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International Journal of Molecular... Nov 2022Bacteriophages have long been considered only as infectious agents that affect bacterial hosts. However, recent studies provide compelling evidence that these viruses... (Review)
Review
Bacteriophages have long been considered only as infectious agents that affect bacterial hosts. However, recent studies provide compelling evidence that these viruses are able to successfully interact with eukaryotic cells at the levels of the binding, entry and expression of their own genes. Currently, bacteriophages are widely used in various areas of biotechnology and medicine, but the most intriguing of them is cancer therapy. There are increasing studies confirming the efficacy and safety of using phage-based vectors as a systemic delivery vehicle of therapeutic genes and drugs in cancer therapy. Engineered bacteriophages, as well as eukaryotic viruses, demonstrate a much greater efficiency of transgene delivery and expression in cancer cells compared to non-viral gene transfer methods. At the same time, phage-based vectors, in contrast to eukaryotic viruses-based vectors, have no natural tropism to mammalian cells and, as a result, provide more selective delivery of therapeutic cargos to target cells. Moreover, numerous data indicate the presence of more complex molecular mechanisms of interaction between bacteriophages and eukaryotic cells, the further study of which is necessary both for the development of gene therapy methods and for understanding the cancer nature. In this review, we summarize the key results of research into aspects of phage-eukaryotic cell interaction and, in particular, the use of phage-based vectors for highly selective and effective systemic cancer gene therapy.
Topics: Animals; Bacteriophages; Gene Transfer Techniques; Genetic Therapy; Pharmaceutical Preparations; Genes, Neoplasm; Mammals; Neoplasms
PubMed: 36430720
DOI: 10.3390/ijms232214245 -
FEMS Microbiology Reviews Feb 2022We are in the midst of a golden age of uncovering defense systems against bacteriophages. Apart from the fundamental interest in these defense systems, and revolutionary... (Review)
Review
We are in the midst of a golden age of uncovering defense systems against bacteriophages. Apart from the fundamental interest in these defense systems, and revolutionary applications that have been derived from them (e.g. CRISPR-Cas9 and restriction endonucleases), it is unknown how defense systems contribute to resistance formation against bacteriophages in clinical settings. Bacteriophages are now being reconsidered as therapeutic agents against bacterial infections due the emergence of multidrug resistance. However, bacteriophage resistance through defense systems and other means could hinder the development of successful phage-based therapies. Here, we review the current state of the field of bacteriophage defense, highlight the relevance of bacteriophage defense for potential clinical use of bacteriophages as therapeutic agents and suggest new directions of research.
Topics: Bacterial Infections; Bacteriophages; CRISPR-Cas Systems; Humans; Phage Therapy
PubMed: 34558600
DOI: 10.1093/femsre/fuab048 -
Journal of Medical Microbiology Feb 2020spp. are commensals of the human microbiota, and a leading cause of opportunistic nosocomial infections. The incidence of multidrug resistant (MDR) strains of causing... (Review)
Review
spp. are commensals of the human microbiota, and a leading cause of opportunistic nosocomial infections. The incidence of multidrug resistant (MDR) strains of causing serious infections is increasing, and is an emerging pathogen. Alternative strategies to tackle infections caused by these bacteria are required as strains become resistant to last-resort antibiotics such as colistin. Bacteriophages (phages) are viruses that can infect and kill bacteria. They and their gene products are now being considered as alternatives or adjuncts to antimicrobial therapies. Several and studies have shown the potential for lytic phages to combat MDR infections. Ready access to cheap sequencing technologies has led to a large increase in the number of genomes available for -infecting phages, with these phages being heterogeneous at the whole-genome level. This review summarizes our current knowledge on phages of spp. and highlights technological and biological issues relevant to the development of phage-based therapies targeting these bacteria.
Topics: Animals; Bacteriophages; Biodiversity; Humans; Klebsiella; Klebsiella Infections; Phage Therapy
PubMed: 31976857
DOI: 10.1099/jmm.0.001141 -
Current Opinion in Virology Apr 2021Viruses are ubiquitous, essential components of any ecosystem, and of multicellular organism holobionts. Numerous viruses cause acute infection, killing the host or... (Review)
Review
Viruses are ubiquitous, essential components of any ecosystem, and of multicellular organism holobionts. Numerous viruses cause acute infection, killing the host or being cleared by immune system. In many other cases, viruses coexist with the host as symbionts, either temporarily or for the duration of the host's life. Apparently, virus-host relationships span the entire range from aggressive parasitism to mutualism. Here we attempt to delineate the healthy human virome, that is, the entirety of viruses that are present in a healthy human body. The bulk of the healthy virome consists of bacteriophages infecting bacteria in the intestine and other locations. However, a variety of viruses, such as anelloviruses and herpesviruses, and the numerous endogenous retroviruses, persist by replicating in human cells, and these are our primary focus. Crucially, the boundary between symbiotic and pathogenic viruses is fluid such that members of the healthy virome can become pathogens under changing conditions.
Topics: Bacteriophages; Host-Pathogen Interactions; Humans; Symbiosis; Virome; Virus Physiological Phenomena; Virus Replication; Viruses
PubMed: 33652230
DOI: 10.1016/j.coviro.2021.02.002 -
Nature Protocols Dec 2020Directed evolution, which applies the principles of Darwinian evolution to a laboratory setting, is a powerful strategy for generating biomolecules with diverse and...
Directed evolution, which applies the principles of Darwinian evolution to a laboratory setting, is a powerful strategy for generating biomolecules with diverse and tailored properties. This technique can be implemented in a highly efficient manner using continuous evolution, which enables the steps of directed evolution to proceed seamlessly over many successive generations with minimal researcher intervention. Phage-assisted continuous evolution (PACE) enables continuous directed evolution in bacteria by mapping the steps of Darwinian evolution onto the bacteriophage life cycle and allows directed evolution to occur on much faster timescales compared to conventional methods. This protocol provides detailed instructions on evolving proteins using PACE and phage-assisted non-continuous evolution (PANCE) and includes information on the preparation of selection phage and host cells, the assembly of a continuous flow apparatus and the performance and analysis of evolution experiments. This protocol can be performed in as little as 2 weeks to complete more than 100 rounds of evolution (complete cycles of mutation, selection and replication) in a single PACE experiment.
Topics: Bacteriophages; Directed Molecular Evolution
PubMed: 33199872
DOI: 10.1038/s41596-020-00410-3 -
Cell Host & Microbe Jun 2019The human gut microbiome is comprised of densely colonizing microorganisms including bacteriophages, which are in dynamic interaction with each other and the mammalian...
The human gut microbiome is comprised of densely colonizing microorganisms including bacteriophages, which are in dynamic interaction with each other and the mammalian host. To address how bacteriophages impact bacterial communities in the gut, we investigated the dynamic effects of phages on a model microbiome. Gnotobiotic mice were colonized with defined human gut commensal bacteria and subjected to predation by cognate lytic phages. We found that phage predation not only directly impacts susceptible bacteria but also leads to cascading effects on other bacterial species via interbacterial interactions. Metabolomic profiling revealed that shifts in the microbiome caused by phage predation have a direct consequence on the gut metabolome. Our work provides insight into the ecological importance of phages as modulators of bacterial colonization, and it additionally suggests the potential impact of gut phages on the mammalian host with implications for their therapeutic use to precisely modulate the microbiome.
Topics: Animals; Bacteriolysis; Bacteriophages; Feces; Gastrointestinal Microbiome; Germ-Free Life; Metabolome; Mice; Microbial Interactions
PubMed: 31175044
DOI: 10.1016/j.chom.2019.05.001 -
Nature Microbiology Dec 2022Jumbo phages such as Pseudomonas aeruginosa ФKZ have potential as antimicrobials and as a model for uncovering basic phage biology. Both pursuits are currently limited...
Jumbo phages such as Pseudomonas aeruginosa ФKZ have potential as antimicrobials and as a model for uncovering basic phage biology. Both pursuits are currently limited by a lack of genetic engineering tools due to a proteinaceous 'phage nucleus' structure that protects from DNA-targeting CRISPR-Cas tools. To provide reverse-genetics tools for DNA jumbo phages from this family, we combined homologous recombination with an RNA-targeting CRISPR-Cas13a enzyme and used an anti-CRISPR gene (acrVIA1) as a selectable marker. We showed that this process can insert foreign genes, delete genes and add fluorescent tags to genes in the ФKZ genome. Fluorescent tagging of endogenous gp93 revealed that it is ejected with the phage DNA while deletion of the tubulin-like protein PhuZ surprisingly had only a modest impact on phage burst size. Editing of two other phages that resist DNA-targeting CRISPR-Cas systems was also achieved. RNA-targeting Cas13a holds great promise for becoming a universal genetic editing tool for intractable phages, enabling the systematic study of phage genes of unknown function.
Topics: Bacteriophages; CRISPR-Cas Systems; Gene Editing; Genetic Engineering; RNA
PubMed: 36316452
DOI: 10.1038/s41564-022-01243-4 -
Viruses Aug 2019Phages have shown a high biotechnological potential with numerous applications. The advent of high-resolution microscopy techniques aligned with omic and molecular tools...
Phages have shown a high biotechnological potential with numerous applications. The advent of high-resolution microscopy techniques aligned with omic and molecular tools are revealing innovative phage features and enabling new processes that can be further exploited for biotechnological applications in a wide variety of fields. This special issue is a collection of original and review articles focusing on the most recent advances in phage-based biotechnology with applications for human benefit.
Topics: Animals; Bacteriophages; Biotechnology; Cell Surface Display Techniques; Humans; Phage Therapy
PubMed: 31405109
DOI: 10.3390/v11080737 -
Annual Review of Virology Sep 2021Bacteriophages-viruses that infect bacteria-are abundant within our bodies, but their significance to human health is only beginning to be explored. Here, we synthesize...
Bacteriophages-viruses that infect bacteria-are abundant within our bodies, but their significance to human health is only beginning to be explored. Here, we synthesize what is currently known about our phageome and its interactions with the immune system. We first review how phages indirectly affect immunity via bacterial expression of phage-encoded proteins. We next review how phages directly influence innate immunity and bacterial clearance. Finally, we discuss adaptive immunity against phages and its implications for phage/bacterial interactions. In light of these data, we propose that our microbiome can be understood as an interconnected network of bacteria, bacteriophages, and human cells and that the stability of these tri-kingdom interactions may be important for maintaining our immunologic and metabolic health. Conversely, the disruption of this balance, through exposure to exogenous phages, microbial dysbiosis, or immune dysregulation, may contribute to disease.
Topics: Bacteria; Bacteriophages; Humans; Immune System; Microbiota; Viruses
PubMed: 34014761
DOI: 10.1146/annurev-virology-091919-074551 -
Periodontology 2000 Jun 2021Oral bacteriophages (or phages), especially periodontal ones, constitute a growing area of interest, but research on oral phages is still in its infancy. Phages are... (Review)
Review
Oral bacteriophages (or phages), especially periodontal ones, constitute a growing area of interest, but research on oral phages is still in its infancy. Phages are bacterial viruses that may persist as intracellular parasitic deoxyribonucleic acid (DNA) or use bacterial metabolism to replicate and cause bacterial lysis. The microbiomes of saliva, oral mucosa, and dental plaque contain active phage virions, bacterial lysogens (ie, carrying dormant prophages), and bacterial strains containing short fragments of phage DNA. In excess of 2000 oral phages have been confirmed or predicted to infect species of the phyla Actinobacteria (>300 phages), Bacteroidetes (>300 phages), Firmicutes (>1000 phages), Fusobacteria (>200 phages), and Proteobacteria (>700 phages) and three additional phyla (few phages only). This article assesses the current knowledge of the diversity of the oral phage population and the mechanisms by which phages may impact the ecology of oral biofilms. The potential use of phage-based therapy to control major periodontal pathogens is also discussed.
Topics: Bacteria; Bacteriophages; Humans; Microbiota; Prophages; Virome
PubMed: 33690937
DOI: 10.1111/prd.12363