Bacteriophage types – Replication cycles & Classification
There are many bacteriophage types, although a few we hear of more than others. Bacteriophages are very complex viruses that have been around since the earliest Earth history and have played a crucial role in maintaining the balance over the population of bacteria on our planet. These ancient forms of life have evolved greatly and we are only beginning to scratch the surface on their unique and vital role in our lives.
Although found everywhere and there are so many bacteriophage types of all shapes and sizes, they are all categorised into one of the two replication methods; lytic and lysogenic. It is important to understand the differentiation of the two as that plays a crucial rule in regards to how phages may interact with us; as one happens to always play on our side, whilst the other has its interests aligned with its survival, which may go against us.
Bacteriophage types - Replication
Virulent bacteriophages – Lytic cycle (cytoplasmic viral replication)
Virulent bacteriophages happen to be those that play in our interest, as well as theirs. This bacteriophage type uses the lytic cycle for replication. Lysis or lytic cycle is a cytoplasmic viral replication process in which the bacteriophage injects its genetic material into a host cell, which allows this genetic material to replica, producing many new phages. Once the host cell is filled with new bacteriophages, the host cell raptures from within, releasing the newly formed phages.
It is important to note that the bacteriophages that are used for phage products and phage therapy are all virulent phages.
Temperate bacteriophages – Lysogenic cycle
Temperate bacteriophages are the bacteriophage type that use the lysogenic cycle for replication. The lysogenc cycle is one where a phage infuses its generic material into a host, but instead of rapidly replicating, this generic material finds its way to the host’s genetic material and infuses itself with it, becoming a prophage. It becomes part of the host’s genetic material and when the host cell divides, the temperate phage genetic material also undergoes a replication process.
Lysogenic bacteriophages remain in this symbiotic state; in which it causes no harm to the host cell but rather quietly uses the resources provided by the host cell. However, when a lysogenic bacteriophage feels under a certain amount of pressure, or its survival is placed at risk, it has the ability to switch from the lysogenic cycle to the lytic cycle, which results in rapid replication of newly formed phages which burst out of the host cell.
Bacteriophages that have the capability to undergo the lysogenic cycle, ie; temperate phages, assess and choose the cycle that they see fit in accordance to the environment they find themselves in, whether to go for the lytic or lysogenic cycle.
Bacteriophage types - Classification
Below is the current known breakdown of bacteriophages. Since phages are still being studied and there is a lot that has not be discovered, the following information may be seen as incomplete.
Bacteriophage types
Order – Caudovirales. Family – Ackermannviridae, Myoviridae, Siphoviridae and Podoviridae.
Ackermannviridae
Belongs to the order of Caudovirales. These phages are nonenveloped and have head-tail structures. Their icosahedral head is approximately 93nm in diameter. They also have a neck with no collar and a base plate. Their tail is approximately 140nm in width and 20nm in length and is contractile. They also have fibers attached to their tail, which are approximately 38nm in length. These bacteriophages use cytoplasmic viral replication.
Myoviridae
Belongs to the order of Caudovirales. These phages have elongated heads (approximately 110nm in length), long tails with a collar (114nm), base plates with spikes and 6 long tail fibers. They have a linear genome of approximately 33kb – 244 kb in length and it encodes for 40 – 415 proteins. These bacteriophages use cytoplasmic viral replication, lytic and lack the genes to become lysogenic.
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Bacteriophage types
This group contains the following subfamilies and genera within:
Sub family – Peduovirinae. Genera – Hpunalikevirus & P2likevirus.
Peduovirinae have virions with heads that are 60nm in diameter and tails that are 135nm by 18nm in length. Their identification marker is the sheaths that slide off the tail core. These bacteriophages use cytoplasmic viral replication.
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Sub family – Spounavirinae. Genera – Spounalikevirus & Twortlikevirus.
Spounavirinae have isometric heads ranging between 87nm - 94nm in diameter, visible capsomers (protein protection of genetic material), long tails between 140nm - 219nm and a double base plate. The tip of their tails, there are globular structures known to be base plate spikes and kinked tail fibers. These phages are all virulent phages (lytic). They attack a broad range of members from the Firmicutes; phylum of bacteria. Phages from this group normally possess large (127-142kb) nonpermuted genomes with 3.1-20kb terminal redundancies. These bacteriophages use cytoplasmic viral replication.
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Sub family – Tevenvirinae. Genera – T4virus & Schizot4virus.
Tevenvirinae are divided on the morphology of the head; T4virus has a head of 137nm in length and Schizot4virus has a head of 111nm in length. Further division within the genera is made depending on the protein homology. These bacteriophages use cytoplasmic viral replication.
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Sub family – Eucampyvirinae. Genera – Cp220likevirus & Cp8unalikevirus.
Eucampyvirinae have a nonenveloped, head-like structure. Their icosahedral head is approximately 93nm – 96nm in diameter. Their tail is approximately 96nm – 140nm in length and 20nm in width is contractile. They also have 38nm long fibers that are attached on the tail. Their linear dsDNA genome is approximately 132kb – 197kb in length and encodes 149 – 245 proteins. These bacteriophages use cytoplasmic viral replication.
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Bacteriophage types
Unassigned family. Genera – Bcep78likevirus, Bcepmulikevirus, Felixounalikevirus, Hapunalikevirus, I3likevirus, Mulikevirus, Pbunalikevirus, Phicd119likevirus, Phihlikevirus, Phikzlikevirus, Punalikevirus & Viunalikevirus.
Siphoviridae
Belongs to the order of Caudovirales. These bacteriophages target both bacteria and archaea. Many bacteriophages from this family have been placed in an unclassified group with no genus, however many of the phages are known to target Lactobacillus, Mycobacterium, Streptococcus, and other bacteria. Currently, there are 313 species in this family with 47 genera. These phages have no enveloped head that is icosahedral. Members are identified by their cross-banded noncontractile tails. Their genomes are double stranded and linear (around 50kb in length) containing 70 genes. These bacteriophages use cytoplasmic viral replication, exiting host cell through lysis.
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Podoviridae
Belongs to the order of Caudovirales. There are 50 species found in this family, with 20 genera. The main characteristic of these phages is their very short and noncontractile tail with 6 short subterminal fibers. Their tail is thick and is built to stack like disks, with a maximum length of approximately 17nm. They are nonenveloped with a head that is icosahedral. The diameter is 60nm and they have 72 capsomers. These bacteriophages have a double stranded DNA with a linear genome approximately 40-43kb in length and encodes approximately 55 genes. The genome encodes 9 structural proteins. They follow the bidirectional DNA replication process. These bacteriophages use cytoplasmic viral replication.
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Bacteriophage types
Order – Ligamenvirales. Family – Lipothrixviridae and Rudiviridae.
Lipothrixviridae
Belongs to the order of Ligamenvirales. These phages target archaea from the kingdom of Crenarchaeota and have 8 species which are divided among 3 genera; Betalipothrixvirus, Gammalipothrixvirus and Deltalipothrixvirus. They share the structural and genomic properties with phages from the Rudiviridae family; nonenveloped and rod shaped. They also have the linear dsDNA genomes with up to 9 genes. They also have the filamentous particles that are built from homologous capsid proteins. These bacteriophages use cytoplasmic viral replication.
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Rudiviridae
Belongs to the order of Ligamenvirales and are the only genus in the family. These bacteriophages target hyper thermophilic archaea from the kingdom of Crenarchaeota. They are nonenveloped and stiff rod shaped with linear dsDNA genomes. They currently have 3 species, including Sulfolobus islandicus rod-shaped virus 2. The family name comes from the Latin word ‘rudis’, meaning thin rod, in reflection to the shape of this virion. These bacteriophages use cytoplasmic, lytic cycle of viral replication.
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Bacteriophage types
Order – Unassigned. Family – Ampullaviridae, Bicaudaviridae, Clavaviridae, Corticoviridae, Cystoviridae, Fuselloviridae, Globuloviridae, Guttaviridae, Inoviridae, Leviviridae, Microviridae, Plasmaviridae, Pleolipoviridae, Portogloboviridae, Sphaerolipoviridae, Spiraviridae, Tectiviridae, Tristromaviridae & Turriviridae.
Ampullaviridae
Does not have an assigned order and only has 1 specie in 1 genus. These bacteriophages target archaea from the genus Acidianus. They have one narrow end which expands into a wider end. Total length is approximately 230nm and width of approximately 75nm. The narrow end has a viral envelope that is used to inject the DNA into hosts. The broad end has 20 thin filaments, each distributed in a ring. The family and genus name comes from the Latin word ‘ampulla’, in reflection to the bottle shape of this virion. These bacteriophages use cytoplasmic viral replication.
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Bicaudaviridae
Does not have an assigned order and only has 1 genus with 1 specie; Acidianus two-tailed virus, however Sulfolobus tengchongensis spindle-shaped viruses 1 and 2 (STSV1 and STSV2) are also listed to belong to this family. These bacteriophages are hyper thermophilic archaea viruses that target species from the genus of Acidianus. They are enveloped and have are lemon-shaped. Their genomes are circular, approximately 62kb in length and the genome has 72 open reading frames. These phages use cytoplasmic viral replication.
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Clavaviridae
Does not have an assigned order and only has 1 genus. These bacteriophages target species archaea. They are bacilliform shaped and 15.8nm in diameter, with one pointed end and the other rounded. Virions are highly thermostable, remaining infectious after being left in incubation of 100°C for 3 hours. They have a circular double-stranded DNA molecule of 5.3kb. DNA contains 14 open reading frames. The DNA is not integrated with host cells, and does not cause host cell lysis. The family and genus name comes from the Latin word ‘clava’, which translates to stick.
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Corticoviridae
Does not have an assigned order and only has 1 genus with 1 specie; Pseudoalteromonas virus PM2. Prophages which are closely related to the PM2 are of aquatic bacteria, which suggest that corticoviruses may be underestimated in their ecological importance. These bacteriophages target species of bacteria. These phages consist of a icosahedral, round, non-enveloped capsid, with a diameter of 60nm, with an internal lipid membrane found in the inner and outer protein shell. These shells have three layers and on the surface have a pattern with bush-like spikes from twelve vertices. These bacteriophages use cytoplasmic viral replication. The family and genus name comes from the Latin word ‘cortex’ or ‘corticis’, which translate to crust or bark.
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Cystoviridae
Does not have an assigned order and only has 1 specie in this genus; Pseudomonas phage phi6. These bacteriophages target species of phaseolicola bacteria. A distinguishing feature is their tripartite dsRNA genome, approximately 14kb in length and the protein and lipid outer layer. No other known bacteriophage has a lipid outer layer. The most identified cystoviruses today are those which target the Pseudomonas species. These phages are enveloped, with an icosahedral and have spherical geometrics. In diameter they are approximately 85nm. Their genomes are linear and segmented; large - 6.4kb in length, Medium – 4kb in length and Small – 2.9kb in length. The genome codes contain 12 proteins. These bacteriophages use cytoplasmic viral replication.
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Fuselloviridae
Does not have an assigned order and is a family of viruses. There are currently 9 species which are divided amongst 2 genera. These bacteriophages target species of archaea, specifically; shibatae, solfataricus, and islandicus. They are enveloped and lemon-shaped. Their diameter is 60nm with a length of 100nm. Their genomes are circular, approximately 17.3kb in length. These phages are present in high temperatures (≥70 °C), acidic (pH ≤4) environments, such as hot springs. These bacteriophages use cytoplasmic viral replication.
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Globuloviridae
Does not have an assigned order and is a family of viruses which are hyperthermophilic archaeal viruses. Currently, they have 1 genus with 2 species in this family; Pyrobaculum spherical virus and Thermoproteus tenax spherical virus 1. These bacteriophages target Crenarchaea from the genera Pyrobaculum and Thermoproteus. These phages are enveloped and spherical. Their diameter is approximately 100nm. Their genomes are linear dsDNA, non-segmentaed and are approximately 20kb – 30kb in length. These bacteriophages use cytoplasmic viral replication.
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Guttaviridae
Does not have an assigned order and is a family of viruses, currently having 2 species divided among 2 genera. These bacteriophages target Sulfolobus newzealandicus. These phages are enveloped with a diameter that is approximately 70nm – 95nm and the length of approximately 110nm – 185nm. The genomes are circular, approximately 20kb in length. They consist of a coat, core, nucleocapsid and fibers found at pointed ends. The surface has a bee-hive ribbed surface with protrusions that are covered with long fibers at the pointed end. Their genome is extremely heavily methylated. These bacteriophages use DNA-templated transcription. The family name comes from the Latin word ‘gutta’, which translate to droplet.
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Inoviridae
Does not have an assigned order and is a family of viruses, currently having 43 species divided among 2 genera. These bacteriophages target bacteria. These phages are nonenveloped, have a rod or filament geometrics. Their diameter is approximately 7nm and length of approximately 2000nm. Their genomes are circular, approximately 8kb in length and the genome codes for 4 to 10 proteins. These bacteriophages use cytoplasmic viral replication.
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Leviviridae
Does not have an assigned order and is a family of viruses, currently having 4 species divided among 2 genera. These bacteriophages target bacteria, including; Enterobacteria, Caulobacter, Pseudomonas, and Acinetobacter. These phages are icosahedral, nonenveloped and have spherical geometrics. Their diameter is approximately 26nm. Their genomes are linear and non-segmented, approximately 4kb in length and the genome codes for 4 proteins. These bacteriophages use the Positive stranded RNA virus transcription method and the lysis to exit the host cell.
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Microviridae
Does not have an assigned order and is a family of viruses, currently having 12 species divided among 7 genera. These bacteriophages target bacteria, specifically; Enterobacteria and Spiroplasma. These phages are icosahedral, nonenveloped and have round geometrics. Their diameter is approximately 25nm – 27nm (Each virion has 60 copies of F, G and J protein and 12 copies of H protein). They also have trumpet-shaped pentamers (each composed of 5 copies of G and one of H protein). Their genome is a single stranded DNA. The majority of these bacteriophages use the lytic life cycle, however a few have a temperate life cycle. The family name comes from the ancient Greek word ‘μικρός’ (mikrós), which translate to small, reflecting the size of their genomes as being amongst the smallest of the DNA viruses.
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Plasmaviridae
Does not have an assigned order and is a family of viruses which has 1 genus with 1 specie. These bacteriophages target bacteria, specifically; Acholeplasma (Acholeplasma virus L2). These phages are quasi-spherical, enveloped and approximately 80nm in diameter (range between 50nm – 125nm). Their genome is condensed, nonsegmented and has a single molecule of a circular, supercoiled doublbe-stranded DNA of 12 kb pairs in length. The genome has 14 open reading frames and encodes at least 15 proteins. These bacteriophages use cytoplasmic viral replication.
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Pleolipoviridae
Does not have an assigned order. These phages are enveloped, pleomorphic approximately 40nm in diameter. They have a circular ssDNA with a genome of 7kb – 10.6kb in length. These bacteriophages use cytoplasmic viral replication.
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Portogloboviridae
Does not have an assigned order. These phages are icosahedral capsid with an 87nm diameter. This capsid encloses an internal membrane made of lipid. They also have a nucleoprotein filament of 3nm in width which is would into 14 spherical coils. Their genome in a circular double-stranded DNA that is 20kb in length, that encodes 45 proteins. These bacteriophages use cytoplasmic viral replication.
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Sphaerolipoviridae
Does not have an assigned order and is a family of viruses which has 3 genera; Alphasphaerolipovirus, Betasphaerolipovirus and Gammasphaerolipovirus. Species belonging to Alphasphaerolipovirus and Betasphaerolipovirus target halophilic archaea and those belonging to the genus Gammasphaerolipovirus target thermophilic bacteria. These phages are tailless icosphedral, with internal lipid membrane and have a double-stranded DNA. They are nonenveloped and the size ranges between 50nm – 80nm.
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Spiraviridae
Does not have an assigned order and is a family of viruses and there is only 1 specie currently recognized. These bacteriophages target archeae. The phages are nonenveloped, hollow and cylindrical. Their size is approximately 200nm x 28nm with appendages of 20nm. They have a single stranded DNA of 24.9kb and it encodes 57 proteins. These bacteriophages use cytoplasmic viral replication.
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Tectiviridae
Does not have an assigned order and is a family of viruses which has 3 genera with 4 species. These bacteriophages target bacteria. They have no head-tail structure, but have the capability of producing a tail-like structure of approximately 60nm – 100nm upon adsorption of after chloroform treatment. They are icosahedral, nonenveloped and the capsid has 2 layers. The outer layer if a protein structure and the inner layer is a proteinaceous lipid membrane which contains the genome. Lipids contribute to 15% of their weight and they have no carbohydrates present. They also have apical spike extending, approximately 20nm. Their genome is a single molecule that is a linear double-stranded DNA of 15kb in length and has 30 open reading frames. These bacteriophages use cytoplasmic viral replication.
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Tristromaviridae
Does not have an assigned order. These phages are enveloped, rod-shaped and are approximately 410nm in length and approximately 38nm in diameter. They have a linear dsDNA genome of 15.9kb in length. Their DNA is packaged in a helical core. These bacteriophages use cytoplasmic viral replication.
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Turriviridae
Does not have an assigned order and is a family of viruses which has 2 species in 1 genus; Alphaturrivirus. These bacteriophages target archaea, specifically Sulfolobus solfataricus. They have an icosahedral structure with an approximate diameter of 74nm and 12 five-fold vertices turrent-like appendages expanding to 13nm, above the capsid shell. The capsid is enclosed in an internal lipid membrane. They have a linear genome of 17kb in length. These bacteriophages use cytoplasmic viral replication.
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Feature image taken from Micro Biology Online
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