tam NM, Cazzato A, Tan S, Urdaci M, Brisson A, Gasbarrini A, Barnes I, Cutting SM | title = Bacillus subtilis isolated from the human gastrointestinal tract | journal = Research in Microbiology | volume = 160 | issue = 2 | pages = 134–43 | date = March 2009 | pmid = 19068230 | doi = 10.1016/j.resmic.2008.11.002 | doi-access = free }} In some bee habitats, B. subtilis appears in the gut flora of honey bees.{{Cite journal| vauthors = Sudhagar S, Reddy PR, Nagalakshmi G |date=April 2017|title=Influence of elevation in structuring the gut bacterial communities of Apis cerana Fab|url=http://www.entomoljournal.com/archives/2017/vol5issue3/PartG/5-2-151-255.pdf|journal=Journal of Entomology and Zoology|volume=5|issue=3|pages=434–440 }} 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.{{Cite journal | vauthors = Tan IS, Ramamurthi KS |date=June 2014 |title=Spore formation in B acillus subtilis: Bacillus subtilis sporulation |journal=Environmental Microbiology Reports |language=en |volume=6 |issue=3 |pages=212–225 |doi=10.1111/1758-2229.12130|pmid=24983526 |pmc=4078662 }} Additionally, B. subtilis has been shown to form biofilms 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.

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Bacillus 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 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 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 off competition. {{Citation needed|date=June 2014}}

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.{{cite journal | vauthors = McKenney PT, Driks A, Eichenberger P | title = The Bacillus subtilis endospore: assembly and functions of the multilayered coat | journal = Nature Reviews. Microbiology | volume = 11 | issue = 1 | pages = 33–44 | date = January 2013 | pmid = 23202530 | doi = 10.1038/nrmicro2921 | pmc = 9910062 | s2cid = 205498395 | doi-access = free }}

{{main|Sporulation in Bacillus subtilis}}

{{further|Sporulation}}

{{excerpt|Sporulation in Bacillus subtilis|Commitment to sporulation}}Once B. subtilis commits to sporulation, the sigma factor sigma F is secreted.{{cite journal | vauthors = Earl AM, Losick R, Kolter R | title = Ecology and genomics of Bacillus subtilis | journal = Trends in Microbiology | volume = 16 | issue = 6 | pages = 269–275 | date = June 2008 | pmid = 18467096 | doi = 10.1016/j.tim.2008.03.004 | pmc = 2819312 }} This factor promotes sporulation. A sporulation septum is formed and a chromosome is slowly moved into the forespore. When a third of one chromosome copy is in the forespore and the remaining two thirds is in the mother cell, the chromosome fragment in the forespore contains the locus for sigma F, which begins to be expressed in the forespore.{{cite journal | vauthors = Higgins D, Dworkin J | title = Recent progress in Bacillus subtilis sporulation | journal = FEMS Microbiology Reviews | volume = 36 | issue = 1 | pages = 131–148 | date = January 2012 | pmid = 22091839 | doi = 10.1111/j.1574-6976.2011.00310.x | pmc = 3237856 }} In order to prevent sigma F expression in the mother cell, an anti-sigma factor, which is encoded by spoIIAB,Slonczewski J, John Watkins Foster, Zinser ER. 2020. Microbiology : an evolving science. New York: W.W. Norton & Company. is expressed. Any residual anti-sigma factor in the forespore (which would otherwise interfere with sporulation) is inhibited by an anti-anti-sigma factor, which is encoded by spoIIAA. SpoIIAA is located near the locus for the sigma factor, so it is consistently expressed in the forespore. Since the spoIIAB locus is not located near the sigma F and spoIIAA loci, it is expressed only in the mother cell and therefore repress sporulation in that cell, allowing sporulation to continue in the forespore. Residual spoIIAA in the mother cell represses spoIIAB, but spoIIAB is constantly replaced so it continues to inhibit sporulation. When the full chromosome localizes to the forespore, spoIIAB can repress sigma F. Therefore, the genetic asymmetry of the B. subtilis chromosome and expression of sigma F, spoIIAB and spoIIAA dictate spore formation in B. subtilis.

File:B._subtilis_sporulation_reg.png

{{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 (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.{{cite book |chapter-url=http://www.horizonpress.com/bac | vauthors = Noirot P|chapter=Replication of the Bacillus subtilis chromosome | title = Bacillus: Cellular and Molecular Biology | veditors = Graumann P | publisher = Caister Academic Press | year = 2007 | isbn = 978-1-904455-12-7 }}{{page needed|date=October 2013}}

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.{{cite journal | vauthors = Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, Boland F, Brignell SC, Bron S, Bunai K, Chapuis J, Christiansen LC, Danchin A, Débarbouille M, Dervyn E, Deuerling E, Devine K, Devine SK, Dreesen O, Errington J, Fillinger S, Foster SJ, Fujita Y, Galizzi A, Gardan R, Eschevins C, Fukushima T, Haga K, Harwood CR, Hecker M, Hosoya D, Hullo MF, Kakeshita H, Karamata D, Kasahara Y, Kawamura F, Koga K, Koski P, Kuwana R, Imamura D, Ishimaru M, Ishikawa S, Ishio I, Le Coq D, Masson A, Mauël C, Meima R, Mellado RP, Moir A, Moriya S, Nagakawa E, Nanamiya H, Nakai S, Nygaard P, Ogura M, Ohanan T, O'Reilly M, O'Rourke M, Pragai Z, Pooley HM, Rapoport G, Rawlins JP, Rivas LA, Rivolta C, Sadaie A, Sadaie Y, Sarvas M, Sato T, Saxild HH, Scanlan E, Schumann W, Seegers JF, Sekiguchi J, Sekowska A, Séror SJ, Simon M, Stragier P, Studer R, Takamatsu H, Tanaka T, Takeuchi M, Thomaides HB, Vagner V, van Dijl JM, Watabe K, Wipat A, Yamamoto H, Yamamoto M, Yamamoto Y, Yamane K, Yata K, Yoshida K, Yoshikawa H, Zuber U, Ogasawara N | display-authors = 6 | title = Essential Bacillus subtilis genes | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 100 | issue = 8 | pages = 4678–83 | date = April 2003 | pmid = 12682299 | pmc = 153615 | doi = 10.1073/pnas.0730515100 | bibcode = 2003PNAS..100.4678K | jstor = 3144001 | doi-access = free }}

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].{{cite journal | vauthors = Yu CS, Yim KY, Tsui SK, Chan TF | title = Complete genome sequence of Bacillus subtilis strain QB928, a strain widely used in B. subtilis genetic studies | journal = Journal of Bacteriology | volume = 194 | issue = 22 | pages = 6308–9 | date = November 2012 | pmid = 23105055 | doi = 10.1128/JB.01533-12 | pmc=3486399}}

Several noncoding RNAs have been characterized in the B. subtilis genome in 2009, including Bsr RNAs.{{cite journal | vauthors = Saito S, Kakeshita H, Nakamura K | title = Novel small RNA-encoding genes in the intergenic regions of Bacillus subtilis | journal = Gene | volume = 428 | issue = 1–2 | pages = 2–8 | date = January 2009 | pmid = 18948176 | doi = 10.1016/j.gene.2008.09.024 }}

Microarray-based comparative genomic analyses have revealed that B. subtilis members show considerable genomic diversity.{{cite journal | vauthors = Earl AM, Losick R, Kolter R | title = Ecology and genomics of Bacillus subtilis | journal = Trends in Microbiology | volume = 16 | issue = 6 | pages = 269–75 | date = June 2008 | pmid = 18467096 | pmc = 2819312 | doi = 10.1016/j.tim.2008.03.004 }}

FsrA is a small RNA found in Bacillus subtilis. It is an effector of the iron sparing response, and acts to down-regulate iron-containing proteins in times of poor iron bioavailability.{{cite journal | vauthors = Gaballa A, Antelmann H, Aguilar C, Khakh SK, Song KB, Smaldone GT, Helmann JD | title = The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 33 | pages = 11927–32 | date = August 2008 | pmid = 18697947 | pmc = 2575260 | doi = 10.1073/pnas.0711752105 | bibcode = 2008PNAS..10511927G | doi-access = free }}{{cite journal | vauthors = Smaldone GT, Antelmann H, Gaballa A, Helmann JD | title = The FsrA sRNA and FbpB protein mediate the iron-dependent induction of the Bacillus subtilis lutABC iron-sulfur-containing oxidases | journal = Journal of Bacteriology | volume = 194 | issue = 10 | pages = 2586–93 | date = May 2012 | pmid = 22427629 | pmc = 3347220 | doi = 10.1128/JB.05567-11 }}

A promising fish probiotic, B. 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.{{cite journal | vauthors = Rahman MM, Paul SI, Akter T, Tay AC, Foysal MJ, Islam MT | title = Whole-Genome Sequence of Bacillus subtilis WS1A, a Promising Fish Probiotic Strain Isolated from Marine Sponge of the Bay of Bengal | journal = Microbiology Resource Announcements | volume = 9 | issue = 39 | date = September 2020 | pmid = 32972930 | pmc = 7516141 | doi = 10.1128/mra.00641-20 }} B. subtilis strain WS1A genome contains many potential genes, such as those encoding proteins involved in the biosynthesis of riboflavin, vitamin B6, and amino acids ([https://www.uniprot.org/uniprot/P51785 ilvD]) and in carbon utilization ([https://www.uniprot.org/uniprot/P39646 pta]).

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).{{cite journal | vauthors = Saito Y, Taguchi H, Akamatsu T | title = Fate of transforming bacterial genome following incorporation into competent cells of Bacillus subtilis: a continuous length of incorporated DNA | journal = Journal of Bioscience and Bioengineering | volume = 101 | issue = 3 | pages = 257–62 | date = March 2006 | pmid = 16716928 | doi = 10.1263/jbb.101.257 }} The transferred DNA is likely double-stranded DNA and is often more than a third of the total chromosome length of 4,215 kb.{{cite journal | vauthors = Saito Y, Taguchi H, Akamatsu T | title = DNA taken into Bacillus subtilis competent cells by lysed-protoplast transformation is not ssDNA but dsDNA | journal = Journal of Bioscience and Bioengineering | volume = 101 | issue = 4 | pages = 334–39 | date = April 2006 | pmid = 16716942 | doi = 10.1263/jbb.101.334 }} It appears that about 7–9% of the recipient cells take up an entire chromosome.{{cite journal | vauthors = Akamatsu T, Taguchi H | title = Incorporation of the whole chromosomal DNA in protoplast lysates into competent cells of Bacillus subtilis | journal = Bioscience, Biotechnology, and Biochemistry | volume = 65 | issue = 4 | pages = 823–29 | date = April 2001 | pmid = 11388459 | doi = 10.1271/bbb.65.823 | s2cid = 30118947 | doi-access = free }}

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.{{cite journal | vauthors = Anagnostopoulos C, Spizizen J | journal = Journal of Bacteriology | volume = 81 | issue = 5 | pages = 741–46 | date = May 1961 | pmid = 16561900 | pmc = 279084 | title = Requirements for Transformation in Bacillus Subtilis | doi = 10.1128/JB.81.5.741-746.1961 }} 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.{{cite journal | vauthors = Hoelzer MA, Michod RE | title = DNA repair and the evolution of transformation in Bacillus subtilis. III. Sex with damaged DNA | journal = Genetics | volume = 128 | issue = 2 | pages = 215–23 | date = June 1991 | doi = 10.1093/genetics/128.2.215 | pmid = 1906416 | pmc = 1204460 | url = http://www.genetics.org/cgi/pmidlookup?view=long&pmid=1906416 }}{{cite journal | vauthors = Michod RE, Wojciechowski MF, Hoelzer MA | title = DNA repair and the evolution of transformation in the bacterium Bacillus subtilis | journal = Genetics | volume = 118 | issue = 1 | pages = 31–39 | date = January 1988 | doi = 10.1093/genetics/118.1.31 | pmid = 8608929 | pmc = 1203263 | url = http://www.genetics.org/cgi/pmidlookup?view=long&pmid=8608929 }}{{cite journal | vauthors = Wojciechowski MF, Hoelzer MA, Michod RE | title = DNA repair and the evolution of transformation in Bacillus subtilis. II. Role of inducible repair | journal = Genetics | volume = 121 | issue = 3 | pages = 411–22 | date = March 1989 | doi = 10.1093/genetics/121.3.411 | pmid = 2497048 | pmc = 1203629 | url = http://www.genetics.org/cgi/pmidlookup?view=long&pmid=2497048 }} 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.{{cite journal | vauthors = Michod RE, Bernstein H, Nedelcu AM | title = Adaptive value of sex in microbial pathogens | journal = Infection, Genetics and Evolution | volume = 8 | issue = 3 | pages = 267–85 | date = May 2008 | pmid = 18295550 | doi = 10.1016/j.meegid.2008.01.002 }}

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.{{cite journal | vauthors = Itaya M, Nagasaku M, Shimada T, Ohtani N, Shiwa Y, Yoshikawa H, Kaneko S, Tomita M, Sato M | display-authors = 6 | title = Stable and efficient delivery of DNA to Bacillus subtilis (natto) using pLS20 conjugational transfer plasmids | journal = FEMS Microbiology Letters | volume = 366 | issue = 4 | date = February 2019 | pmid = 30726909 | doi = 10.1093/femsle/fnz032 }}

By adopting Green Chemistry{{buzzword inline|date=June 2025}} in the use of less hazardous materials, while saving cost, researchers{{Who|date=June 2025}} 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 bacteria 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.{{Cite web |title=Chemistry AU naturel: mimicking nature's clean and efficient ways. - Free Online Library |url=https://www.thefreelibrary.com/Chemistry+AU+naturel:+mimicking+nature%27s+clean+and+efficient+ways.-a0129629071 |access-date=2023-04-29 |website=www.thefreelibrary.com}}

Image:Bacillus subtilis Gram.jpg

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{{cite journal | vauthors = Ciprandi G, Scordamaglia A, Venuti D, Caria M, Canonica GW | title = In vitro effects of Bacillus subtilis on the immune response | journal = Chemioterapia | volume = 5 | issue = 6 | pages = 404–07 | date = December 1986 | pmid = 3100070 }} and release of CpG dinucleotides inducing interferon IFN-α/IFNγ producing activity of leukocytes and cytokines important in the development of cytotoxicity towards tumor cells.{{cite journal | vauthors= Shylakhovenko VA | title=Anticancer and Immunostimulatory effects of Nucleoprotein Fraction of 'Bacillus subtilis' | journal=Experimental Oncology |volume=25 |date=June 2003 | pages=119–23}} 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 how a biological agent dispensed around the subway trains would disperse and potentially affect unsuspecting passengers.{{cite book|url=https://searchworks.stanford.edu/view/13147679 |title=A study of the vulnerability of subway passengers in New York City to covert action with biological agents |series=Miscellaneous publication |publisher=Department of the Army, Fort Detrick |year=1968}} Due to its ability to survive, it is thought to still be present there.{{cite book | vauthors = Rosoff S, Pontell H, Tillman R |date= 2020 |title= Profit Without Honor: White Collar Crime and the Looting of America |publisher= Pearson |pages= 352–3 |isbn= 9780134871486}}

The antibiotic bacitracin was first isolated from a variety of Bacillus licheniformis named "Tracy I"{{cite web | vauthors = Podstawka A |title=Bacillus licheniformis Tracy I {{!}} DSM 603, ATCC 10716, CCM 2181, IFO 12199, NBRC 12199, NCIB 8874, FDA BT1 {{!}} BacDiveID:686 |url=https://bacdive.dsmz.de/strain/686 |website=bacdive.dsmz.de |language=en}} 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.{{cite journal | vauthors = Johnson BA, Anker H, Meleney FL | title = Bacitracin: a new antibiotic produced by a member of the B. subtilis group | journal = Science | volume = 102 | issue = 2650 | pages = 376–7 | date = October 1945 | pmid = 17770204 | doi = 10.1126/science.102.2650.376 | bibcode = 1945Sci...102..376J | s2cid = 51066 }}

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.{{cite journal | vauthors = Horneck G, Klaus DM, Mancinelli RL | title = Space microbiology | journal = Microbiology and Molecular Biology Reviews | volume = 74 | issue = 1 | pages = 121–56 | date = March 2010 | pmid = 20197502 | pmc = 2832349 | doi = 10.1128/mmbr.00016-09 | bibcode = 2010MMBR...74..121H }} It has been used as an extremophile survival indicator in outer space such as Exobiology Radiation Assembly,{{cite journal | vauthors = Dose K, Bieger-Dose A, Dillmann R, Gill M, Kerz O, Klein A, Meinert H, Nawroth T, Risi S, Stridde C | display-authors = 6 | title = ERA-experiment "Space Biochemistry" | journal = Advances in Space Research | volume = 16 | issue = 8 | pages = 119–29 | year = 1995 | pmid = 11542696 | doi = 10.1016/0273-1177(95)00280-R | bibcode = 1995AdSpR..16h.119D }}{{cite journal |doi=10.1016/0273-1177(95)00217-3 |title=Ion populations in the tail of Venus |year=1995 | vauthors = Vaisberg O, Fedorov A, Dunjushkin F, Kozhukhovsky A, Smirnov V, Avanov L, Russell CT, Luhmann JG | display-authors = 6 |journal=Advances in Space Research |volume=16 |issue=4 |pages=105–18 |bibcode=1995AdSpR..16d.105V}} EXOSTACK,{{cite book | vauthors = Clancy P | title = Looking for Life, Searching the Solar System | publisher = Cambridge University Press | date = Jun 23, 2005}}{{page needed|date=October 2013}}{{cite journal | vauthors = Horneck G, Klaus DM, Mancinelli RL | title = Space microbiology | journal = Microbiology and Molecular Biology Reviews | volume = 74 | issue = 1 | pages = 121–56 | date = March 2010 | pmid = 20197502 | pmc = 2832349 | doi = 10.1128/MMBR.00016-09 | bibcode = 2010MMBR...74..121H }} and EXPOSE orbital missions.{{cite journal | vauthors = Fajardo-Cavazos P, Link L, Melosh HJ, Nicholson WL | title = Bacillus subtilis spores on artificial meteorites survive hypervelocity atmospheric entry: implications for Lithopanspermia | journal = Astrobiology | volume = 5 | issue = 6 | pages = 726–36 | date = December 2005 | pmid = 16379527 | doi = 10.1089/ast.2005.5.726 | bibcode = 2005AsBio...5..726F }}{{cite journal |doi=10.1016/j.pss.2007.12.014 |title=Mineralogical alteration of artificial meteorites during atmospheric entry. The STONE-5 experiment |year=2008 | vauthors = Brandstätter F, Brack A, Baglioni P, Cockell CS, Demets R, Edwards HG, Kurat G, Osinski GR, Pillinger JM, Roten CA, Sancisi-Frey S | display-authors = 6 |journal=Planetary and Space Science |volume=56 |issue=7 |pages=976–84 |bibcode=2008P&SS...56..976B|citeseerx=10.1.1.549.4307 }}{{cite journal | vauthors = Wassmann M, Moeller R, Rabbow E, Panitz C, Horneck G, Reitz G, Douki T, Cadet J, Stan-Lotter H, Cockell CS, Rettberg P | display-authors = 6 | title = Survival of spores of the UV-resistant Bacillus subtilis strain MW01 after exposure to low-earth orbit and simulated martian conditions: data from the space experiment ADAPT on EXPOSE-E | journal = Astrobiology | volume = 12 | issue = 5 | pages = 498–507 | date = May 2012 | pmid = 22680695 | doi = 10.1089/ast.2011.0772 | bibcode = 2012AsBio..12..498W }}

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.{{cite journal | vauthors = Zeigler DR, Prágai Z, Rodriguez S, Chevreux B, Muffler A, Albert T, Bai R, Wyss M, Perkins JB | display-authors = 6 | title = The origins of 168, W23, and other Bacillus subtilis legacy strains | journal = Journal of Bacteriology | volume = 190 | issue = 21 | pages = 6983–95 | date = November 2008 | pmid = 18723616 | pmc = 2580678 | doi = 10.1128/JB.00722-08 }}

Image:Bacillus subtilis colonies.jpg in a molecular biology laboratory]]

Bacillus globigii, a closely related but phylogenetically distinct species now known as Bacillus atrophaeus{{cite journal |doi=10.1099/00207713-39-3-295 |title=Taxonomic Relationship of Black-Pigmented Bacillus subtilis Strains and a Proposal for Bacillus atrophaeus sp. nov |year=1989 | vauthors = Nakamura LK | journal=International Journal of Systematic Bacteriology |volume=39 |issue=3 |pages=295–300|doi-access=free }}{{cite journal | vauthors = Burke SA, Wright JD, Robinson MK, Bronk BV, Warren RL | title = Detection of molecular diversity in Bacillus atrophaeus by amplified fragment length polymorphism analysis | journal = Applied and Environmental Microbiology | volume = 70 | issue = 5 | pages = 2786–90 | date = May 2004 | pmid = 15128533 | pmc = 404429 | doi = 10.1128/AEM.70.5.2786-2790.2004 | bibcode = 2004ApEnM..70.2786B }} was used as a biowarfare simulant during Project SHAD (aka Project 112).{{cite web|title=Project 112/SHAD - Shipboard Hazard and Defense |url=http://mcm.fhpr.osd.mil/cb_exposures/project112_shad/shad.aspx |publisher=U.S. Department of Veterans' Affairs |access-date=25 February 2015 |url-status=dead |archive-url=https://web.archive.org/web/20150221192452/http://mcm.fhpr.osd.mil/cb_exposures/project112_shad/shad.aspx |archive-date=21 February 2015 }} 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.{{cite journal | vauthors = Gibbons HS, Broomall SM, McNew LA, Daligault H, Chapman C, Bruce D, Karavis M, Krepps M, McGregor PA, Hong C, Park KH, Akmal A, Feldman A, Lin JS, Chang WE, Higgs BW, Demirev P, Lindquist J, Liem A, Fochler E, Read TD, Tapia R, Johnson S, Bishop-Lilly KA, Detter C, Han C, Sozhamannan S, Rosenzweig CN, Skowronski EW | title = Genomic signatures of strain selection and enhancement in Bacillus atrophaeus var. globigii, a historical biowarfare simulant | journal = PLOS ONE | volume = 6 | issue = 3 | pages = e17836 | date = March 2011 | pmid = 21464989 | pmc = 3064580 | doi = 10.1371/journal.pone.0017836 | bibcode = 2011PLoSO...617836G | doi-access = free }}

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.

• 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 [e.g. thorium (IV) and plutonium (IV)] disposal.{{citation needed|date=March 2020}}
• 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.{{cite journal | vauthors = van Dijl JM, Hecker M | title = Bacillus subtilis: from soil bacterium to super-secreting cell factory | journal = Microbial Cell Factories | volume = 12 | issue = 3 | pages = 3 | date = January 2013 | pmid = 23311580 | doi = 10.1186/1475-2859-12-3 | pmc=3564730 | doi-access = free }}
• B. subtilis is used as a soil inoculant in horticulture and agriculture.{{Cite web |url=http://www.eppo.int/QUARANTINE/fungi/Monilinia_fructicola/MONIFC_ds.pdf |title=Monilinia fructicola | work = Data Sheets on Quarantine Pests | publisher = European Public Prosecutor's Office (EPPO) |access-date=2015-07-21 |archive-date=2015-06-04 |archive-url=https://web.archive.org/web/20150604195059/http://www.eppo.int/QUARANTINE/fungi/Monilinia_fructicola/MONIFC_ds.pdf |url-status=dead }}{{cite journal | vauthors = Swain MR, Ray RC | title = Biocontrol and other beneficial activities of Bacillus subtilis isolated from cowdung microflora | journal = Microbiological Research | volume = 164 | issue = 2 | pages = 121–30 | pmid = 17320363 | doi = 10.1016/j.micres.2006.10.009 | year=2009| doi-access = }}{{cite journal|title=Biological control of peach brown rot (Monilinia spp.) by Bacillus subtilis CPA-8 is based on production of fengycin-like lipopeptides| doi=10.1007/s10658-011-9905-0|volume=132|issue = 4|journal=European Journal of Plant Pathology|pages=609–19|year=2011|vauthors=Yánez-Mendizábal V| s2cid=15761522}}
• It may provide some benefit to saffron growers by speeding corn growth and increasing stigma biomass yield.{{cite journal | vauthors = Sharaf-Eldin M, Elkholy S, Fernández JA, Junge H, Cheetham R, Guardiola J, Weathers P | title = Bacillus subtilis FZB24 affects flower quantity and quality of saffron (Crocus sativus) | journal = Planta Medica | volume = 74 | issue = 10 | pages = 1316–20 | date = August 2008 | pmid = 18622904 | pmc = 3947403 | doi = 10.1055/s-2008-1081293 }}
• It is used as an "indicator organism" during gas sterilization procedures, to ensure a sterilization cycle has completed successfully. Specifically B. subtilis endospores are used to verify that a cycle has reached spore-destroying conditions.{{cite web|url=https://www.who.int/phint/en/d/Jb.7.5.9/|archive-url=https://web.archive.org/web/20081208010853/http://www.who.int/phint/en/d/Jb.7.5.9/|url-status=dead|archive-date=December 8, 2008|title=The International Pharmacopoeia – Fourth Supplement: Methods of Analysis: 5. Pharmaceutical technical procedures: 5.8 Methods of sterilization}}{{cite web|url=http://www.andersenproducts.com/accessories/AN2203/index.html|work=Andersen Products|title=AN-2203 Biological Indicator for EO (25/box)|access-date=2013-05-24|archive-date=2013-10-06|archive-url=https://web.archive.org/web/20131006020504/http://www.andersenproducts.com/accessories/AN2203/index.html|url-status=dead}}
• B. subtilis has been found to act as a useful bioproduct fungicide that prevents the growth of Monilinia vaccinii-corymbosi, a.k.a. the mummy berry fungus, without interfering with pollination or fruit qualities.{{Cite journal|date=2005-04-01|title=Effect of flower-applied Serenade biofungicide (Bacillus subtilis) on pollination-related variables in rabbiteye blueberry|journal=Biological Control|volume=33|issue=1|pages=32–38|doi=10.1016/j.biocontrol.2005.01.002|issn=1049-9644|vauthors=Ngugi HK, Dedej S, Delaplane KS, Savelle AT, Scherm H}}
• 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.
• Pairing bacillus subtilis and with chitosan has been shown to reduce green mold decay in citrus fruits.{{Cite journal |last1=Waewthongrak |first1=Waree |last2=Pisuchpen |first2=Supachai |last3=Leelasuphakul |first3=Wanchai |year=2015 |title=Effect of Bacillus subtilis and chitosan applications on green mold (Penicillium digitatum Sacc.) decay in citrus fruit |url=https://doi.org/10.1016/j.postharvbio.2014.07.010 |journal=Postharvest Biology and Technology |volume=99 |pages=44–49 |doi=10.1016/j.postharvbio.2014.07.010 |issn=0925-5214}}

• 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.{{cite journal | vauthors = Yu AC, Yim AK, Mat WK, Tong AH, Lok S, Xue H, Tsui SK, Wong JT, Chan TF | title = Mutations enabling displacement of tryptophan by 4-fluorotryptophan as a canonical amino acid of the genetic code | journal = Genome Biology and Evolution | volume = 6 | issue = 3 | pages = 629–41 | date = March 2014 | pmid = 24572018 | doi = 10.1093/gbe/evu044 | url= | pmc=3971595}}
• 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.{{citation needed|date=January 2015}}
• It is used to produce hyaluronic acid, which is used in the joint-care sector in healthcare{{cite web |url=http://www.biopharma.novozymes.com/en/hyaluronic-acid/Frequently-asked-questions/Pages/default.aspx |title=Sodium hyaluronate frequently asked questions, hyaluronic acid FAQs, HA – Hyasis® | Novozymes Biopharma |access-date=2013-08-13 |url-status=dead |archive-url=https://web.archive.org/web/20130828202453/http://www.biopharma.novozymes.com/en/hyaluronic-acid/Frequently-asked-questions/Pages/default.aspx |archive-date=2013-08-28 }} and cosmetics.
• 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.{{cite journal | vauthors = Harrigan GG, Ridley WP, Miller KD, Sorbet R, Riordan SG, Nemeth MA, Reeves W, Pester TA | display-authors = 6 | title = The forage and grain of MON 87460, a drought-tolerant corn hybrid, are compositionally equivalent to that of conventional corn | journal = Journal of Agricultural and Food Chemistry | volume = 57 | issue = 20 | pages = 9754–63 | date = October 2009 | pmid = 19778059 | doi = 10.1021/jf9021515 }}[http://www.aphis.usda.gov/brs/aphisdocs/09_05501p_det.pdf USDA: Determination of Nonregulated Status for MON 87460 Corn (Zea mays L)]
• A new strain has been modified to convert nectar into honey by secreting enzymes.{{Cite web|url=http://www.israel21c.org/israeli-students-win-award-for-making-honey-without-bees/|title=Israeli students win award for making honey without bees| vauthors = Blum B |date=2019-11-17|website=Israel21c|language=en-US|access-date=2019-11-24}}

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".{{citation needed|date=January 2015}}

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.{{citation needed|date=January 2015}}

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.

Bacillus subtilis spores can survive the extreme heat generated during cooking. Some B. subtilis strains are responsible for causing ropiness or rope spoilage – a sticky, stringy consistency caused by bacterial production of long-chain polysaccharides – in spoiled bread dough and baked goods.{{Cite web|title=Rope Spoilage {{!}} Baking Processes|url=https://bakerpedia.com/processes/rope-spoilage/|access-date=2021-02-07|website=BAKERpedia|date=21 June 2016 |language=en-US}} 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.{{cite journal | vauthors = Pepe O, Blaiotta G, Moschetti G, Greco T, Villani F | title = Rope-producing strains of Bacillus spp. from wheat bread and strategy for their control by lactic acid bacteria | journal = Applied and Environmental Microbiology | volume = 69 | issue = 4 | pages = 2321–9 | date = April 2003 | pmid = 12676716 | pmc = 154770 | doi = 10.1128/AEM.69.4.2321-2329.2003 | bibcode = 2003ApEnM..69.2321P }}

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.{{cite journal | vauthors = Lefevre M, Racedo SM, Denayrolles M, Ripert G, Desfougères T, Lobach AR, Simon R, Pélerin F, Jüsten P, Urdaci MC | display-authors = 6 | title = Safety assessment of Bacillus subtilis CU1 for use as a probiotic in humans | journal = Regulatory Toxicology and Pharmacology | volume = 83 | pages = 54–65 | date = February 2017 | pmid = 27825987 | doi = 10.1016/j.yrtph.2016.11.010 | doi-access = free }}

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.{{cite web|url=https://www.fda.gov/Food/FoodIngredientsPackaging/ucm078956.htm|title= FDA partial list of microorganisms|year= 2002|publisher=Food and Drug Administration}}{{dead link|date=May 2025|bot=medic}}{{cbignore|bot=medic}} 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 intake; during this long history of widespread use, natto has not been implicated in adverse events potentially attributable to the presence of B. subtilis.{{citation needed|date=January 2015}} 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.{{cite book | vauthors = Shortt C | chapter = Perspectives on foods for specific health uses (FOSHU) | pages = 7–1 | veditors = Gibson GR|title=Food Science and Technology Bulletin : Functional Foods | volume = 1 |date=September 2005 |publisher=IFIS Publishing |location=Reading |isbn=978-0-86014-193-8}}

Bacillus subtilis has been granted "Qualified Presumption of Safety" status by the European Food Safety Authority.{{cite journal | author = EFSA Panel on Biological Hazards (BIOHAZ) | title = Scientific opinion on the maintenance of the list of QPS microorganisms intentionally added to food or feed (2010 update) | journal = EFSA Journal | volume = 8 | issue = 12 | pages = 1944 | year = 2010 |doi= 10.2903/j.efsa.2010.1944 | url = http://www.efsa.europa.eu/en/efsajournal/pub/1944| doi-access = free }}

• Adenylosuccinate lyase deficiency
• Extremophile
• Guthrie test
• YlbH leader

{{Reflist}}

• {{Commons category-inline}}
• [http://www.subtiwiki.uni-goettingen.de/ SubtiWiki] "up-to-date information for all genes of Bacillus subtilis"
• [http://epa.gov/biotech_rule/pubs/fra/fra009.htm Bacillus subtilis Final Risk Assessment] on EPA.gov. [https://web.archive.org/web/20150909034145/http://epa.gov/biotech_rule/pubs/fra/fra009.htm Archived from the original on 2015-09-09].
• [http://genolist.pasteur.fr/SubtiList/ Bacillus subtilis genome browser]
• [http://bacdive.dsmz.de/index.php?search=1172&submit=Search Type strain of Bacillus subtilis at BacDive - the Bacterial Diversity Metadatabase]

{{Extremophile}}

{{Taxonbar|from=Q131238}}

{{Authority control}}

subtilis

Category:Bacteria described in 1872

Category:Extremophiles

Category:Food microbiology