HOME
The Info List - Bacteriophage


--- Advertisement ---



A bacteriophage (/ˈbækˈtɪərioʊˌfeɪdʒ/), also known informally as a phage (/feɪdʒ/), is a virus that infects and replicates within Bacteria
Bacteria
and Archaea. The term was derived from "bacteria" and the Greek: φαγεῖν (phagein), "to devour". Bacteriophages are composed of proteins that encapsulate a DNA
DNA
or RNA
RNA
genome, and may have relatively simple or elaborate structures. Their genomes may encode as few as four genes, and as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm. Bacteriophages are among the most common and diverse entities in the biosphere.[1] Bacteriophages are ubiquitous viruses, found wherever bacteria exist. It is estimated there are more than 1031 bacteriophages on the planet, more than every other organism on Earth, including bacteria, combined.[2] Phages are widely distributed in locations populated by bacterial 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 per milliliter have been found in microbial mats at the surface,[3] and up to 70% of marine bacteria may be infected by phages.[4] They have been used for over 90 years as an alternative to antibiotics in the former Soviet Union
Soviet Union
and Central Europe, as well as in France.[5] They are seen as a possible therapy against multi-drug-resistant strains of many bacteria (see phage therapy).[6] Nevertheless, phages of Inoviridae have been shown to complicate biofilms involved in pneumonia and cystic fibrosis, and shelter the bacteria from drugs meant to eradicate disease and promote persistent infection.[7]

Contents

1 Classification 2 History 3 Phage therapy 4 Replication

4.1 Attachment and penetration 4.2 Synthesis of proteins and nucleic acid 4.3 Virion assembly 4.4 Release of virions

5 Genome
Genome
structure 6 Systems biology 7 In the environment 8 Other areas of use 9 In the dairy industry 10 Model bacteriophages 11 See also 12 References 13 External links

Classification[edit] Bacteriophages occur abundantly in the biosphere, with different virions, genomes, and lifestyles. Phages are classified by the International Committee on Taxonomy of Viruses (ICTV) according to morphology and nucleic acid. Nineteen families are currently recognized by the ICTV that infect bacteria and archaea. Of these, only two families have RNA
RNA
genomes, and only five families are enveloped. Of the viral families with DNA genomes, only two have single-stranded genomes. Eight of the viral families with DNA
DNA
genomes have circular genomes while nine have linear genomes. Nine families infect bacteria only, nine infect archaea only, and one (Tectiviridae) infects both bacteria and archaea.

Bacteriophage
Bacteriophage
P22, a member of the Podoviridae
Podoviridae
by morphology due to its short, non-contractile tail

ICTV classification of prokaryotic (bacterial and archaeal) viruses[1]

Order Family Morphology Nucleic acid Examples

Caudovirales Myoviridae Nonenveloped, contractile tail Linear dsDNA T4 phage, Mu, PBSX, P1Puna-like, P2, I3, Bcep 1, Bcep 43, Bcep 78

Siphoviridae Nonenveloped, noncontractile tail (long) Linear dsDNA λ phage, T5 phage, phi, C2, L5, HK97, N15

Podoviridae Nonenveloped, noncontractile tail (short) Linear dsDNA T7 phage, T3 phage, Φ29, P22, P37

Ligamenvirales Lipothrixviridae Enveloped, rod-shaped Linear dsDNA Acidianus filamentous virus 1

Rudiviridae Nonenveloped, rod-shaped Linear dsDNA Sulfolobus islandicus rod-shaped virus 1

Unassigned Ampullaviridae Enveloped, bottle-shaped Linear dsDNA

Bicaudaviridae Nonenveloped, lemon-shaped Circular dsDNA

Clavaviridae Nonenveloped, rod-shaped Circular dsDNA

Corticoviridae Nonenveloped, isometric Circular dsDNA

Cystoviridae Enveloped, spherical Segmented dsRNA

Fuselloviridae Nonenveloped, lemon-shaped Circular dsDNA

Globuloviridae Enveloped, isometric Linear dsDNA

Guttaviridae Nonenveloped, ovoid Circular dsDNA

Inoviridae Nonenveloped, filamentous Circular ssDNA M13

Leviviridae Nonenveloped, isometric Linear ssRNA MS2, Qβ

Microviridae Nonenveloped, isometric Circular ssDNA ΦX174

Plasmaviridae Enveloped, pleomorphic Circular dsDNA

Tectiviridae Nonenveloped, isometric Linear dsDNA

History[edit] In 1896, Ernest Hanbury Hankin
Ernest Hanbury Hankin
reported that something in the waters of the Ganges
Ganges
and Yamuna
Yamuna
rivers in India
India
had marked antibacterial action against cholera and could pass through a very fine porcelain filter.[8] In 1915, British bacteriologist Frederick Twort, superintendent of the Brown Institution of London, discovered a small agent that infected and killed bacteria. He believed the agent must be one of the following:

a stage in the life cycle of the bacteria; an enzyme produced by the bacteria themselves; or a virus that grew on and destroyed the bacteria.[9]

Twort's work was interrupted by the onset of World War I
World War I
and shortage of funding. Independently, French-Canadian
French-Canadian
microbiologist Félix d'Hérelle, working at the Pasteur Institute
Pasteur Institute
in Paris, announced on 3 September 1917, that he had discovered "an invisible, antagonistic microbe of the dysentery 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."[10] D'Hérelle called the virus a bacteriophage or bacteria-eater (from the Greek phagein meaning "to devour"). He also recorded a dramatic account of a man suffering from dysentery who was restored to good health by the bacteriophages.[11] It was D'Herelle who conducted much research into bacteriophages and introduced the concept of phage therapy.[12] In 1969, Max Delbrück, Alfred Hershey
Alfred Hershey
and Salvador Luria
Salvador Luria
were awarded the Nobel Prize in Physiology or Medicine
Nobel Prize in Physiology or Medicine
for their discoveries of the replication of viruses and their genetic structure.[13] Phage therapy[edit] Main article: Phage therapy Phages were discovered to be antibacterial agents and were used in the former Soviet
Soviet
Republic of Georgia (pioneered there by Giorgi Eliava with help from the co-discoverer of bacteriophages, Felix d'Herelle) and the United States
United States
during the 1920s and 1930s for treating bacterial infections. They had widespread use, including treatment of 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.[14] Antibiotics were discovered and marketed widely. They were easier to make, store and to prescribe. Former Soviet
Soviet
research continued, but publications were mainly in Russian or Georgian languages and were unavailable internationally for many years.

Their use has continued since the end of the Cold War in Georgia and elsewhere in Central and Eastern Europe. The first regulated, randomized, double-blind clinical trial was reported in the Journal of Wound Care in June 2009, which evaluated the safety and efficacy of a bacteriophage cocktail to treat infected venous leg ulcers in human patients.[15] The FDA approved the study as a Phase I clinical trial. The study's results demonstrated the safety of therapeutic application of bacteriophages but did not show efficacy. The authors explain that the use of certain chemicals that are part of standard wound care (e.g. lactoferrin or silver) may have interfered with bacteriophage viability.[15] Another controlled clinical trial in Western Europe (treatment of ear infections caused by Pseudomonas aeruginosa) was reported shortly after in the journal Clinical Otolaryngology in August 2009.[16] The study concludes that bacteriophage preparations were safe and effective for treatment of chronic ear infections in humans. Additionally, there have been numerous animal and other experimental clinical trials evaluating the efficacy of bacteriophages for various diseases, such as infected burns and wounds, and cystic fibrosis associated lung infections, among others.[17] Meanwhile, bacteriophage researchers are developing engineered viruses to overcome antibiotic resistance, and engineering the phage genes responsible for coding enzymes which degrade the biofilm matrix, phage structural proteins and also enzymes responsible for lysis of bacterial cell wall.[3][4][5] There have been results showing that T4 phages that are small in size and short-tailed can be helpful in detecting E.coli in the human body.[18] D'Herelle "quickly learned that bacteriophages are found wherever bacteria thrive: in sewers, in rivers that catch waste runoff from pipes, and in the stools of convalescent patients."[19] This includes rivers traditionally thought to have healing powers, including India's Ganges
Ganges
River.[20] Replication[edit]

Diagram of the DNA
DNA
injection process

Bacteriophages may have a lytic cycle 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. Some lytic phages undergo a phenomenon known as lysis inhibition, where completed phage progeny will not immediately lyse out of the cell if extracellular phage concentrations are high. 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
DNA
and replicate along with it relatively harmlessly, or may even become established as a plasmid. The virus remains dormant until host conditions deteriorate, perhaps due to depletion of nutrients; then, the endogenous phages (known as prophages) 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 replicated in all of the cell’s offspring. An example of a bacteriophage known to follow the lysogenic cycle and the lytic cycle is the phage lambda of E. coli.[21] Sometimes prophages may provide benefits to the host bacterium while they are dormant by adding new functions to the bacterial genome in a phenomenon called lysogenic conversion. Examples are the conversion of harmless strains of Corynebacterium diphtheriae
Corynebacterium diphtheriae
or Vibrio cholerae
Vibrio cholerae
by bacteriophages to highly virulent ones, which cause diphtheria or cholera, respectively.[22][23] Strategies to combat certain bacterial infections by targeting these toxin-encoding prophages have been proposed.[24] Attachment and penetration[edit]

In this electron micrograph of bacteriophages attached to a bacterial cell, the viruses are the size and shape of coliphage T1.

To enter a host cell, bacteriophages attach to specific receptors on the surface of bacteria, including lipopolysaccharides, teichoic acids, proteins, or even flagella. This specificity means 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 them.[25] 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 present in the tail,[4] injecting genetic material through the bacterial membrane. Podoviruses lack an elongated tail sheath similar to that of a myovirus, so they instead use their small, tooth-like tail fibers enzymatically to degrade a portion of the cell membrane before inserting their genetic material. Synthesis of proteins and nucleic acid[edit] Within minutes, bacterial ribosomes start translating viral m RNA
RNA
into protein. For RNA-based phages, RNA
RNA
replicase is synthesized early in the process. Proteins modify the bacterial RNA
RNA
polymerase so 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. Walter Fiers (University of Ghent, Belgium) was the first to establish the complete nucleotide sequence of a gene (1972) and of the viral genome of bacteriophage MS2 (1976).[26] Virion assembly[edit] 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 afterward. The head capsids, constructed separately, will spontaneously assemble with the tails. The DNA
DNA
is packed efficiently within the heads. The whole process takes about 15 minutes.

Diagram of a typical tailed bacteriophage structure

Release of virions[edit] 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, which attacks and breaks down the cell wall peptidoglycan. 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
phages. In contrast to virion release, phages displaying a lysogenic cycle do not kill the host but, rather, become long-term residents as prophage. Genome
Genome
structure[edit] Given the millions of different phages in the environment, phages' genomes come in a variety of forms and sizes. RNA
RNA
phage such as MS2 have the smallest genomes of only a few kilobases. However, some DNA phages such as T4 may have large genomes with hundreds of genes; the size and shape of the capsid varies along with the size of the genome.[27] Bacteriophage
Bacteriophage
genomes can be highly mosaic, i.e. the genome of many phage species appear to be composed of numerous individual modules. These modules may be found in other phage species in different arrangements. Mycobacteriophages – bacteriophages with mycobacterial hosts – have provided excellent examples of this mosaicism. In these mycobacteriophages, genetic assortment may be the result of repeated instances of site-specific recombination and illegitimate recombination (the result of phage genome acquisition of bacterial host genetic sequences).[28] Evolutionary mechanisms shaping the genomes of bacterial viruses vary between different families and depend on the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the viral life cycle.[29] Systems biology[edit] Phages often have dramatic effects on their hosts. As a consequence, the transcription pattern of the infected bacterium may change considerably. For instance, infection of Pseudomonas aeruginosa
Pseudomonas aeruginosa
by the temperate phage PaP3 changed the expression of 38% (2160/5633) of its host's genes. Many of these effects are probably indirect, hence the challenge becomes to identify the direct interactions among bacteria and phage.[30] Several attempts have been made to map Protein–protein interactions among phage and their host. For instance, bacteriophage lambda was found to interact with its host E. coli by 31 interactions. However, a large-scale study revealed 62 interactions, most of which were new. Again, the significance of many of these interactions remains unclear, but these studies suggest that there are most likely several key interactions and many indirect interactions whose role remains uncharacterized.[31] In the environment[edit] Main article: Marine bacteriophage Metagenomics
Metagenomics
has allowed the in-water detection of bacteriophages that was not possible previously.[32] Bacteriophages have also been used in hydrological tracing and modelling in river systems, especially where surface water and groundwater interactions occur. The use of phages is preferred to the more conventional dye marker because they are significantly less absorbed when passing through ground waters and they are readily detected at very low concentrations.[33] Non-polluted water may contain ca. 2×108 bacteriophages per mL.[34] Bacteriophages are thought to extensively contribute to horizontal gene transfer in natural environments, principally via transduction but also via transformation.[35] Metagenomics-based studies have also revealed that viromes from a variety of environments harbor antibiotic resistance genes, including those that could confer multidrug resistance.[36] Other areas of use[edit] Since 2006, the United States
United States
Food and Drug Administration (FDA) and United States
United States
Department of Agriculture (USDA) have approved several bacteriophage products. LMP-102 (Intralytix) was approved for treating ready-to-eat (RTE) poultry and meat products. In that same year, the FDA approved LISTEX (developed and produced by Micreos) using bacteriophages on cheese to kill Listeria monocytogenes
Listeria monocytogenes
bacteria, giving them generally recognized as safe (GRAS) status.[37] In July 2007, the same bacteriophage were approved for use on all food products.[38] In 2011 USDA confirmed that LISTEX is a clean label processing aid and is included in USDA.[39] Research in the field of food safety is continuing to see if lytic phages are a viable option to control other food-borne pathogens in various food products. In 2011 the FDA cleared the first bacteriophage-based product for in vitro diagnostic use.[40] The KeyPath MRSA/MSSA Blood Culture Test uses a cocktail of bacteriophage to detect Staphylococcus aureus
Staphylococcus aureus
in positive blood cultures and determine methicillin resistance or susceptibility. The test returns results in about 5 hours, compared to 2–3 days for standard microbial identification and susceptibility test methods. It was the first accelerated antibiotic susceptibility test approved by the FDA.[41] Government agencies in the West have for several years been looking to Georgia and the former Soviet Union
Soviet Union
for help with exploiting phages for counteracting bioweapons and toxins, such as anthrax and botulism.[42] Developments are continuing 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 biocides for environmental surfaces, e.g., in hospitals, and as preventative treatments for catheters and medical devices before use in clinical settings. The technology for phages to be applied to dry surfaces, e.g., uniforms, curtains, or even sutures for surgery now exists. Clinical trials reported in Clinical Otolaryngology[43] show success in veterinary treatment of pet dogs with otitis. Phage display
Phage display
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 reinfecting a susceptible bacterial strain, thus allowing them to retrieve the peptides encoded in them for further study.[44] The SEPTIC bacterium sensing and identification method uses the ion emission and its dynamics during phage infection and offers high specificity and speed for detection.[45] Phage-ligand technology makes use of proteins, which are identified from bacteriophages, characterized and recombinantly expressed for various applications such as binding of bacteria and bacterial components (e.g. endotoxin) and lysis of bacteria.[46] Bacteriophages are also important model organisms for studying principles of evolution and ecology.[47] In the dairy industry[edit] Bacteriophages present in the environment can cause fermentation failures of cheese starter cultures. In order to avoid this, mixed-strain starter cultures and culture rotation regimes can be used.[48] Model bacteriophages[edit] The following bacteriophages are extensively studied:

λ phage T2 phage T4 phage
T4 phage
(169 kbp genome,[49] 200 nm long[50]) T7 phage T12 phage R17 phage M13 phage MS2 phage
MS2 phage
(23–28 nm in size[51]) G4 phage P1 phage Enterobacteria phage P2 P4 phage Phi X 174
Phi X 174
phage N4 phage Pseudomonas phage Φ6 Φ29 phage 186 phage

See also[edit]

Viruses portal

Bacterivore CrAssphage DNA
DNA
viruses Phage ecology Phage monographs (a comprehensive listing of phage and phage-associated monographs, 1921 – present) Polyphage RNA
RNA
viruses Transduction Viriome CRISPR

References[edit]

^ a b Mc Grath S and van Sinderen D (editors). (2007). Bacteriophage: Genetics and Molecular Biology (1st ed.). Caister Academic Press. ISBN 978-1-904455-14-1. [1].  ^ http://outbreaknewstoday.com/bacteriophage-therapy-treats-patient-near-death-mdr-acinetobacter-baumannii-45488/ ^ a b Wommack, K. E.; Colwell, R. R. (2000). "Virioplankton: Viruses in Aquatic Ecosystems". Microbiology
Microbiology
and Molecular Biology Reviews. 64 (1): 69–114. doi:10.1128/MMBR.64.1.69-114.2000. PMC 98987 . PMID 10704475.  ^ a b c Prescott, L. (1993). Microbiology, Wm. C. Brown Publishers, ISBN 0-697-01372-3 ^ a b BBC Horizon (1997): The Virus
Virus
that Cures – Documentary about the history of phage medicine in Russia and the West ^ Keen, E. C. (2012). "Phage Therapy: Concept to Cure". Frontiers in Microbiology. 3: 238. doi:10.3389/fmicb.2012.00238. PMC 3400130 . PMID 22833738.  ^ http://phys.org/news/2015-11-bacteria-bacteriophages-collude-formation-clinically.html ^ Hankin E H. (1896). "L'action bactericide des eaux de la Jumna et du Gange sur le vibrion du cholera". Annales de l'Institut Pasteur (in French). 10: 511–523.  ^ Twort, F. W. (1915). "An Investigation on the Nature of Ultra-Microscopic Viruses". The Lancet. 186 (4814): 1241–1243. doi:10.1016/S0140-6736(01)20383-3.  ^ Félix d'Hérelles (1917). "Sur un microbe invisible antagoniste des bacilles dysentériques" (PDF). Comptes Rendus de l'Académie des Sciences de Paris. 165: 373–5. Archived (PDF) from the original on 4 December 2010. Retrieved 5 September 2010.  ^ Félix d'Hérelle (1949). "The bacteriophage" (PDF). Science News. 14: 44–59. Retrieved 5 September 2010.  ^ Keen EC (2012). "Felix d'Herelle and Our Microbial Future". Future Microbiology. 7 (12): 1337–1339. doi:10.2217/fmb.12.115. PMID 23231482.  ^ "The Nobel Prize in Physiology or Medicine
Nobel Prize in Physiology or Medicine
1969". Nobel Foundation. Retrieved 2007-07-28.  ^ Kutter, Elizabeth; De Vos, Daniel; Gvasalia, Guram; Alavidze, Zemphira; Gogokhia, Lasha; Kuhl, Sarah; Abedon, Stephen (1 January 2010). "Phage Therapy in Clinical Practice: Treatment of Human Infections". Current Pharmaceutical Biotechnology. 11 (1): 69–86. doi:10.2174/138920110790725401. PMID 20214609.  ^ a b Rhoads, DD; Wolcott, RD; Kuskowski, MA; Wolcott, BM; Ward, LS; Sulakvelidze, A (June 2009). " Bacteriophage
Bacteriophage
therapy of venous leg ulcers in humans: results of a phase I safety trial". Journal of wound care. 18 (6): 237–8, 240–3. doi:10.12968/jowc.2009.18.6.42801. PMID 19661847.  ^ Wright, A.; Hawkins, C.H.; Änggård, E.E.; Harper, D.R. (August 2009). "A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy". Clinical Otolaryngology. 34 (4): 349–357. doi:10.1111/j.1749-4486.2009.01973.x. PMID 19673983.  ^ Wright, A; Hawkins, CH; Anggård, EE; Harper, DR (August 2009). "A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy". Clinical Otolaryngology. 34 (4): 349–57. doi:10.1111/j.1749-4486.2009.01973.x. PMID 19673983.  ^ Tawil, Nancy (April 2012). "Surface plasmon resonance detection of E. coli and mathicillin-resistant S. aureus bacteriophages". Elsevier. 3 (5): e78. doi:10.1371/journal.pgen.0030078 – via Science Direct.  ^ Kuchment, Anna (2012), The Forgotten Cure: The past and future of phage therapy, Springer, p. 11, ISBN 978-1-4614-0250-3  ^ Deresinski, Stan (15 April 2009). " Bacteriophage
Bacteriophage
Therapy: Exploiting Smaller Fleas". Clinical Infectious Diseases. 48 (8): 1096–1101. doi:10.1086/597405. PMID 19275495.  ^ Mason, Kenneth A., Jonathan B. Losos, Susan R. Singer, Peter H Raven, and George B. Johnson. (2011). Biology, p. 533. McGraw-Hill, New York. ISBN 978-0-07-893649-4. ^ Mokrousov I (January 2009). "Corynebacterium diphtheriae: genome diversity, population structure and genotyping perspectives". Infection, Genetics and Evolution. 9 (1): 1–15. doi:10.1016/j.meegid.2008.09.011. PMID 19007916.  ^ Charles RC, Ryan ET (October 2011). " Cholera
Cholera
in the 21st century". Current Opinion in Infectious Diseases. 24 (5): 472–7. doi:10.1097/QCO.0b013e32834a88af. PMID 21799407.  ^ Keen, E. C. (December 2012). "Paradigms of pathogenesis: Targeting the mobile genetic elements of disease". Frontiers in Cellular and Infection Microbiology. 2: 161. doi:10.3389/fcimb.2012.00161. PMC 3522046 . PMID 23248780.  ^ Gabashvili, I.; Khan, S.; Hayes, S.; Serwer, P. (1997). "Polymorphism of bacteriophage T7". Journal of Molecular Biology. 273 (3): 658–67. doi:10.1006/jmbi.1997.1353. PMID 9356254.  ^ Fiers, W.; Contreras, R.; Duerinck, F.; Haegeman, G.; Iserentant, D.; Merregaert, J.; Min Jou, W.; Molemans, F.; Raeymaekers, A.; Van Den Berghe, A.; Volckaert, G.; Ysebaert, M. (1976). "Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene". Nature. 260 (5551): 500–507. Bibcode:1976Natur.260..500F. doi:10.1038/260500a0. PMID 1264203.  ^ Black, LW; Thomas, JA (2012). "Condensed genome structure". Advances in Experimental Medicine and Biology. Advances in Experimental Medicine and Biology. 726: 469–87. doi:10.1007/978-1-4614-0980-9_21. ISBN 978-1-4614-0979-3. PMC 3559133 . PMID 22297527.  ^ Morris P, Marinelli LJ, Jacobs-Sera D, Hendrix RW, Hatfull GF (March 2008). "Genomic characterization of mycobacteriophage Giles: evidence for phage acquisition of host DNA
DNA
by illegitimate recombination". Journal of Bacteriology. 190 (6): 2172–82. doi:10.1128/JB.01657-07. PMC 2258872 . PMID 18178732.  ^ Krupovic M, Prangishvili D, Hendrix RW, Bamford DH (December 2011). "Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere". Microbiology
Microbiology
and Molecular Biology Reviews : MMBR. 75 (4): 610–35. doi:10.1128/MMBR.00011-11. PMC 3232739 . PMID 22126996.  ^ Zhao X, Chen C, Shen W, Huang G, Le S, Lu S, Li M, Zhao Y, Wang J, Rao X, Li G, Shen M, Guo K, Yang Y, Tan Y, Hu F (2016). "Global Transcriptomic Analysis of Interactions between Pseudomonas aeruginosa and Bacteriophage
Bacteriophage
PaP3". Sci Rep. 6: 19237. Bibcode:2016NatSR...619237Z. doi:10.1038/srep19237. PMC 4707531 . PMID 26750429.  ^ Blasche S, Wuchty S, Rajagopala SV, Uetz P (2013). "The protein interaction network of bacteriophage lambda with its host, Escherichia coli". J. Virol. 87 (23): 12745–55. doi:10.1128/JVI.02495-13. PMC 3838138 . PMID 24049175.  ^ Breitbart, M, P Salamon, B Andresen, J Mahaffy, A Segall, D Mead, F Azam, F Rohwer (2002) Genomic analysis of uncultured marine viral communities. Proceedings of the National Academy USA. 99:14250-14255. ^ Martin, C. (1988). "The Application of Bacteriophage
Bacteriophage
Tracer Techniques in South West Water". Water and Environment Journal. 2 (6): 638–642. doi:10.1111/j.1747-6593.1988.tb01352.x.  ^ Bergh, O (1989). "HIGH ABUNDANCE OF VIRUSES FOUND IN AQUATIC ENVIRONMENTS" (PDF). Nature. 340 (6233): 467–468. Bibcode:1989Natur.340..467B. doi:10.1038/340467a0. PMID 2755508. Retrieved 17 November 2015.  ^ Keen, Eric C.; Bliskovsky, Valery V.; Malagon, Francisco; Baker, James D.; Prince, Jeffrey S.; Klaus, James S.; Adhya, Sankar L.; Groisman, Eduardo A. (2017). "Novel "Superspreader" Bacteriophages Promote Horizontal Gene Transfer by Transformation". MBio. 8 (1): e02115–16. doi:10.1128/mBio.02115-16. ISSN 2150-7511. PMC 5241400 . PMID 28096488.  ^ Lekunberri, Itziar; Subirats, Jessica; Borrego, Carles M.; Balcazar, Jose L. (2017). "Exploring the contribution of bacteriophages to antibiotic resistance". Environmental Pollution. 220 (Pt B): 981–984. doi:10.1016/j.envpol.2016.11.059. ISSN 0269-7491. PMID 27890586.  ^ U.S. FDA/CFSAN: Agency Response Letter, GRAS Notice No. 000198 ^ (U.S. FDA/CFSAN: Agency Response Letter, GRAS Notice No. 000218) ^ FSIS Directive 7120 Archived 18 October 2011 at the Wayback Machine. ^ [2] ^ [3] ^ The New York Times: Studying anthrax in a Soviet-era lab – with Western funding ^ Wright, A.; Hawkins, C.; Anggård, E.; Harper, D. (2009). "A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy". Clinical Otolaryngology. 34 (4): 349–357. doi:10.1111/j.1749-4486.2009.01973.x. PMID 19673983.  ^ Smith GP, Petrenko VA (April 1997). "Phage Display". Chem. Rev. 97 (2): 391–410. doi:10.1021/cr960065d. PMID 11848876.  ^ "M. Dobozi-King, S. Seo, J.U. Kim, R. Young, M. Cheng, L.B. Kish, "Rapid detection and identification of bacteria: SEnsing of Phage-Triggered Ion Cascade (SEPTIC)", Journal of Biological Physics and Chemistry 5 (2005) 3–7." (PDF).  ^ Technological background Phage-ligand technology ^ Keen, E. C. (2014). "Tradeoffs in bacteriophage life histories". Bacteriophage. 4 (1): e28365. doi:10.4161/bact.28365. PMC 3942329 . PMID 24616839.  ^ Atamer, Zeynep; Samtlebe, Meike; Neve, Horst; J. Heller, Knut; Hinrichs, Joerg (2013-07-16). "Review: elimination of bacteriophages in whey and whey products". Frontiers in Microbiology. 4: 191. doi:10.3389/fmicb.2013.00191. ISSN 1664-302X. PMC 3712493 . PMID 23882262.  ^ Miller, ES; Kutter, E; Mosig, G; Arisaka, F; Kunisawa, T; Rüger, W (March 2003). " Bacteriophage
Bacteriophage
T4 genome". Microbiology
Microbiology
and molecular biology reviews : MMBR. 67 (1): 86–156, table of contents. doi:10.1128/MMBR.67.1.86-156.2003. PMC 150520 . PMID 12626685.  ^ Ackermann, H.-W.; Krisch, H. M. (6 April 2014). "A catalogue of T4-type bacteriophages". Archives of Virology. 142 (12): 2329–2345. doi:10.1007/s007050050246. PMID 9672598.  ^ Strauss, James H.; Sinsheimer, Robert L. (July 1963). "Purification and properties of bacteriophage MS2 and of its ribonucleic acid". Journal of Molecular Biology. 7 (1): 43–54. doi:10.1016/S0022-2836(63)80017-0. 

External links[edit]

Animation of bacteriophage targeting E. coli bacteria Häusler, T. (2006) "Viruses vs. Superbugs", Macmillan Phage.org general information on bacteriophages bacteriophages illustrations and genomics Bacteriophages get a foothold on their prey NPR Science Friday podcast, "Using 'Phage' Viruses to Help Fight Infection", April 2008 Animation by Hybrid Animation Medical for a T4 Bacteriophage
Bacteriophage
targeting E. coli bacteria. Bacteriophages: What are they. Presentation by Professor Graham Hatfull, University of Pittsburgh on YouTube

v t e

Ecology: Modelling ecosystems: Trophic components

General

Abiotic component Abiotic stress Behaviour Biogeochemical cycle Biomass Biotic component Biotic stress Carrying capacity Competition Ecosystem Ecosystem
Ecosystem
ecology Ecosystem
Ecosystem
model Keystone species List of feeding behaviours Metabolic theory of ecology Productivity Resource

Producers

Autotrophs Chemosynthesis Chemotrophs Foundation species Mixotrophs Myco-heterotrophy Mycotroph Organotrophs Photoheterotrophs Photosynthesis Photosynthetic efficiency Phototrophs Primary nutritional groups Primary production

Consumers

Apex predator Bacterivore Carnivores Chemoorganotroph Foraging Generalist and specialist species Intraguild predation Herbivores Heterotroph Heterotrophic nutrition Insectivore Mesopredators Mesopredator
Mesopredator
release hypothesis Omnivores Optimal foraging theory Predation Prey switching

Decomposers

Chemoorganoheterotrophy Decomposition Detritivores Detritus

Microorganisms

Archaea Bacteriophage Environmental microbiology Lithoautotroph Lithotrophy Microbial cooperation Microbial ecology Microbial food web Microbial intelligence Microbial loop Microbial mat Microbial metabolism Phage ecology

Food webs

Biomagnification Ecological efficiency Ecological pyramid Energy flow Food chain Trophic level

Example webs

Cold seeps Hydrothermal vents Intertidal Kelp forests Lakes North Pacific Subtropical Gyre Rivers San Francisco Estuary Soil Tide pool

Processes

Ascendency Bioaccumulation Cascade effect Climax community Competitive exclusion principle Consumer-resource systems Copiotrophs Dominance Ecological network Ecological succession Energy quality Energy Systems Language f-ratio Feed conversion ratio Feeding frenzy Mesotrophic soil Nutrient cycle Oligotroph Paradox of the plankton Trophic cascade Trophic mutualism Trophic state index

Defense, counter

Animal coloration Antipredator adaptations Camouflage Deimatic behaviour Herbivore
Herbivore
adaptations to plant defense Mimicry Plant defense against herbivory Predator avoidance in schooling fish

v t e

Ecology: Modelling ecosystems: Other components

Population ecology

Abundance Allee effect Depensation Ecological yield Effective population size Intraspecific competition Logistic function Malthusian growth model Maximum sustainable yield Overpopulation in wild animals Overexploitation Population cycle Population dynamics Population modeling Population size Predator–prey (Lotka–Volterra) equations Recruitment Resilience Small population size Stability

Species

Biodiversity Density-dependent inhibition Ecological effects of biodiversity Ecological extinction Endemic species Flagship species Gradient analysis Indicator species Introduced species Invasive species Latitudinal gradients in species diversity Minimum viable population Neutral theory Occupancy–abundance relationship Population viability analysis Priority effect Rapoport's rule Relative abundance distribution Relative species abundance Species diversity Species homogeneity Species richness Species distribution Species-area curve Umbrella species

Species interaction

Antibiosis Biological interaction Commensalism Community ecology Ecological facilitation Interspecific competition Mutualism Storage effect

Spatial ecology

Biogeography Cross-boundary subsidy Ecocline Ecotone Ecotype Disturbance Edge effects Foster's rule Habitat
Habitat
fragmentation Ideal free distribution Intermediate Disturbance Hypothesis Island biogeography Landscape ecology Landscape epidemiology Landscape limnology Metapopulation Patch dynamics r/K selection theory Resource selection function Source–sink dynamics

Niche

Ecological niche Ecological trap Ecosystem
Ecosystem
engineer Environmental niche modelling Guild Habitat Marine habitats Limiting similarity Niche apportionment models Niche construction Niche differentiation

Other networks

Assembly rules Bateman's principle Bioluminescence Ecological collapse Ecological debt Ecological deficit Ecological energetics Ecological indicator Ecological threshold Ecosystem
Ecosystem
diversity Emergence Extinction debt Kleiber's law Liebig's law of the minimum Marginal value theorem Thorson's rule Xerosere

Other

Allometry Alternative stable state Balance of nature Biological data visualization Ecocline Ecological economics Ecological footprint Ecological forecasting Ecological humanities Ecological stoichiometry Ecopath Ecosystem
Ecosystem
based fisheries Endolith Evolutionary ecology Functional ecology Industrial ecology Macroecology Microecosystem Natural environment Regime shift Systems ecology Urban ecology Theoretical ecology

List of ecology topics

v t e

Microbiology: Virus

Components

Viral envelope Capsid Viral protein

Viral life cycle

Viral entry Viral replication Viral shedding Virus
Virus
latency Viroplasm

Genetics

Reassortment Antigenic shift Antigenic drift Phenotype mixing

By host

Bacteriophage Virophage Mycovirus Plant virus
Plant virus
(Plant to Human) Animal virus Human virome Archea virus Amoeba virus

Other

Viral disease Helper virus Laboratory diagnosis of viral infections Viral load Virus-like particle Viral quantification Antiviral drug Neurotropic virus Oncovirus Social history of viruses Satellite

.