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![Comparison of phage genome sizes as differentiated by family. Genome sizes are as provided by NCBI (follow the Viruses link from http://www.ncbi.nlm.nih.gov/genome). Phage morphologies are provided also by NCBI but we defer to the International Committee for Virus Taxonomy given conflict between the two (http://www.ictvonline.org/). In addition, there are older sequences along with one newer sequence (phage G) that are not yet found on the above NCBI database page that we have included. These are for Enterobacteria phage SP (microvirus), Enterobacteria phage Fr (microvirus), Enterobacteria phage GA (microvirus), Bacillus phage G (myovirus), Bacillus phage PZA (podovirus), and Streptococcus phage SMP (siphovirus). Not included are genome sizes associated with unclassified phages. Total numbers of genomes included are as follows (if there are two numbers then the first is as found in the earlier version of this figure [19] and the second as found here): Leviviridae (10), Microviridae (17), Inoviridae (28→31), Corticoviridae (1), Plasmaviridae (1), Cystoviridae (5), Tectiviridae (4), Podoviridae (92→108), Siphoviridae (253→291), and Myoviridae (115→147). Purple refers to RNA genomes, red to ssDNA genomes, blue to dsDNA genomes as found in lipid-containing and tailless virions, and green, as indicated in the figure, are dsDNA in tailed and lipid-less virus particles.](profile/Paul-Hyman/publication/258924310/figure/fig2/AS:202568669110307@1425307542875/Comparison-of-phage-genome-sizes-as-differentiated-by-family-Genome-sizes-are-as.png)
Comparison of phage genome sizes as differentiated by family. Genome sizes are as provided by NCBI (follow the Viruses link from http://www.ncbi.nlm.nih.gov/genome). Phage morphologies are provided also by NCBI but we defer to the International Committee for Virus Taxonomy given conflict between the two (http://www.ictvonline.org/). In addition, there are older sequences along with one newer sequence (phage G) that are not yet found on the above NCBI database page that we have included. These are for Enterobacteria phage SP (microvirus), Enterobacteria phage Fr (microvirus), Enterobacteria phage GA (microvirus), Bacillus phage G (myovirus), Bacillus phage PZA (podovirus), and Streptococcus phage SMP (siphovirus). Not included are genome sizes associated with unclassified phages. Total numbers of genomes included are as follows (if there are two numbers then the first is as found in the earlier version of this figure [19] and the second as found here): Leviviridae (10), Microviridae (17), Inoviridae (28→31), Corticoviridae (1), Plasmaviridae (1), Cystoviridae (5), Tectiviridae (4), Podoviridae (92→108), Siphoviridae (253→291), and Myoviridae (115→147). Purple refers to RNA genomes, red to ssDNA genomes, blue to dsDNA genomes as found in lipid-containing and tailless virions, and green, as indicated in the figure, are dsDNA in tailed and lipid-less virus particles.
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Life forms can be roughly differentiated into those that are microscopic versus those that are not as well as those that are multicellular and those that, instead, are unicellular. Cellular organisms seem generally able to host viruses, and this propensity carries over to those that are both microscopic and less than truly multicellular. These viru...
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... [5] Bacteriophages, first and foremost, are viruses of Bacteria, sharing the world with viruses of Archaea and viruses of domain Eukarya. An alternative ecological categorization separates those that infect primarily "macro"-organisms (animals, plants, macrofungi, and larger multicellular algae) from those that infect microorganisms (bacteria, archaea, single-celled protists, micro-fungi, and microscopic algae) [17,18]. For the latter, virus dissemination between individual cells (e.g., between bacterial cells) and between whole organisms (also, e.g., between bacterial cells) are more or less the same thing. ...
... These morphologies vary in terms of whether or not virions contain lipids, have tails, or contain DNA or RNA genomes, as well as whether those genomes are singlestranded or double-stranded. Smaller-genomed phages (under approximately 10 kb) generally possess single-stranded nucleic acid (DNA or RNA), middle-sized genomed phages (also RNA or DNA, but double stranded, and with genomes ranging in size from roughly 10 to 15 kb) seem to typically have virions that contain lipids, while larger-genomed phages (generally greater than 15 kb) appear to lack these lipids, have double-stranded DNA genomes, and possess tails [17,23,24]. It is tailed phages, members of virus order Caudovirales (to be replaced with class Caudoviricetes; [20]), that represent most of the phages employed in therapy. ...
Phage therapy is a medical form of biological control of bacterial infections, one that uses naturally occurring viruses, called bacteriophages or phages, as antibacterial agents. Pioneered over 100 years ago, phage therapy nonetheless is currently experiencing a resurgence in interest, with growing numbers of clinical case studies being published. This renewed enthusiasm is due in large part to phage therapy holding promise for providing safe and effective cures for bacterial infections that traditional antibiotics acting alone have been unable to clear. This Essay introduces basic phage biology, provides an outline of the long history of phage therapy, highlights some advantages of using phages as antibacterial agents, and provides an overview of recent phage therapy clinical successes. Although phage therapy has clear clinical potential, it faces biological, regulatory, and economic challenges to its further implementation and more mainstream acceptance.
... Until now the epidemic of viral infections is still a global problem with the potential for death which continues to increase. Viruses are indeed very small, even smaller than bacteria (Hyman and Abedon, 2012). However, they have the ability to multiply and move from one organism to other organisms very quickly. ...
Most drugs, including antiviral drugs, show low solubility in water, which affects dissolution, bioavailability, and therapeutic effectiveness. Therefore, many antiviral drugs are given in very large doses. One of the efforts to overcome these problems is the application of solid dispersions in which polymers and surfactants can trap drug molecules that are in the amorphous phase. Drugs in a hydrophilic carrier will increase wettability, water absorption capacity, and porosity of particles, so that the drug is released better. This review article will discuss the development of technology in solid-state, how solid dispersion overcomes the lack of solubility and the rate of dissolution of antiviral drugs, and solid dispersion preparation techniques. We also discuss some examples of successful applications of solid dispersion methods to antiviral drugs that have been circulating on the market. Overall, this review article offers information of innovation in the development of antiviral drugs to provide more solid dispersion antiviral drug products.
... [1]. In this life process, microorganisms interact and collaborate to carry out various multicellular behavior, including migration, feeding, biofilm formation, chemical warfare, and quorum sensing. ...
This review provides an understanding of biopolymers and its classes that is applicable for antimicrobial activity. Biocompatibility and bioactivity of biopolymers made from natural sources are unparalleled. Ethnopharmacologists, botanists, microbiologists, and natural-products chemists all look to plants for the phytochemicals and leads utilized in the treatment of infectious diseases. This review also discusses about antimicrobial peptides that penetrate microbes by destroying the membrane. Antimicrobial resistance has risen to the position of the world’s third largest cause of mortality. Bio-composites from biopolymers and reinforced with natural fibers and plant active components has indicated improved antimicrobial capabilities. Biodegradable nanocomposite films have enhanced antibacterial and antioxidant properties. Green nanoparticles produced via the process of biosynthesis using plant extracts pose a lower risk to the surrounding environment. Nanomaterials provide several benefits, including a high surface-area-to-volume ratio and better potential to interact with the membranes and cell walls of pathogens. They are exceedingly small, which also makes them advantageous. Metal oxide nanoparticles have antibacterial properties, and researchers have investigated how that relates to mechanism of photogenerated reactive oxygen species. This review focuses on the correlation can link the reactive oxygen generating capabilities of nanoparticle to their antibacterial activity, even though specific nanoparticles possess antimicrobial activity.
... Такие вирусы обнаружены у бацилл, которые также относятся к порядку Firmicutes, как и энтерококки [18]. Также встречаются фаги с одноцепочечной молекулой ДНК и РНК-содержащие вирусы [19]. Вполне возможно, что со временем все эти группы вирусов будут найдены, охарактеризованы, и схема идентификации вирусов должна быть дополнена новыми праймерами. ...
Introduction. The development and use of therapeutic drugs based on bacterial viruses, or bacteriophages, is a promising direction in the fight against bacterial infections. The composition of phage preparations must be constantly updated, which requires the search for new viruses through the screening of biological material and samples from the environment.
Purpose. Development of a method for the search and identification of virulent enterococcal bacteriophages based on the polymerase chain reaction (PCR).
Materials and methods. The known diversity of enterococcal viruses was assessed by database searches of the National Center for Biotechnology Information (NCBI) and the International Committee on Taxonomy of Viruses (ICTV). Primers were selected using the NCBI PrimerBlast and Primer3 programs. Primers were tested on seven commercial phage cocktails and 46 biomaterial samples. The specificity of PCR was confirmed by determining the nucleotide sequences of PCR products.
Results. The obligately virulent enterococcal bacteriophages described in the literature belong to five ICTV approved genera: Copernicusvirus , Efquatrovirus , Kochikohdavirus , Saphexavirus , and Schiekvirus . Representatives of the sixth genus, Phifelvirus , have a temperate life cycle. The PCR scheme developed by us is intended for specific amplification of fragments of the gene of the main capsid protein of the mentioned genera of bacteriophages. It was used to identify representatives of all five genera of virulent enterococcal bacteriophages in commercial phage cocktails. In samples of biological material, we identified representatives of the genera Efquatrovirus , Kochikohdavirus , Saphexavirus and Schiekvirus .
Conclusion. The PCR scheme presented in this work makes it possible to detect all currently described obligately virulent bacteriophages infecting Enterococcus spp. in phagolysates and samples of biological material, and can also be used to determine the genera of viruses.
... Early observations linking symbiotic dinoflagellates from anemones with viruses, stresses, and coral diseases (Wilson et al. 2001) led to the hypothesis that the algal cells harbored latent proviruses. In this type of infection, a virus persists in the cytoplasm as an episome (an extrachromosomal molecule) or becomes integrated into the host genome, replicating as a (latent) provirus, synchronized with the host cell (Hyman and Abedon 2012). After exposure to stress, the latent provirus enters a lytic cycle, lysing the host cell and invading other susceptible hosts. ...
Dinoflagellates from the family Symbiodiniaceae are phototrophic marine protists that engage in symbiosis with diverse hosts. Their large and distinct genomes are characterized by pervasive gene duplication and large-scale retroposition events. However, little is known about the role and scale of horizontal gene transfer (HGT) in the evolution of this algal family. In other dinoflagellates, high levels of HGTs have been observed, linked to major genomic transitions, such as the appearance of a viral-acquired nucleoprotein that originated via HGT from a large DNA algal virus. Previous work showed that Symbiodiniaceae from different hosts are actively infected by viral groups, such as giant DNA viruses and ssRNA viruses, that may play an important role in coral health. Latent viral infections may also occur, whereby viruses could persist in the cytoplasm or integrate into the host genome as a provirus. This hypothesis received experimental support; however, the cellular localization of putative latent viruses and their taxonomic affiliation are still unknown. In addition, despite the finding of viral sequences in some genomes of Symbiodiniaceae, viral origin, taxonomic breadth, and metabolic potential have not been explored. To address these questions, we searched for putative viral-derived proteins in thirteen Symbiodiniaceae genomes. We found fifty-nine candidate viral-derived HGTs that gave rise to twelve phylogenies across ten genomes. We also describe the taxonomic affiliation of these virus-related sequences, their structure, and their genomic context. These results lead us to propose a model to explain the origin and fate of Symbiodiniaceae viral acquisitions.
... The current diversity of viruses of marine protists is substantial with most of the cultured viruses being those that infect photoautotrophs (Hyman and Abedon 2012). The diversity of known viruses of protists includes viruses made up of ssDNA, dsDNA, ssRNA, and dsRNA and ranges in size from a few genes (thousands of bases) to the thousands of genes (1-2 million bp), with the latter being akin to the size of small bacterial genomes. ...
Diversity within marine microbiomes spans the three domains of life: microbial eukaryotes (i.e., protists), bacteria, and archaea. Although protists were the first microbes observed by microscopy, it took the advent of molecular techniques to begin to resolve their complex and reticulate evolutionary history. Symbioses between microbial entities have been key in this journey, and such interactions continue to shape the ecology of marine microbiomes. Nowadays, photosynthetic marine protists are appreciated for their activities as primary producers, rivalling land plant contributions in the global carbon cycle. Predatory protists are known for consuming prokaryotes and other protists, with some combining metabolisms into a mixotrophic lifestyle. Still, much must be learned about specific interactions and lifestyles, especially for uncultured groups recognized just by environmental sequences. With respect to the fate of protists in food webs, there are many paths to consider. Despite being in early stages of identifying interactions, whether mutualistic or death-inducing infections by parasites and viruses, knowledge is advancing rapidly via methods for interrogation in nature without culturing. Here, we review marine protists, their evolutionary histories, diversity, ecological roles, and lifestyles in all layers of the ocean, with reference to how views have shifted over time through extensive investigation.KeywordsCarbon cycleEukaryotic evolutionMarine food websPhytoplanktonProtistan evolutionProtistan interactions
... Viruses are ubiquitous in every ecosystem and infect all forms of life, from prokaryotes to eukaryotes (Hyman and Abedon, 2012). Food fermentation is driven by dense microbial consortia consisting mainly of bacteria and fungi . ...
The emergence of Coronavirus disease 2019 as a global pandemic has increased popular concerns about diseases caused by viruses. Fermented foods containing high loads of viable fungi and bacteria are potential sources for virus contamination. The most common include viruses that infect bacteria (bacteriophage) and yeasts reported in fermented milks, sausages, vegetables, wine, sourdough, and cocoa beans. Recent molecular studies have also associated fermented foods as vehicles for pathogenic human viruses. Human noroviruses, rotavirus, and hepatitis virus have been identified in different fermented foods through multiple routes. No severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) virus or close members were found in fermented foods to date. However, the occurrence/persistence of other pathogenic viruses reveals a potential vulnerability of fermented foods to SARS-CoV-2 contamination. On the other side of the coin, some bacteriophages are being suggested for improving the fermentation process and food safety, as well as owing potential probiotic properties in modern fermented foods. This review will address the diversity and characteristics of viruses associated with fermented foods and what has been changed after a short introduction to the most common next generation sequencing platforms. Also, the risk of SARS-CoV-2 transmission via fermented foods and preventive measures will be discussed.
... Viruses are the most abundant biological entities in the biosphere, being found in every environment and infecting a wide range of organisms, such as plants, insects, mammals, and microorganisms [1][2][3]. Surveys to detect, identify, and characterize viral diversity are challenging due to the limited ability to isolate and grow viruses and their hosts in laboratory [4]. Furthermore, viruses do not have universally conserved sequences in their genomes that can be used as targets for PCR-based assays, such as the ribosomal genes of prokaryotes and eukaryotes [5,6]. ...
Hematophagous insects act as the major reservoirs of infectious agents due to their intimate contact with a large variety of vertebrate hosts. Lutzomyia longipalpis is the main vector of Leishmania chagasi in the New World, but its role as a host of viruses is poorly understood. In this work, Lu. longipalpis RNA libraries were subjected to progressive assembly using viral profile HMMs as seeds. A sequence phylogenetically related to fungal viruses of the genus Mitovirus was identified and this novel virus was named Lul-MV-1. The 2697-base genome presents a single gene coding for an RNA-directed RNA polymerase with an organellar genetic code. To determine the possible host of Lul-MV-1, we analyzed the molecular characteristics of the viral genome. Dinucleotide composition and codon usage showed profiles similar to mitochondrial DNA of invertebrate hosts. Also, the virus-derived small RNA profile was consistent with the activation of the siRNA pathway, with size distribution and 5′ base enrichment analogous to those observed in viruses of sand flies, reinforcing Lu. longipalpis as a putative host. Finally, RT-PCR of different insect pools and sequences of public Lu. longipalpis RNA libraries confirmed the high prevalence of Lul-MV-1. This is the first report of a mitovirus infecting an insect host.
... In the present study, we have isolated and characterized a novel jumbo bacteriophage, vB_VhaM_pir03 with broad host lytic activity against Vibrio harveyi type strain DSM19623 and analyzed its therapeutic potential for aquaculture. Transmission electron microscopy revealed that vB_VhaM_pir03 is related to the Myoviridae family based on the presence of an icosahedral head and long contractile tail [39]. In addition, vB_VhaM_pir03 also had relatively large structural dimensions compared to other Myoviruses infecting Vibrio spp. ...
Vibrio harveyi is a Gram-negative marine bacterium that causes major disease outbreaks and economic losses in aquaculture. Phage therapy has been considered as a potential alternative to antibiotics however, candidate bacteriophages require comprehensive characterization for a safe and practical phage therapy. In this work, a lytic novel jumbo bacteriophage, vB_VhaM_pir03 belonging to the Myoviridae family was isolated and characterized against V. harveyi type strain DSM19623. It had broad host lytic activity against 31 antibiotic-resistant strains of V. harveyi, V. alginolyticus, V. campbellii and V. owensii. Adsorption time of vB_VhaM_pir03 was determined at 6 min while the latent-phase was at 40 min and burst-size at 75 pfu/mL. vB_VhaM_pir03 was able to lyse several host strains at multiplicity-of-infections (MOI) 0.1 to 10. The genome of vB_VhaM_pir03 consists of 286,284 base pairs with 334 predicted open reading frames (ORFs). No virulence, antibiotic resistance, integrase encoding genes and transducing potential were detected. Phylogenetic and phylogenomic analysis showed that vB_VhaM_pir03 is a novel bacteriophage displaying the highest similarity to another jumbo phage, vB_BONAISHI infecting Vibrio coralliilyticus. Experimental phage therapy trial using brine shrimp, Artemia salina infected with V. harveyi demonstrated that vB_VhaM_pir03 was able to significantly reduce mortality 24 h post infection when administered at MOI 0.1 which suggests that it can be an excellent candidate for phage therapy.
... Bacteriophages, or phages, are the viruses of bacteria (Calendar and Abedon, 2006;Hyman and Abedon, 2012;Lehman, 2018). As phages can be biologically active within bodies, they also can be considered to be drug-like, i.e., as medicaments. ...
Pharmacology can be differentiated into two key aspects, pharmacodynamics and pharmacokinetics. Pharmacodynamics describes a drug's impact on the body while pharmacokinetics describes the body's impact on a drug. Another way of understanding these terms is that pharmacodynamics is a description of both the positive and negative consequences of drugs attaining certain concentrations in the body while pharmacokinetics is concerned with our ability to reach and then sustain those concentrations. Unlike the drugs for which these concepts were developed, including antibiotics, the bacteriophages (or 'phages') that we consider here are not chemotherapeutics but instead are the viruses of bacteria. Here we review the pharmacology of these viruses, particularly as they can be employed to combat bacterial infections (phage therapy). Overall, an improved pharmacological understanding of phage therapy should allow for more informed development of phages as antibacterial 'drugs', allow for more rational post hoc debugging of phage therapy experiments, and encourage improved design of phage therapy protocols. Contrasting with antibiotics, however, phages as viruses impact individual bacterial cells as single virions rather than as swarms of molecules, and while they are killing bacteria, bacteriophages also can amplify phage numbers, in situ. Explorations of phage therapy pharmacology consequently can often be informed as well by basic principles of the ecological interactions between phages and bacteria as by study of the pharmacology of drugs. Bacteriophages in phage therapy thus can display somewhat unique as well as more traditional pharmacological aspects.
