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Current Opinion in Virology Oct 2011Bacteriophages occupy a unique position in biology, representing an absolute majority of all organisms in the biosphere. Because their genomes are relatively small,... (Review)
Review
Bacteriophages occupy a unique position in biology, representing an absolute majority of all organisms in the biosphere. Because their genomes are relatively small, elucidating the genetic diversity of the phage population, deciphering their origins, and identifying the evolutionary mechanisms that shape the population would seem readily feasible. And yet the pace of phage genome characterization has slowed over the past three years, reflecting in part a need to transition from sequencing known and well-characterized bacteriophages to the isolation and comparative analysis of new isolates. The current state of bacteriophage genomics shows that the genetic diversity of the population is very high, that phages have been actively evolving for billions of years with active engagement of horizontal genetic exchange, and that their genomes are consequently pervasively mosaic in their architectures. But we have barely scratched the surface and the next years of phage genome exploration promise to be especially revealing.
Topics: Bacteriophages; Biological Evolution; Genetic Variation; Genome, Viral; Phylogeny
PubMed: 22034588
DOI: 10.1016/j.coviro.2011.06.009 -
Viruses Mar 2011Bacteriophages have been a model system to study assembly processes for over half a century. Formation of infectious phage particles involves specific protein-protein... (Review)
Review
Bacteriophages have been a model system to study assembly processes for over half a century. Formation of infectious phage particles involves specific protein-protein and protein-nucleic acid interactions, as well as large conformational changes of assembly precursors. The sequence and molecular mechanisms of phage assembly have been elucidated by a variety of methods. Differences and similarities of assembly processes in several different groups of bacteriophages are discussed in this review. The general principles of phage assembly are applicable to many macromolecular complexes.
Topics: Bacteriophages; Viral Proteins; Virus Assembly
PubMed: 21994726
DOI: 10.3390/v3030172 -
Microbiological Research 2018Bacteriophage particles are the most abundant biological entities on our planet, infecting specific bacterial hosts in every known environment and being major drivers of... (Review)
Review
Bacteriophage particles are the most abundant biological entities on our planet, infecting specific bacterial hosts in every known environment and being major drivers of bacterial adaptive evolution. The study of bacteriophage particles potentially sheds light on the development of new biotechnology products. Bacteriophage therapy, although not new, makes use of strictly lytic phage particles as an alternative in the antimicrobial treatment of resistant bacterial infections and is being rediscovered as a safe method due to the fact that these biological entities devoid of any metabolic machinery do not have affinity to eukaryotic cells. Furthermore, bacteriophage-based vaccination is emerging as one of the most promising preventive strategies. This review paper discusses the biological nature of bacteriophage particles, their mode(s) of action and potential exploitation in modern biotechnology. Topics covered in detail include the potential of bacteriophage particles in human infections (bacteriophage therapy), nanocages for gene delivery, food biopreservation and safety, biocontrol of plant pathogens, phage display, bacterial biosensing devices, vaccines and vaccine carriers, biofilm and bacterial growth control, surface disinfection, corrosion control, together with structural and functional stabilization issues.
Topics: Anti-Bacterial Agents; Bacteria; Bacterial Infections; Bacteriophages; Biofilms; Biological Control Agents; Biosensing Techniques; Biotechnology; Corrosion; DNA Packaging; Dental Caries; Disinfection; Food Preservation; Food Safety; Gene Transfer Techniques; Humans; Nanostructures; Phage Therapy; Vaccination; Vaccines
PubMed: 29853167
DOI: 10.1016/j.micres.2018.04.007 -
Antimicrobial Agents and Chemotherapy Mar 2001
Comparative Study Review
Topics: Animals; Anti-Bacterial Agents; Bacterial Infections; Bacteriophages; Biological Therapy; Disease Models, Animal; Humans
PubMed: 11181338
DOI: 10.1128/AAC.45.3.649-659.2001 -
Archives of Virology Aug 2018High-throughput sequencing (HTS) and its use in recovering and assembling novel virus sequences from environmental, human clinical, veterinary and plant samples has... (Review)
Review
High-throughput sequencing (HTS) and its use in recovering and assembling novel virus sequences from environmental, human clinical, veterinary and plant samples has unearthed a vast new catalogue of viruses. Their classification, known by their sequences alone, sets a major challenge to traditional virus taxonomy, especially at the family and species levels, which have been historically based largely on descriptive taxon definitions. These typically entail some knowledge of their phenotypic properties, including replication strategies, virion structure and clinical and epidemiological features, such as host range, geographical distribution and disease outcomes. Little to no information on these attributes is available, however, for viruses identified in metagenomic datasets. If such viruses are to be included in virus taxonomy, their assignments will have to be guided largely or entirely by metrics of genetic relatedness. The immediate problem here is that the International Committee on Taxonomy of Viruses (ICTV), an organisation that authorises the taxonomic classification of viruses, provides little or no guidance on how similar or how divergent viruses must be in order to be considered members of new species or new families. We have recently developed a method for scoring genomic (dis)similarity between viruses (Genome Relationships Applied to Virus Taxonomy - GRAViTy) among the eukaryotic and prokaryotic viruses currently classified by the ICTV. At the family and genus levels, we found large-scale consistency between genetic relationships and their taxonomic assignments for eukaryotic viruses of all genome configurations and genome sizes. Family assignments of prokaryotic viruses have, however, been made at a quite different genetic level, and groupings currently classified as sub-families are a much better match to the eukaryotic virus family level. These findings support the ongoing reorganisation of bacteriophage taxonomy by the ICTV Phage Study Group. A rapid and objective means to explore metagenomic viral diversity and make evidence-based assignments for such viruses at each taxonomic layer is essential. Analysis of sequences by GRAViTy provides evidence that family (and genus) assignments of currently classified viruses are largely underpinned by genomic relatedness, and these features could serve as a guide towards an evidence-based classification of metagenomic viruses in the future.
Topics: Animals; Bacteriophages; Genome, Viral; Humans; Phylogeny; Virus Diseases; Viruses
PubMed: 30039318
DOI: 10.1007/s00705-018-3938-z -
Annual Review of Biophysics 2012We examine virus maturation of selected nonenveloped and enveloped single-stranded RNA viruses, retroviruses, bacteriophages, and herpesviruses. Processes associated... (Review)
Review
We examine virus maturation of selected nonenveloped and enveloped single-stranded RNA viruses, retroviruses, bacteriophages, and herpesviruses. Processes associated with maturation in the RNA viruses range from subtle (nodaviruses and picornaviruses) to dramatic (tetraviruses and togaviruses). The elaborate assembly and maturation pathway of HIV is discussed in contrast to the less sophisticated but highly efficient processes associated with togaviruses. Bacteriophage assembly and maturation are discussed in general terms, with specific examples chosen for emphasis. Finally the herpesviruses are compared with bacteriophages. The data support divergent evolution of nodaviruses, picornaviruses, and tetraviruses from a common ancestor and divergent evolution of alphaviruses and flaviviruses from a common ancestor. Likewise, bacteriophages and herpesviruses almost certainly share a common ancestor in their evolution. Comparing all the viruses, we conclude that maturation is a convergent process that is required to solve conflicting requirements in biological dynamics and function.
Topics: Animals; Bacteriophages; Biological Evolution; Humans; Virus Assembly; Virus Physiological Phenomena; Viruses
PubMed: 22404678
DOI: 10.1146/annurev-biophys-042910-155407 -
Virologica Sinica Feb 2015Phages are credited with having been first described in what we now, officially, are commemorating as the 100(th) anniversary of their discovery. Those one-hundred years... (Review)
Review
Phages are credited with having been first described in what we now, officially, are commemorating as the 100(th) anniversary of their discovery. Those one-hundred years of phage history have not been lacking in excitement, controversy, and occasional convolution. One such complication is the concept of secondary infection, which can take on multiple forms with myriad consequences. The terms secondary infection and secondary adsorption, for example, can be used almost synonymously to describe virion interaction with already phage-infected bacteria, and which can result in what are described as superinfection exclusion or superinfection immunity. The phrase secondary infection also may be used equivalently to superinfection or coinfection, with each of these terms borrowed from medical microbiology, and can result in genetic exchange between phages, phage-on-phage parasitism, and various partial reductions in phage productivity that have been termed mutual exclusion, partial exclusion, or the depressor effect. Alternatively, and drawing from epidemiology, secondary infection has been used to describe phage population growth as that can occur during active phage therapy as well as upon phage contamination of industrial ferments. Here primary infections represent initial bacterial population exposure to phages while consequent phage replication can lead to additional, that is, secondary infections of what otherwise are not yet phage-infected bacteria. Here I explore the varying meanings and resultant ambiguity that has been associated with the term secondary infection. I suggest in particular that secondary infection, as distinctly different phenomena, can in multiple ways influence the success of phage-mediated biocontrol of bacteria, also known as, phage therapy.
Topics: Animals; Bacteria; Bacterial Physiological Phenomena; Bacteriophages; Biological Therapy; Coinfection; Humans
PubMed: 25595214
DOI: 10.1007/s12250-014-3547-2 -
Mediators of Inflammation 2019The human gut is an extremely active immunological site interfacing with the densest microbial community known to colonize the human body, the gut microbiota. Despite... (Review)
Review
The human gut is an extremely active immunological site interfacing with the densest microbial community known to colonize the human body, the gut microbiota. Despite tremendous advances in our comprehension of how the gut microbiota is involved in human health and interacts with the mammalian immune system, most studies are incomplete as they typically do not consider bacteriophages. These bacterial viruses are estimated to be as numerous as their bacterial hosts, with tremendous and mostly uncharacterized genetic diversity. In addition, bacteriophages are not passive members of the gut microbiota, as highlighted by the recent evidence for their active involvement in human health. Yet, how bacteriophages interact with their bacterial hosts and the immune system in the human gut remains poorly described. Here, we aim to fill this gap by providing an overview of bacteriophage communities in the gut during human development, detailing recent findings for their bacterial-mediated effects on the immune response and summarizing the latest evidence for direct interactions between them and the immune system. The dramatic increase in antibiotic-resistant bacterial pathogens has spurred a renewed interest in using bacteriophages for therapy, despite the many unknowns about bacteriophages in the human body. Going forward, more studies encompassing the communities of bacteria, bacteriophages, and the immune system in diverse health and disease settings will provide invaluable insight into this dynamic trio essential for human health.
Topics: Animals; Bacteria; Bacteriophages; Gastrointestinal Microbiome; Humans; Immune System; Microbiota
PubMed: 31582898
DOI: 10.1155/2019/3730519 -
Annual Review of Virology Sep 2020Actinobacteriophages are viruses that infect bacterial hosts in the phylum . More than 17,000 actinobacteriophages have been described and over 3,000 complete genome... (Review)
Review
Actinobacteriophages are viruses that infect bacterial hosts in the phylum . More than 17,000 actinobacteriophages have been described and over 3,000 complete genome sequences reported, resulting from large-scale, high-impact, integrated research-education initiatives such as the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Sciences (SEA-PHAGES) program. Their genomic diversity is enormous; actinobacteriophages comprise many architecturally mosaic genomes with distinct DNA sequences. Their genome diversity is driven by the highly dynamic interactions between phages and their hosts, and prophages can confer a variety of systems that defend against attack by genetically distinct phages; phages can neutralize these defense systems by coding for counter-defense proteins. These phages not only provide insights into diverse and dynamic phage populations but also have provided numerous tools for mycobacterial genetics. A case study using a three-phage cocktail to treat a patient with a drug-resistant suggests that phages may have considerable potential for the therapeutic treatment of mycobacterial infections.
Topics: Actinobacteria; Bacteriophages; Base Sequence; Genetic Variation; Genome, Viral; Genomics; Mycobacterium Infections; Phage Therapy; Phylogeny
PubMed: 32991269
DOI: 10.1146/annurev-virology-122019-070009 -
Viruses Oct 2023Half a century has passed since the discovery of Pseudomonas phage phi6, the first enveloped dsRNA bacteriophage to be isolated. It remained the sole known dsRNA phage... (Review)
Review
Half a century has passed since the discovery of Pseudomonas phage phi6, the first enveloped dsRNA bacteriophage to be isolated. It remained the sole known dsRNA phage for a quarter of a century and the only recognised member of the family until the year 2018. After the initial discovery of phi6, additional dsRNA phages have been isolated from globally distant locations and identified in metatranscriptomic datasets, suggesting that this virus type is more ubiquitous in nature than previously acknowledged. Most identified dsRNA phages infect strains and utilise either pilus or lipopolysaccharide components of the host as the primary receptor. In addition to the receptor-mediated strictly lytic lifestyle, an alternative persistent infection strategy has been described for some dsRNA phages. To date, complete genome sequences of fourteen dsRNA phage isolates are available. Despite the high sequence diversity, similar sets of genes can typically be found in the genomes of dsRNA phages, suggesting shared evolutionary trajectories. This review provides a brief overview of the recognised members of the virus family and related dsRNA phage isolates, outlines the current classification of dsRNA phages, and discusses their relationships with eukaryotic RNA viruses.
Topics: Bacteriophages; Pseudomonas Phages; Pseudomonas; Genome, Viral
PubMed: 38005832
DOI: 10.3390/v15112154