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Viruses Mar 2013Studying the coevolutionary dynamics between bacteria and the bacteriophage viruses that infect them is critical to understanding both microbial diversity and ecosystem... (Review)
Review
Studying the coevolutionary dynamics between bacteria and the bacteriophage viruses that infect them is critical to understanding both microbial diversity and ecosystem functioning. Phages can play a key role in shaping bacterial population dynamics and can significantly alter both intra- and inter-specific competition among bacterial hosts. Predicting how phages might influence community stability and apparent competition, however, requires an understanding of how bacteria-phage interaction networks evolve as a function of host diversity and community dynamics. Here, we first review the progress that has been made in understanding phage specificity, including the use of experimental evolution, we then introduce a new dataset on natural bacteriophages collected from the phyllosphere of horse chestnut trees, and finally we highlight that bacterial sensitivity to phage is rarely a binary trait and that this variation should be taken into account and reported. We emphasize that there is currently insufficient evidence to make broad generalizations about phage host range in natural populations, the limits of phage adaptation to novel hosts, or the implications of phage specificity in shaping microbial communities. However, the combination of experimental and genomic approaches with the study of natural communities will allow new insight to the evolution and impact of phage specificity within complex bacterial communities.
Topics: Bacteria; Bacterial Physiological Phenomena; Bacteriophages; Biological Evolution; Host Specificity
PubMed: 23478639
DOI: 10.3390/v5030806 -
Current Opinion in Microbiology Feb 2023Bacteriophages are the most abundant biological entity on earth, acting as the predators and evolutionary drivers of bacteria. Owing to their inherent ability to... (Review)
Review
Bacteriophages are the most abundant biological entity on earth, acting as the predators and evolutionary drivers of bacteria. Owing to their inherent ability to specifically infect and kill bacteria, phages and their encoded endolysins and receptor-binding proteins (RBPs) have enormous potential for development into precision antimicrobials for treatment of bacterial infections and microbial disbalances; or as biocontrol agents to tackle bacterial contaminations during various biotechnological processes. The extraordinary binding specificity of phages and RBPs can be exploited in various areas of bacterial diagnostics and monitoring, from food production to health care. We review and describe the distinctive features of phage RBPs, explain why they are attractive candidates for use as therapeutics and in diagnostics, discuss recent applications using RBPs, and finally provide our perspective on how synthetic technology and artificial intelligence-driven approaches will revolutionize how we use these tools in the future.
Topics: Carrier Proteins; Bacteriophage Receptors; Artificial Intelligence; Bacteriophages; Bacteria
PubMed: 36446275
DOI: 10.1016/j.mib.2022.102240 -
Current Opinion in Structural Biology Apr 2010Similar modes of virus maturation have been observed in dsDNA bacteriophages and the structurally related herpes viruses and some type of maturation occur in most animal... (Review)
Review
Similar modes of virus maturation have been observed in dsDNA bacteriophages and the structurally related herpes viruses and some type of maturation occur in most animal viruses. Recently a variety of biophysical studies of maturation intermediates of bacteriophages P22, lambda, and HK97 have suggested an energy landscape that drives the transitions and structure-based mechanisms for its formation. Near-atomic resolution models of subunit tertiary structures in an early intermediate of bacteriophage HK97 maturation revealed a remarkable distortion of the secondary structures when compared to the mature particle. Scaffolding proteins may induce the distortion that is maintained by quaternary structure interactions following scaffold release, making the intermediate particle metastable.
Topics: Bacteriophage P22; Bacteriophages; Capsid Proteins; Models, Biological; Virion
PubMed: 20149636
DOI: 10.1016/j.sbi.2010.01.004 -
Virology Mar 2022Bacteriophage T7 is an extensively studied virulent phage, and its taxonomic family, the Autographiviridae, is broadly synonymous with a strictly virulent lifestyle. It...
Bacteriophage T7 is an extensively studied virulent phage, and its taxonomic family, the Autographiviridae, is broadly synonymous with a strictly virulent lifestyle. It is difficult to imagine how a T7-like phage could function in a "domesticated" temperate lifestyle, in which it is incorporated into the host's genome. Here we describe two temperate T7-like bacteriophages: ProddE, a Desulfovibrio phage, and Pasto, an Agrobacterium phage. Each contains recognizable T7-like proteins in the canonical T7-like gene order, but with the addition of lysogeny gene modules. While ProddE contains a phage-like repressor, Pasto lysogeny appears to be controlled by a novel MarR-like transcriptional regulator. In addition, we identify similar T7-like prophage elements in a wide variety of Gram-negative bacterial genomes and a small number of Gram-positive genomes. Identification of these elements in diverse bacterial species raises interesting evolutionary questions about the origins of T7-like phages and which lifestyle, temperate or virulent, is the ancestral form.
Topics: Bacteriophages; Biological Evolution; Caudovirales; Evolution, Molecular; Gene Expression Regulation, Viral; Host-Pathogen Interactions; Lysogeny; Phylogeny; Prophages; Virus Replication
PubMed: 35149347
DOI: 10.1016/j.virol.2022.01.013 -
Viruses May 2023The year 2023 marks the fiftieth anniversary of the discovery of the bacteriophage φ6. The review provides a look back on the initial discovery and classification of... (Review)
Review
The year 2023 marks the fiftieth anniversary of the discovery of the bacteriophage φ6. The review provides a look back on the initial discovery and classification of the lipid-containing and segmented double-stranded RNA (dsRNA) genome-containing bacteriophage-the first identified cystovirus. The historical discussion describes, for the most part, the first 10 years of the research employing contemporary mutation techniques, biochemical, and structural analysis to describe the basic outline of the virus replication mechanisms and structure. The physical nature of φ6 was initially controversial as it was the first bacteriophage found that contained segmented dsRNA, resulting in a series of early publications that defined the unusual genomic quality. The technology and methods utilized in the initial research (crude by current standards) meant that the first studies were quite time-consuming, hence the lengthy period covered by this review. Yet when the data were accepted, the relationship to the reoviruses was apparent, launching great interest in cystoviruses, research that continues to this day.
Topics: RNA, Viral; Bacteriophage phi 6; Bacteriophages; Cystoviridae; Virus Replication; RNA, Double-Stranded
PubMed: 37376608
DOI: 10.3390/v15061308 -
Environment International Aug 2019The emerging contamination of pathogenic bacteria in the soil has caused a serious threat to public health and environmental security. Therefore, effective methods to... (Review)
Review
The emerging contamination of pathogenic bacteria in the soil has caused a serious threat to public health and environmental security. Therefore, effective methods to inactivate pathogenic bacteria and decrease the environmental risks are urgently required. As a century-old technique, bacteriophage (phage) therapy has a high efficiency in targeting and inactivating pathogenic bacteria in different environmental systems. This review provides an update on the status of bacteriophage therapy for the inactivation of pathogenic bacteria in the soil environment. Specifically, the applications of phage therapy in soil-plant and soil-groundwater systems are summarized. In addition, the impact of phage therapy on soil functioning is described, including soil function gene transmission, soil microbial community stability, and soil nutrient cycling. Soil factors, such as soil temperature, pH, clay mineral, water content, and nutrient components, influence the survival and activity of phages in the soil. Finally, the future research prospects of phage therapy in soil environments are described.
Topics: Bacteria; Bacteriophages; Plant Diseases; Soil Microbiology; Temperature
PubMed: 31158595
DOI: 10.1016/j.envint.2019.05.062 -
Virologica Sinica Feb 2015The lysogenic phage CTXΦ of Vibrio cholerae can transfer the cholera toxin gene both horizontally (inter-strain) and vertically (cell proliferation). Due to its... (Review)
Review
The lysogenic phage CTXΦ of Vibrio cholerae can transfer the cholera toxin gene both horizontally (inter-strain) and vertically (cell proliferation). Due to its diversity in form and species, the complexity of regulatory mechanisms, and the important role of the infection mechanism in the production of new virulent strains of V. cholerae, the study of the lysogenic phage CTXΦ has attracted much attention. Based on the progress of current research, the genomic features and their arrangement, the host-dependent regulatory mechanisms of CTXΦ phage survival, proliferation and propagation were reviewed to further understand the phage's role in the evolutionary and epidemiological mechanisms of V. cholerae.
Topics: Bacteriophages; Biological Evolution; Cholera; Humans; Vibrio cholerae
PubMed: 25613689
DOI: 10.1007/s12250-014-3550-7 -
MBio Aug 2017The global bacteriophage population is large, dynamic, old, and highly diverse genetically. Many phages are tailed and contain double-stranded DNA, but these remain...
The global bacteriophage population is large, dynamic, old, and highly diverse genetically. Many phages are tailed and contain double-stranded DNA, but these remain poorly characterized genomically. A collection of over 1,000 phages infecting reveals the diversity of phages of a common bacterial host, but their relationships to phages of phylogenetically proximal hosts are not known. Comparative sequence analysis of 79 phages isolated on shows these also to be diverse and that the phages can be grouped into 14 clusters of related genomes, with an additional 14 phages that are "singletons" with no closely related genomes. One group of six phages is closely related to Cluster A mycobacteriophages, but the other phages are distant relatives and share only 10% of their genes with the mycobacteriophages. The phage genomes vary in genome length (17.1 to 103.4 kb), percentage of GC content (47 to 68.8%), and genome architecture and contain a variety of features not seen in other phage genomes. Like the mycobacteriophages, the highly mosaic phages demonstrate a spectrum of genetic relationships. We show this is a general property of bacteriophages and suggest that any barriers to genetic exchange are soft and readily violable. Despite the numerical dominance of bacteriophages in the biosphere, there is a dearth of complete genomic sequences. Current genomic information reveals that phages are highly diverse genomically and have mosaic architectures formed by extensive horizontal genetic exchange. Comparative analysis of 79 phages of shows them to not only be highly diverse, but to present a spectrum of relatedness. Most are distantly related to phages of the phylogenetically proximal host , although one group of phages is more closely related to mycobacteriophages than to the other phages. Phage genome sequence space remains largely unexplored, but further isolation and genomic comparison of phages targeted at related groups of hosts promise to reveal pathways of bacteriophage evolution.
Topics: Bacteriophages; Base Composition; DNA, Viral; Genetic Variation; Genome, Viral; Genomics; Gordonia Bacterium; Mycobacteriophages; Phylogeny; Sequence Analysis, DNA
PubMed: 28811342
DOI: 10.1128/mBio.01069-17 -
MBio Feb 2022In this study, we describe the isolation and characterization of novel bacteriophage vB_EcoP_Kapi1 (Kapi1) isolated from a strain of commensal Escherichia coli...
Isolation and Characterization of a Novel Temperate Escherichia coli Bacteriophage, Kapi1, Which Modifies the O-Antigen and Contributes to the Competitiveness of Its Host during Colonization of the Murine Gastrointestinal Tract.
In this study, we describe the isolation and characterization of novel bacteriophage vB_EcoP_Kapi1 (Kapi1) isolated from a strain of commensal Escherichia coli inhabiting the gastrointestinal tract of healthy mice. We show that Kapi1 is a temperate phage integrated into tRNA of strain MP1 and describe its genome annotation and structure. Kapi1 shows limited homology to other characterized prophages but is most similar to the seroconverting phages of Shigella flexneri and clusters taxonomically with P22-like phages. The receptor for Kapi1 is the lipopolysaccharide O-antigen, and we further show that Kapi1 alters the structure of its host's O-antigen in multiple ways. Kapi1 displays unstable lysogeny, and we find that the lysogenic state is more stable during growth in simulated intestinal fluid. Furthermore, Kapi1 lysogens have a competitive advantage over their nonlysogenic counterparts both and , suggesting a role for Kapi1 during colonization. We thus report the use of MP1 and Kapi1 as a model system to explore the molecular mechanisms of mammalian colonization by E. coli to ask what the role(s) of prophages in this context might be. Although research exploring the microbiome has exploded in recent years, our understanding of the viral component of the microbiome is lagging far behind our understanding of the bacterial component. The vast majority of intestinal bacteria carry prophages integrated into their chromosomes, but most of these bacteriophages remain uncharacterized and unexplored. Here, we isolate and characterize a novel temperate bacteriophage infecting a commensal strain of Escherichia coli. We aim to explore the interactions between bacteriophages and their hosts in the context of the gastrointestinal tract, asking what role(s) temperate bacteriophages may play in growth and survival of bacteria in the gut. Understanding the fundamental biology of gut commensal bacteria can inform the development of novel antimicrobial or probiotic strategies for intestinal infections.
Topics: Mice; Animals; O Antigens; Escherichia coli; Bacteriophages; Coliphages; Lysogeny; Prophages; Gastrointestinal Tract; Bacteria; Mammals
PubMed: 35073745
DOI: 10.1128/mbio.02085-21 -
Poultry Science Jun 2017This study evaluated the effectiveness of bacteriophage treatment for reducing Salmonella attachment and biofilms on hard surfaces. Bacteriophages (n = 6) were selected...
This study evaluated the effectiveness of bacteriophage treatment for reducing Salmonella attachment and biofilms on hard surfaces. Bacteriophages (n = 6) were selected for bacteriophage treatment based on host ranges against Salmonella isolates (n = 10) obtained from rendering plants. The effectiveness of bacteriophage treatment (104-108 PFU/mL) was initially evaluated against strong Salmonella biofilm formers in 96-well microplate. Then, the bacteriophage treatment (109 PFU/mL) was applied for 7 d to reduce Salmonella attached to the stainless steel surfaces under laboratory and greenhouse conditions. The inhibition of biofilm formation and reduction of pre-formed biofilm in 96-well microplate with bacteriophage treatment reached up to 90 and 66%, respectively. Under laboratory conditions, bacteriophage treatment reduced up to 2.9 and 3.0 log CFU/cm2 of attachment and slightly formed biofilm of selected top 10 Salmonella strains and an avirulent Salmonella Typhimurium strain 8243, respectively, as compared with reductions of 3.4, 1.4, and 3.0 log CFU/cm2 of S. Typhimurium strain 8243 in summer, fall/winter, and spring seasons under greenhouse conditions, respectively. Clearly, bacteriophages were effective on reducing Salmonella attachment and biofilms formed on hard surfaces under both laboratory and greenhouse conditions. The use of bacteriophages on hard surfaces may have merits in reducing the likelihood of finished rendered products being recontaminated with Salmonella in rendering plants.
Topics: Animals; Bacterial Adhesion; Bacteriophages; Biofilms; Chickens; Food-Processing Industry; Microscopy, Electron, Transmission; Salmonella; Seasons; Stainless Steel
PubMed: 28339743
DOI: 10.3382/ps/pew463