Bacteriophage
Overview
A bacteriophage is any one of a number of viruses that infect
Infection
An infection is the colonization of a host organism by parasite species. Infecting parasites seek to use the host's resources to reproduce, often resulting in disease...

 bacteria. They do this by injecting genetic material, which they carry enclosed in an outer protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

 capsid
Capsid
A capsid is the protein shell of a virus. It consists of several oligomeric structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or may not correspond to individual proteins, are called capsomeres. The capsid encloses the genetic...

. The genetic material can be ssRNA, dsRNA, ssDNA, or dsDNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

 ('ss-' or 'ds-' prefix denotes single-strand or double-strand) along with either circular or linear arrangement.

Bacteriophages are among the most common and diverse entities in the biosphere
Biosphere
The biosphere is the global sum of all ecosystems. It can also be called the zone of life on Earth, a closed and self-regulating system...

.
Discussions
Encyclopedia
A bacteriophage is any one of a number of viruses that infect
Infection
An infection is the colonization of a host organism by parasite species. Infecting parasites seek to use the host's resources to reproduce, often resulting in disease...

 bacteria. They do this by injecting genetic material, which they carry enclosed in an outer protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

 capsid
Capsid
A capsid is the protein shell of a virus. It consists of several oligomeric structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or may not correspond to individual proteins, are called capsomeres. The capsid encloses the genetic...

. The genetic material can be ssRNA, dsRNA, ssDNA, or dsDNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

 ('ss-' or 'ds-' prefix denotes single-strand or double-strand) along with either circular or linear arrangement.

Bacteriophages are among the most common and diverse entities in the biosphere
Biosphere
The biosphere is the global sum of all ecosystems. It can also be called the zone of life on Earth, a closed and self-regulating system...

. The term is commonly used in its shortened form, phage.

Phages are widely distributed in locations populated by bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...

l hosts, such as soil or the intestines of animals. One of the densest natural sources for phages and other viruses is sea water, where up to 9×108 virions
Virus
A virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea...

 per milliliter have been found in microbial mats at the surface, and up to 70% of marine bacteria may be infected by phages.
They have been used for over 90 years as an alternative to antibiotics in the former Soviet Union
Soviet Union
The Soviet Union , officially the Union of Soviet Socialist Republics , was a constitutionally socialist state that existed in Eurasia between 1922 and 1991....

 and Eastern Europe as well in France. They are seen as a possible therapy against multi-drug-resistant strains of many bacteria.

Classification

The dsDNA tailed phages, or Caudovirales, account for 95% of all the phages reported in the scientific literature, and possibly make up the majority of phages on the planet. However, there are other phages that occur abundantly in the biosphere, phages with different virions, genomes and lifestyles. Phages are classified by the International Committee on Taxonomy of Viruses
International Committee on Taxonomy of Viruses
The International Committee on Taxonomy of Viruses is a committee which authorizes and organizes the taxonomic classification of viruses. They have developed a universal taxonomic scheme for viruses and aim to describe all the viruses of living organisms. Members of the committee are considered to...

 (ICTV) according to morphology and nucleic acid.
| rowspan=3 | Caudovirales
Caudovirales
The Caudovirales are an order of viruses also known as the tailed bacteriophages. Under the Baltimore classification scheme, the Caudovirales are group I viruses as they have double stranded DNA genomes, which can be anywhere from 18,000 base pairs to 500,000 base pairs in length...

> | rowspan=10 | Unassigned >
ICTV classification of phages
Order Family Morphology Nucleic acid Examples
Myoviridae
Myoviridae
The Myoviridae is a family of bacteriophages. It has been divided into three subfamiles and a number of genera not yet assigned to a subfamily. There are at least 130 species in this family.-Virology:...

Non-enveloped
Viral envelope
Many viruses have viral envelopes covering their protein capsids. The envelopes typically are derived from portions of the host cell membranes , but include some viral glycoproteins. Functionally, viral envelopes are used to help viruses enter host cells...

, contractile tail
Linear dsDNA T4 phage
Siphoviridae
Siphoviridae
Siphoviridae are a family of double-stranded DNA viruses infecting only bacteria. The characteristic features of this family is the presence of a head and non contractile tail.There are at least 256 species in this family.-Virology:...

Non-enveloped, non-contractile tail (long) Linear dsDNA λ phage
Lambda phage
Enterobacteria phage λ is a temperate bacteriophage that infects Escherichia coli.Lambda phage is a virus particle consisting of a head, containing double-stranded linear DNA as its genetic material, and a tail that can have tail fibers. The phage particle recognizes and binds to its host, E...

, Bacteriophage T5
Bacteriophage T5
T5 bacteriophage is a caudal virus who belongs to siphoviridae family. It's a lytic phage that infect E. coli. T5 consists of a 90 nm large icosahedral capsid containing a 121750 bp dsDNA and a 250 nm long flexible and non contractile tail ....

Podoviridae
Podoviridae
The Podoviridae are a family of bacteriophages. Unlike the other families of tailed viruses this family has short tails that are non contractile.There are at least 74 species in this family.-Virology:...

Non-enveloped, non-contractile tail (short) Linear dsDNA T7 phage
T7 phage
Bacteriophage T7 is a bacteriophage capable of infecting susceptible bacterial cells. It infects most strains of Escherichia coli Bacteriophage T7 is a bacteriophage capable of infecting susceptible bacterial cells. It infects most strains of Escherichia coli Bacteriophage T7 is a bacteriophage...

Tectiviridae Non-enveloped, isometric Linear dsDNA
Rudiviridae Non-enveloped, rod-shaped Linear dsDNA
Leviviridae
Leviviridae
The Leviviridae are a family of viruses, including the following genera:*Genus Levivirus; type species: Enterobacteria phage MS2*Genus Allolevivirus; type species: Enterobacteria phage Qβ-External links:*...

Non-enveloped, isometric Linear ssRNA
Corticoviridae Non-enveloped, isometric Circular dsDNA
Fuselloviridae Non-enveloped, lemon-shaped Circular dsDNA
Inoviridae
Inoviridae
The Inoviridae are a family of filamentous bacteriophages. The name of the family is derived from the Greek word 'nos' meaning 'muscle'.-Virology:...

Non-enveloped, filamentous Circular ssDNA
Microviridae
Microviridae
The Microviridae are a family of bacteriophages with a single stranded DNA genome. The name of this family is derived from the Greek word 'micro' meaning small. This refers to the size of their genomes which are among the smallest of the DNA viruses....

Non-enveloped, isometric Circular ssDNA
Lipothrixviridae
Lipothrixviridae
The Lipothrixviridae family consists of a family of viruses that infect archaea.-Taxonomy:These viruses share characteristics from the Rudiviridae family and both have are filamentous viruses with linear dsDNA genomes that infect thermophilic archaea in the kingdom Crenarchaeota.There are four...

Enveloped, rod-shaped Linear dsDNA
Plasmaviridae Enveloped, pleomorphic Circular dsDNA
Cystoviridae Enveloped, spherical Segmented dsRNA

History

Since ancient times, there have been documented reports of river waters having the ability to cure infectious diseases, such as leprosy
Leprosy
Leprosy or Hansen's disease is a chronic disease caused by the bacteria Mycobacterium leprae and Mycobacterium lepromatosis. Named after physician Gerhard Armauer Hansen, leprosy is primarily a granulomatous disease of the peripheral nerves and mucosa of the upper respiratory tract; skin lesions...

. In 1896, Ernest Hanbury Hankin
Ernest Hanbury Hankin
Ernest Hanbury Hankin , was a British bacteriologist, aeronautical theorist and naturalist. Working mainly in India, he studied malaria, cholera and other diseases...

 reported that something in the waters of the Ganges and Yamuna
Yamuna
The Yamuna is the largest tributary river of the Ganges in northern India...

 rivers in India
India
India , officially the Republic of India , is a country in South Asia. It is the seventh-largest country by geographical area, the second-most populous country with over 1.2 billion people, and the most populous democracy in the world...

 had marked antibacterial action against cholera
Cholera
Cholera is an infection of the small intestine that is caused by the bacterium Vibrio cholerae. The main symptoms are profuse watery diarrhea and vomiting. Transmission occurs primarily by drinking or eating water or food that has been contaminated by the diarrhea of an infected person or the feces...

 and could pass through a very fine porcelain filter. In 1915, British
United Kingdom
The United Kingdom of Great Britain and Northern IrelandIn the United Kingdom and Dependencies, other languages have been officially recognised as legitimate autochthonous languages under the European Charter for Regional or Minority Languages...

 bacteriologist Frederick Twort
Frederick Twort
Frederick William Twort was an English bacteriologist and was the original discoverer in 1915 of bacteriophages . He studied medicine at St Thomas's Hospital, London, was superintendent of the Brown Institute for Animals , and he was also professor of bacteriology at the University of London...

, superintendent of the Brown Institution of London, discovered a small agent that infected and killed bacteria. He believed that the agent must be one of the following:
  1. a stage in the life cycle
    Biological life cycle
    A life cycle is a period involving all different generations of a species succeeding each other through means of reproduction, whether through asexual reproduction or sexual reproduction...

     of the bacteria;
  2. an enzyme
    Enzyme
    Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...

     produced by the bacteria themselves; or
  3. a virus that grew on and destroyed the bacteria.


Twort's work was interrupted by the onset of World War I
World War I
World War I , which was predominantly called the World War or the Great War from its occurrence until 1939, and the First World War or World War I thereafter, was a major war centred in Europe that began on 28 July 1914 and lasted until 11 November 1918...

 and shortage of funding.

Independently, French-Canadian microbiologist
Microbiology
Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell , cell clusters or no cell at all . This includes eukaryotes, such as fungi and protists, and prokaryotes...

 Félix d'Hérelle
Félix d'Herelle
Félix d'Herelle was a French-Canadian microbiologist, the co-discoverer of bacteriophages and experimented with the possibility of phage therapy.-Early years:...

, working at the Pasteur Institute
Pasteur Institute
The Pasteur Institute is a French non-profit private foundation dedicated to the study of biology, micro-organisms, diseases, and vaccines. It is named after Louis Pasteur, who made some of the greatest breakthroughs in modern medicine at the time, including pasteurization and vaccines for anthrax...

 in Paris
Paris
Paris is the capital and largest city in France, situated on the river Seine, in northern France, at the heart of the Île-de-France region...

, announced on September 3, 1917, that he had discovered "an invisible, antagonistic microbe of the dysentery
Dysentery
Dysentery is an inflammatory disorder of the intestine, especially of the colon, that results in severe diarrhea containing mucus and/or blood in the faeces with fever and abdominal pain. If left untreated, dysentery can be fatal.There are differences between dysentery and normal bloody diarrhoea...

 bacillus". For d’Hérelle, there was no question as to the nature of his discovery: "In a flash I had understood: what caused my clear spots was in fact an invisible microbe ... a virus parasitic on bacteria." D'Hérelle called the virus a bacteriophage or bacteria-eater (from the Greek phagein meaning to eat). He also recorded a dramatic account of a man suffering from dysentery who was restored to good health by the bacteriophages.

In 1923, the Eliava Institute
George Eliava Institute
The George Eliava Institute of Bacteriophage, Microbiology and Virology has been active since the 1930s in the field of phage therapy, which is used to combat microbial infection .- History :...

 was opened in Tbilisi, Georgia, to research this new science and put it into practice.

In 1969 Max Delbrück, Alfred Hershey
Alfred Hershey
Alfred Day Hershey was an American Nobel Prize-winning bacteriologist and geneticist.He was born in Owosso, Michigan and received his B.S. in chemistry at Michigan State University in 1930 and his Ph.D. in bacteriology in 1934, taking a position shortly thereafter at the Department of Bacteriology...

 and Salvador Luria were awarded the Nobel Prize in Physiology and Medicine for their discoveries of the replication of viruses and their genetic structure.

Replication

Bacteriophages may have a lytic cycle
Lytic cycle
The lytic cycle is one of the two cycles of viral reproduction, the other being the lysogenic cycle. The lytic cycle is typically considered the main method of viral replication, since it results in the destruction of the infected cell...

 or a lysogenic cycle, and a few viruses are capable of carrying out both. With lytic phages such as the T4 phage, bacterial cells are broken open (lysed) and destroyed after immediate replication of the virion. As soon as the cell is destroyed, the phage progeny can find new hosts to infect. Lytic phages are more suitable for phage therapy
Phage therapy
Phage therapy is the therapeutic use of bacteriophages to treat pathogenic bacterial infections. Although extensively used and developed mainly in former Soviet Union countries circa 1920, this method of therapy is still being tested for treatment of a variety of bacterial and poly-microbial...

. Some lytic phage undergo a phenomenon known as lysis inhibition where completed phage progeny will not immediately lyse out of the cell if there is a high extracellular phage concentrations. This mechanism is not identical to that of temperate phage going dormant and is usually temporary.

In contrast, the lysogenic cycle does not result in immediate lysing of the host cell. Those phages able to undergo lysogeny are known as temperate phages. Their viral genome will integrate with host DNA and replicate along with it fairly harmlessly, or may even become established as a plasmid
Plasmid
In microbiology and genetics, a plasmid is a DNA molecule that is separate from, and can replicate independently of, the chromosomal DNA. They are double-stranded and, in many cases, circular...

. The virus remains dormant until host conditions deteriorate, perhaps due to depletion of nutrients, then the endogenous
Endogenous
Endogenous substances are those that originate from within an organism, tissue, or cell. Endogenous retroviruses are caused by ancient infections of germ cells in humans, mammals and other vertebrates...

 phages (known as prophage
Prophage
A prophage is a phage genome inserted and integrated into the circular bacterial DNA chromosome. A prophage, also known as a temperate phage, is any virus in the lysogenic cycle; it is integrated into the host chromosome or exists as an extrachromosomal plasmid. Technically, a virus may be called...

s) become active. At this point they initiate the reproductive cycle, resulting in lysis of the host cell. As the lysogenic cycle allows the host cell to continue to survive and reproduce, the virus is reproduced in all of the cell’s offspring.

Sometimes prophages may provide benefits to the host bacterium while they are dormant by adding new functions to the bacterial genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....

 in a phenomenon called lysogenic conversion. An eminent example is the conversion of a harmless strain of Vibrio cholerae
Vibrio cholerae
Vibrio cholerae is a Gram-negative, comma-shaped bacterium. Some strains of V. cholerae cause the disease cholera. V. cholerae is facultatively anaerobic and has a flagella at one cell pole. V...

by a phage into a highly virulent one, which causes cholera
Cholera
Cholera is an infection of the small intestine that is caused by the bacterium Vibrio cholerae. The main symptoms are profuse watery diarrhea and vomiting. Transmission occurs primarily by drinking or eating water or food that has been contaminated by the diarrhea of an infected person or the feces...

. This is why temperate phages are not suitable for phage therapy.

Attachment and penetration

To enter a host cell, bacteriophages attach to specific receptors on the surface of bacteria, including lipopolysaccharide
Lipopolysaccharide
Lipopolysaccharides , also known as lipoglycans, are large molecules consisting of a lipid and a polysaccharide joined by a covalent bond; they are found in the outer membrane of Gram-negative bacteria, act as endotoxins and elicit strong immune responses in animals.-Functions:LPS is the major...

s, teichoic acid
Teichoic acid
Teichoic acids are bacterial polysaccharides of glycerol phosphate or ribitol phosphate linked via phosphodiester bonds.-Location and structure:...

s, protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

s, or even flagella. This specificity means that a bacteriophage can infect only certain bacteria bearing receptors to which they can bind, which in turn determines the phage's host range. Host growth conditions also influence the ability of the phage to attach and invade bacteria. As phage virions do not move independently, they must rely on random encounters with the right receptors when in solution (blood, lymphatic circulation, irrigation, soil water, etc.).

Myovirus bacteriophages use a hypodermic syringe-like motion to inject their genetic material into the cell. After making contact with the appropriate receptor, the tail fibers flex to bring the base plate closer to the surface of the cell; this is known as reversible binding. Once attached completely, irreversible binding is initiated and the tail contracts, possibly with the help of ATP
Adenosine triphosphate
Adenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...

 present in the tail, injecting genetic material through the bacterial membrane.
Podoviruses lack a elongated tail sheath similar to that of a myovirus, so they instead use their small tooth-like tail fibers to enzymatically degrade a portion of the cell membrane before inserting its genetic material.

Synthesis of proteins and nucleic acid

Within minutes, bacterial ribosome
Ribosome
A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....

s start translating viral mRNA into protein. For RNA-based phages, RNA replicase is synthesized early in the process. Proteins modify the bacterial RNA polymerase
RNA polymerase
RNA polymerase is an enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses...

 so that it preferentially transcribes viral mRNA. The host’s normal synthesis of proteins and nucleic acids is disrupted, and it is forced to manufacture viral products instead. These products go on to become part of new virions within the cell, helper proteins that help assemble the new virions, or proteins involved in cell lysis
Lysis
Lysis refers to the breaking down of a cell, often by viral, enzymic, or osmotic mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a "lysate"....

. Walter Fiers
Walter Fiers
Walter Fiers is a Belgian molecular biologist.He obtained a degree of Engineer for Chemistry and Agricultural Industries at the University of Ghent in 1954, and started his research career as an enzymologist in the laboratory of Laurent Vandendriessche in Ghent. In 1956-57, he worked with Heinz...

 (University of Ghent, Belgium
Belgium
Belgium , officially the Kingdom of Belgium, is a federal state in Western Europe. It is a founding member of the European Union and hosts the EU's headquarters, and those of several other major international organisations such as NATO.Belgium is also a member of, or affiliated to, many...

) was the first to establish the complete nucleotide sequence of a gene (1972) and of the viral genome of Bacteriophage MS2
Bacteriophage MS2
The bacteriophage MS2 is an icosahedral, positive-sense single-stranded RNA virus that infects the bacterium Escherichia coli.-History:...

 (1976).

Virion assembly

In the case of the T4 phage, the construction of new virus particles involves the assistance of helper proteins. The base plates are assembled first, with the tails being built upon them afterwards. The head capsids, constructed separately, will spontaneously assemble with the tails. The DNA is packed efficiently within the heads. The whole process takes about 15 minutes.

Release of virions

Phages may be released via cell lysis, by extrusion, or, in a few cases, by budding. Lysis, by tailed phages, is achieved by an enzyme called endolysin
Endolysin
Endolysin is a generic term describing an enzyme that degrades the bacterial peptidoglycan cell wall, resulting in lysis of the bacterial cell....

, which attacks and breaks down the cell wall peptidoglycan
Peptidoglycan
Peptidoglycan, also known as murein, is a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of bacteria , forming the cell wall. The sugar component consists of alternating residues of β- linked N-acetylglucosamine and N-acetylmuramic acid...

. An altogether different phage type, the filamentous phages, make the host cell continually secrete new virus particles. Released virions are described as free, and, unless defective, are capable of infecting a new bacterium. Budding is associated with certain Mycoplasma
Mycoplasma
Mycoplasma refers to a genus of bacteria that lack a cell wall. Without a cell wall, they are unaffected by many common antibiotics such as penicillin or other beta-lactam antibiotics that target cell wall synthesis. They can be parasitic or saprotrophic. Several species are pathogenic in humans,...

 phages. In contrast to virion release, phages displaying a lysogenic cycle do not kill the host but, rather, become long-term residents as prophage
Prophage
A prophage is a phage genome inserted and integrated into the circular bacterial DNA chromosome. A prophage, also known as a temperate phage, is any virus in the lysogenic cycle; it is integrated into the host chromosome or exists as an extrachromosomal plasmid. Technically, a virus may be called...

.

Phage therapy

Phages were discovered to be anti-bacterial agents and were used throughout the 1940s in the Soviet Union
Soviet Union
The Soviet Union , officially the Union of Soviet Socialist Republics , was a constitutionally socialist state that existed in Eurasia between 1922 and 1991....

 for treating bacterial infections. They had widespread use including treating soldiers in the Red Army. However, they were abandoned for general use in the west for several reasons:
  • Medical trials were carried out, but a basic lack of understanding of phages made these invalid.
  • Phage therapy was seen as untrustworthy, because many of the trials were conducted on totally unrelated diseases such as allergies and viral infections.
  • Antibiotics were discovered and marketed widely. They were easier to make, store and to prescribe.
  • Russian research continued but was published in Russian or Georgian, and was unavailable internationally for many years.


Their use has continued since the end of the Cold War in Georgia
Georgia (country)
Georgia is a sovereign state in the Caucasus region of Eurasia. Located at the crossroads of Western Asia and Eastern Europe, it is bounded to the west by the Black Sea, to the north by Russia, to the southwest by Turkey, to the south by Armenia, and to the southeast by Azerbaijan. The capital of...

  and elsewhere in Eastern Europe. A monograph written by Nina Chanishvili in 2009, in Tbilisi, Georgia gave a thorough analysis of the results of phage therapy. It was based on the data given in the old Soviet scientific literature.

The first regulated clinical trial of efficacy in Western Europe (against ear infections caused by Pseudomonas aeruginosa) was reported in the journal Clinical Otolaryngology in August 2009. Meanwhile, Western scientists are developing engineered viruses to overcome antibiotic resistance, and experimenting with tumor-suppressing agents. One potential treatment currently under development is a phage designed to destroy MRSA.

In the environment

Metagenomics
Metagenomics
Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. Traditional microbiology and microbial genome sequencing rely upon cultivated clonal cultures...

 has allowed the in-water detection of bacteriophages that was not possible previously. These investigations revealed that phage are much more abundant in the water column of both freshwater and marine habitats than previously thought and that they can cause significant mortality of bacterioplankton
Bacterioplankton
Bacterioplankton refers to the bacterial component of the plankton that drifts in the water column. The name comes from the Ancient Greek word , meaning "wanderer" or "drifter" , and , a Latin neologism coined in the 19th century by Christian Gottfried Ehrenberg...

. Methods in phage community ecology have been developed to assess phage-induced mortality of bacterioplankton and its role for food web process and biogeochemical cycle to genetically fingerprint phage communities or populations and estimate viral biodiversity
Biodiversity
Biodiversity is the degree of variation of life forms within a given ecosystem, biome, or an entire planet. Biodiversity is a measure of the health of ecosystems. Biodiversity is in part a function of climate. In terrestrial habitats, tropical regions are typically rich whereas polar regions...

 by metagenomics. The lysis
Lysis
Lysis refers to the breaking down of a cell, often by viral, enzymic, or osmotic mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a "lysate"....

 of bacteria by phages releases organic carbon that was previously particulate (cells) into dissolved forms, which makes the carbon more available to other organisms. Phages are not only the most abundant biological entities but probably also the most diverse ones. The majority of the sequence data obtained from phage communities has no equivalent in databases. These data and other detailed analyses indicate that phage-specific genes and ecological traits are much more frequent than previously thought. In order to reveal the meaning of this genetic and ecological versatility, studies have to be performed with communities and at spatiotemporal scales relevant for microorganisms.

Bacteriophages have also been used in hydrological
Hydrology
Hydrology is the study of the movement, distribution, and quality of water on Earth and other planets, including the hydrologic cycle, water resources and environmental watershed sustainability...

 tracing and modelling in river
River
A river is a natural watercourse, usually freshwater, flowing towards an ocean, a lake, a sea, or another river. In a few cases, a river simply flows into the ground or dries up completely before reaching another body of water. Small rivers may also be called by several other names, including...

 systems especially where surface water and groundwater
Groundwater
Groundwater is water located beneath the ground surface in soil pore spaces and in the fractures of rock formations. A unit of rock or an unconsolidated deposit is called an aquifer when it can yield a usable quantity of water. The depth at which soil pore spaces or fractures and voids in rock...

 interactions occur. The use of phages is preferred to the more conventional dye
Dye
A dye is a colored substance that has an affinity to the substrate to which it is being applied. The dye is generally applied in an aqueous solution, and requires a mordant to improve the fastness of the dye on the fiber....

 marker because they are significantly less absorbed when passing through ground-waters and they are readily detected at very low concentrations.

Role in food fermentation

A broad number of food products, commodity chemicals, and biotechnology
Biotechnology
Biotechnology is a field of applied biology that involves the use of living organisms and bioprocesses in engineering, technology, medicine and other fields requiring bioproducts. Biotechnology also utilizes these products for manufacturing purpose...

 products are manufactured industrially by large-scale bacterial fermentation
Industrial fermentation
Industrial fermentation is the intentional use of fermentation by microorganisms such as bacteria and fungi to make products useful to humans. Fermented products have applications as food as well as in general industry.- Food fermentation :...

 of various organic substrates. Because enormous amounts of bacteria are being cultivated each day in large fermentation vats, the risk of bacteriophage contamination
Contamination
Contamination is the presence of a minor and unwanted constituent in material, physical body, natural environment, at a workplace, etc.-Specifics:"Contamination" also has more specific meanings in science:...

 could rapidly bring fermentation to a halt. The resulting economic setback is a serious threat in these industries. The relationship between bacteriophages and their bacterial hosts is very important in the context of the food fermentation industry. Sources of phage contamination, measures to control their propagation
Self-replication
Self-replication is any behavior of a dynamical system that yields construction of an identical copy of that dynamical system. Biological cells, given suitable environments, reproduce by cell division. During cell division, DNA is replicated and can be transmitted to offspring during reproduction...

 and dissemination
Dissemination
To disseminate , in terms of the field of communication, means to broadcast a message to the public without direct feedback from the audience. Dissemination takes on the theory of the traditional view of communication, which involves a sender and receiver...

, and biotechnological defense strategies developed to restrain phages are of interest. The dairy fermentation industry has openly acknowledged the problem of phages and has been working with academia and starter culture companies to develop defense strategies and systems to curtail the propagation and evolution of phages for decades.

Other areas of use

In August 2006, the United States Food and Drug Administration (FDA) approved LMP-102 (now ListShield) as a food additive to target and kill Listeria monocytogenes. LMP-102 was approved for treating ready-to-eat (RTE) poultry and meat products. In October of that year, following the food additive approval of LMP-102 by Intralytix, the FDA approved a product by EBI using bacteriophages on cheese to kill the Listeria monocytogenes bacteria, giving them GRAS status (Generally Recognized As Safe). In July 2007, the same bacteriophages were approved for use on all food products. There is on going research in the field of food safety to see if lytic phage are a viable option to control other food-borne pathogens in various food products.

Government agencies in the West have for several years been looking to Georgia and the Former Soviet Union for help with exploiting phages for counteracting bioweapons and toxins, such as anthrax
Anthrax
Anthrax is an acute disease caused by the bacterium Bacillus anthracis. Most forms of the disease are lethal, and it affects both humans and other animals...

 and botulism
Botulism
Botulism also known as botulinus intoxication is a rare but serious paralytic illness caused by botulinum toxin which is metabolic waste produced under anaerobic conditions by the bacterium Clostridium botulinum, and affecting a wide range of mammals, birds and fish...

. There are many developments with this among research groups in the US. Other uses include spray application in horticulture for protecting plants and vegetable produce from decay and the spread of bacterial disease. Other applications for bacteriophages are as a biocide for environmental surfaces, e.g., in hospitals, and as a preventative treatment for catheters and medical devices prior to use in clinical settings. The technology for phages to be applied to dry surfaces, e.g., uniforms, curtains, even sutures for surgery now exists. Clinical trials reported in the Lancet show success in veterinary treatment of pet dogs with otitis.

Phage display
Phage display
Phage display is a method for the study of protein–protein, protein–peptide, and protein–DNA interactions that uses bacteriophages to connect proteins with the genetic information that encodes them. Phage Display was originally invented by George P...

 is a different use of phages involving a library of phages with a variable peptide linked to a surface protein. Each phage's genome encodes the variant of the protein displayed on its surface (hence the name), providing a link between the peptide variant and its encoding gene. Variant phages from the library can be selected through their binding affinity to an immobilized molecule (e.g., Botulism toxin) to neutralize it. The bound selected phages can be multiplied by re-infecting a susceptible bacterial strain, thus allowing them to retrieve the peptides encoded in them for further study.

The SEPTIC
Sensing of phage-triggered ion cascades (SEPTIC)
Sensing of phage-triggered ion cascades is a bacterium identification method based on fluctuation-enhanced sensing in fluid medium. The advantages of SEPTIC are the specificity and speed offered by the characteristics of phage infection, the sensitivity due to fluctuation-enhanced sensing, and...

 bacterium sensing and identification method utilizes the ion emission and its dynamics during phage infection and offers high specificity and speed for detection.

Cultural references

  • In 1926 in the Pulitzer prize-winning novel Arrowsmith
    Arrowsmith (novel)
    Arrowsmith is a novel by American author and playwright Sinclair Lewis that was published in 1925. It won the 1926 Pulitzer Prize for Lewis but he refused to accept it. Lewis was greatly assisted in its preparation by science writer Dr. Paul de Kruif, who received 25% of the royalties on sales, but...

    , Sinclair Lewis
    Sinclair Lewis
    Harry Sinclair Lewis was an American novelist, short-story writer, and playwright. In 1930, he became the first writer from the United States to be awarded the Nobel Prize in Literature, "for his vigorous and graphic art of description and his ability to create, with wit and humor, new types of...

     fictionalized the application of bacteriophages as a therapeutic agent.

See also

  • Bacterivore
    Bacterivore
    Bacterivores are free-living, generally heterotrophic organisms, exclusively microscopic, which obtain energy and nutrients primarily or entirely from the consumption of bacteria. Many species of amoeba are bacterivores, as well as other types of protozoans. In common all species of bacteria will...

  • DNA viruses
  • RNA viruses
  • Polyphage
    Polyphage
    For the dietary behaviour term, see polyphagy.Polyphage are genomic multimers of bacteriophage all encapsulated, one after the other, within the same set of coat proteins....

  • Phage ecology
    Phage ecology
    Bacteriophages , potentially the most numerous "organisms" on Earth, are the viruses of bacteria . Phage ecology is the study of the interaction of bacteriophages with their environments...

  • Phage monographs
    Phage monographs
    Bacteriophage are viruses of bacteria and arguably are the most numerous "organisms" on Earth. The history of phage study is captured, in part, in the books published on the topic. This is a list of over 100 monograph on or related to phages....

     (a comprehensive listing of phage and phage-associated monographs, 1921 – present)
  • Transduction
    Transduction (genetics)
    Transduction is the process by which DNA is transferred from one bacterium to another by a virus. It also refers to the process whereby foreign DNA is introduced into another cell via a viral vector. Transduction does not require cell-to-cell contact , and it is DNAase resistant...


External links

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