Virology and Bioinformatics from Virology.ca
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Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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HostPhinder: A Phage Host Prediction Tool

The current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. Meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput approaches for phage characterization within reach. Here, we present HostPhinder, a tool aimed at predicting the bacterial host of phages by examining the phage genome sequence. Using a reference database of 2196 phages with known hosts, HostPhinder predicts the host species of a query phage as the host of the most genomically similar reference phages. As a measure of genomic similarity the number of co-occurring k-mers (DNA sequences of length k) is used. Using an independent evaluation set, HostPhinder was able to correctly predict host genus and species for 81% and 74% of the phages respectively, giving predictions for more phages than BLAST and significantly outperforming BLAST on phages for which both had predictions. HostPhinder predictions on phage draft genomes from the INTESTI phage cocktail corresponded well with the advertised targets of the cocktail. Our study indicates that for most phages genomic similarity correlates well with related bacterial hosts. HostPhinder is available as an interactive web service [1] and as a stand alone download from the Docker registry [2].
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Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome : Nature : Nature Publishing Group

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome : Nature : Nature Publishing Group | Virology and Bioinformatics from Virology.ca | Scoop.it
The mammalian gut ecosystem has considerable influence on host physiology, but the mechanisms that sustain this complex environment in the face of different stresses remain obscure. Perturbations to the gut ecosystem, such as through antibiotic treatment or diet, are at present interpreted at the level of bacterial phylogeny. Less is known about the contributions of the abundant population of phages to this ecological network. Here we explore the phageome as a potential genetic reservoir for bacterial adaptation by sequencing murine faecal phage populations following antibiotic perturbation. We show that antibiotic treatment leads to the enrichment of phage-encoded genes that confer resistance via disparate mechanisms to the administered drug, as well as genes that confer resistance to antibiotics unrelated to the administered drug, and we demonstrate experimentally that phages from treated mice provide aerobically cultured naive microbiota with increased resistance. Systems-wide analyses uncovered post-treatment phage-encoded processes related to host colonization and growth adaptation, indicating that the phageome becomes broadly enriched for functionally beneficial genes under stress-related conditions. We also show that antibiotic treatment expands the interactions between phage and bacterial species, leading to a more highly connected phage-bacterial network for gene exchange. Our work implicates the phageome in the emergence of multidrug resistance, and indicates that the adaptive capacity of the phageome may represent a community-based mechanism for protecting the gut microflora, preserving its functional robustness during antibiotic stress.
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A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students

A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students | Virology and Bioinformatics from Virology.ca | Scoop.it
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Viruses might provide mucosal immunity

Viruses might provide mucosal immunity | Virology and Bioinformatics from Virology.ca | Scoop.it
Mucosal membranes are common portals of entry for microbes. Viruses that infect bacteria might also be part of the mucosal antimicrobial defense system.
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Researchers Set Record For Detecting Smallest Virus

Researchers Set Record For Detecting Smallest Virus | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers have created an ultra-sensitive biosensor capable of identifying the smallest single virus particles in solution, an advance that may revolutionize early disease detection in a point-of-care setting and shrink test result wait times...
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Could Bacteria-Fighting Viruses Replace Overused Antibiotics?: Scientific American

Could Bacteria-Fighting Viruses Replace Overused Antibiotics?: Scientific American | Virology and Bioinformatics from Virology.ca | Scoop.it
Long ignored by mainstream researchers, the viruses that infect bacteria have a role to play in modern medicine, Vincent Fischetti says...
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Ed Rybicki's comment, August 9, 2012 4:35 AM
Anyone interested in early microbiology / virology should look for a paper in the online Annales de l'Institut Pasteur from 1896, entitled "Les Microbes des Rivieres de l'Inde", in which one M Hankin describes how Indian river water was an incredibly effective means of killing Vibrio cholerae - almost certainly, in retrospect, because of the amazingly high titre of vibriophages in it.
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Bacteriophage T4 and Its Relatives. A Series of Critical Reviews: Amazon.co.uk: Jim D Karam, Eric S Miller: Books

Bacteriophage T4 and Its Relatives.A Series of Critical Reviews: Amazon.co.uk: Jim D Karam, Eric S Miller: Books...

 

Gotta love phages.  There's so damn MANY of them.

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Bacteria-Killing Viruses Wield an Iron Spike

Bacteria-Killing Viruses Wield an Iron Spike | Virology and Bioinformatics from Virology.ca | Scoop.it

Forget needles in haystacks. Try finding the tip of a needle in a virus. Scientists have long known that a group of viruses called bacteriophages have a knack for infiltrating bacteria and that some begin their attack with a protein spike. But the tip of this spike is so small that no one knew what it was made of or exactly how it worked. Now a team of researchers has found a single iron atom at the head of the spike, a discovery that suggests phages enter bacteria in a different way than surmised.


Via AJCann
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What Can We Learn from a Metagenomic Analysis of a Georgian Bacteriophage Cocktail?

Phage therapy, a practice widespread in Eastern Europe, has untapped potential in the combat against antibiotic-resistant bacterial infections. However, technology transfer to Western medicine is proving challenging. Bioinformatics analysis could help to facilitate this endeavor.
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MicroMicrobe • Microbial image of the month I’ve previously...

MicroMicrobe • Microbial image of the month I’ve previously... | Virology and Bioinformatics from Virology.ca | Scoop.it
Microbial image of the month


I’ve previously posted an image of a single phage, but this month’s image shows phages in action, infecting a bacterial cell.
Naomi Osborne's insight:

Fab image of phages in action

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Russian Doll Genetics - MicrobiologyBytes

Russian Doll Genetics - MicrobiologyBytes | Virology and Bioinformatics from Virology.ca | Scoop.it
Viruses within viruses - the curious world of bacteriophage genetics.
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Genome and proteome analysis of 7-7-1, a flagellotropic phage infecting Agrobacterium sp H13-3

Genome and proteome analysis of 7-7-1, a flagellotropic phage infecting Agrobacterium sp H13-3 | Virology and Bioinformatics from Virology.ca | Scoop.it

"The flagellotropic phage 7-7-1 infects motile cells of Agrobacterium sp H13-3 by attaching to and traveling along the rotating flagellar filament to the secondary receptor at the base, where it injects its DNA into the host cell."

 

This is an interesting paper, because it describes a phage infecting Agrobacterium - and touches on a subject that has intrigued me for years, which is: How does a phage which attaches to a flagellum, get its genome inside the cell?  This throws some mud onto a previous model, which suggested a passive mode of transport like a well-oiled nut moving towards the head of a bolt, as in this case that would result in transport the other way.  Expect more on this topic!

 

Image sourced from the paper

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Future Virology Introducing yesterday’s phage therapy in today’s medicine

The worldwide emergence of ‘superbugs’ and a dry antibiotic pipeline threaten modern society with a return to the preantibiotic era. Phages – the viruses of bacteria – could help fight antibiotic-resistant bacteria. Phage therapy was first attempted in 1919 by Felix d’Herelle and was commercially developed in the 1930s before being replaced by antibiotics in most of the western world.

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PhiSiGns

PhiSiGns | Virology and Bioinformatics from Virology.ca | Scoop.it

PhiSiGns is a web-based and standalone application that provides a simple and convenient tool to identify signature genes and design primers for PCR amplification of related genes from environmental samples.

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