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STAR Protocols Sep 2021Interactions between bacteriophages and mammalian cells are poorly understood. Establishing common methodologies investigating these interactions is important for...
Interactions between bacteriophages and mammalian cells are poorly understood. Establishing common methodologies investigating these interactions is important for advancing our understanding in this area. The protocols presented here provide an overview of key approaches investigating interactions between bacteriophages and eukaryotic cells using a variety of techniques, including transwells, microscopy, and whole-cell analysis. These techniques allow for the direct measurement of phage-cellular interactions and characterization of how the presence of phages affects cellular pathways, cell biology, immunology, and the microbiome. For complete details on the use and execution of this protocol, please refer to Nguyen et al. (2017) and Bichet et al. (2021).
Topics: Animals; Bacteriophages; Cell Culture Techniques; Epithelial Cells; Humans; Microscopy; Patch-Clamp Techniques
PubMed: 34382021
DOI: 10.1016/j.xpro.2021.100697 -
Research in Microbiology May 2003Bacteriophages are classified into one order and 13 families. Over 5100 phages have been examined in the electron microscope since 1959. At least 4950 phages (96%) are...
Bacteriophages are classified into one order and 13 families. Over 5100 phages have been examined in the electron microscope since 1959. At least 4950 phages (96%) are tailed. They constitute the order Caudovirales and three families. Siphoviridae or phages with long, noncontractile tails predominate (61% of tailed phages). Polyhedral, filamentous, and pleomorphic phages comprise less than 4% of bacterial viruses. Bacteriophages occur in over 140 bacterial or archaeal genera. Their distribution reflects their origin and bacterial phylogeny. Bacteriophages are polyphyletic, arose repeatedly in different hosts, and constitute 11 lines of descent. Tailed phages appear as monophyletic and as the oldest known virus group.
Topics: Bacteriophages; Biological Evolution; Caudovirales; Corticoviridae; Cystoviridae; Fuselloviridae; Inoviridae; Leviviridae; Lipothrixviridae; Microviridae; Rudiviridae; Tectiviridae
PubMed: 12798228
DOI: 10.1016/S0923-2508(03)00067-6 -
Journal of Applied Microbiology Jan 2000Low concentrations of all types of bacteriophages in groundwater limit their power to predict the presence of enteric viruses. There is little concordance in the... (Review)
Review
Low concentrations of all types of bacteriophages in groundwater limit their power to predict the presence of enteric viruses. There is little concordance in the literature regarding phage detection methods, thus making comparisons extremely difficult. Different authors have used different hosts, phage concentration methods, and end-point determinations. Also, markedly different volumes of sample have been employed, varying from 1 litre to 400 l. Bacteriophage concentration methods are not reproducible. There has been marked variability among groups in the natural substrates used (for example, beef extract), the type of adsorbing filter used, centrifugation instruments and conditions, and the delivery of the concentrate to the host cells. There is no consensus on the best bacterial host strain. Currently, several are employed with each showing differential sensitivities and specificities. In particular, host stability must be considered. Host stability has two components: the ability of the host to continue to be receptive to the bacteriophage after continued sub-culture, and the lack of lysogenic or temperate bacteriophage in the host cell line which may be randomly and unpredictably activated. There is a lack of consistent recovery of bacteriophages from individual faecal specimens. In particular, only approximately 3% of individual humans carry the FRNA phages. While there is some evidence to indicate that the phages multiply in sewage, it is not clear how they do so since the host pili should not be produced at lower temperatures. These ecological factors need to be understood. Of all the phages thus far studied, Bacteroides fragilis HSP40 has the highest recovery rate from individual people. However, Bacteroides, being an anaerobe, is a difficult host for routine laboratory analysis. Methods for the enumeration of F(+)-specific phages and Bacteroides phages are complex, time-consuming, costly and not reproducible. Conversely, somatic coliphage methods are simpler and results can be available in 4-6 h. The occurrence of phages and viruses in groundwater depends on physicochemical characteristics that control their fate and transport in the groundwater/aquifer environment. There are very little actual data taken from the field that allow an understanding of the ecology and life span of phages in their natural environment. Moreover, the ability of phages to serve as a source of food for other microbes needs to be understood. There has been a lack of association of bacteriophage recovery with gastroenteritis outbreaks due to enteric viruses. There is only a small epidemiological database concerning the occurrence of enteric viruses in groundwater.
Topics: Animals; Bacteriophages; Bacteroides fragilis; Coliphages; Fresh Water; Humans; Inoviridae; Leviviridae; Public Health; Risk Assessment; Salmonella
PubMed: 10735238
DOI: 10.1046/j.1365-2672.2000.00949.x -
Trends in Biochemical Sciences Nov 1998The rolling-circle mechanism of DNA replication is used by small prokaryotic genomes, such as single-stranded phages and plasmids. However, phages and plasmids have... (Review)
Review
The rolling-circle mechanism of DNA replication is used by small prokaryotic genomes, such as single-stranded phages and plasmids. However, phages and plasmids have adapted the rolling-circle mechanism differently to suit their contrasting biological needs. The phi X174 phage uses a monomeric initiator protein catalytically, displays incomplete termination and recycles the initiator protein, in order to mass-produce phage progeny. By contrast, to control replication precisely, the pT181 plasmid uses a dimeric initiator protein stochiometrically, completes termination and inactivates the initiator after each replication cycle. The phi X174 phage and the pT181 plasmid represent paradigmatic adaptations of the rolling-circle mechanism and could provide models for other replicons.
Topics: Bacteriophage phi X 174; Bacteriophages; Catalysis; DNA Replication; Dimerization; Models, Genetic; Plasmids
PubMed: 9852762
DOI: 10.1016/s0968-0004(98)01302-4 -
Viruses Jan 2019Half a century of research on membrane-containing phages has had a major impact on virology, providing new insights into virus diversity, evolution and ecological... (Review)
Review
Half a century of research on membrane-containing phages has had a major impact on virology, providing new insights into virus diversity, evolution and ecological importance. The recent revolutionary technical advances in imaging, sequencing and lipid analysis have significantly boosted the depth and volume of knowledge on these viruses. This has resulted in new concepts of virus assembly, understanding of virion stability and dynamics, and the description of novel processes for viral genome packaging and membrane-driven genome delivery to the host. The detailed analyses of such processes have given novel insights into DNA transport across the protein-rich lipid bilayer and the transformation of spherical membrane structures into tubular nanotubes, resulting in the description of unexpectedly dynamic functions of the membrane structures. Membrane-containing phages have provided a framework for understanding virus evolution. The original observation on membrane-containing bacteriophage PRD1 and human pathogenic adenovirus has been fundamental in delineating the concept of "viral lineages", postulating that the fold of the major capsid protein can be used as an evolutionary fingerprint to trace long-distance evolutionary relationships that are unrecognizable from the primary sequences. This has brought the early evolutionary paths of certain eukaryotic, bacterial, and archaeal viruses together, and potentially enables the reorganization of the nearly immeasurable virus population (~1 × 10) on Earth into a reasonably low number of groups representing different architectural principles. In addition, the research on membrane-containing phages can support the development of novel tools and strategies for human therapy and crop protection.
Topics: Archaeal Viruses; Bacteriophage PRD1; Bacteriophages; Capsid Proteins; DNA, Viral; Evolution, Molecular; Membranes; Models, Molecular; Virion; Virus Assembly
PubMed: 30669250
DOI: 10.3390/v11010076 -
BMC Microbiology Jun 2020Repetitive-PCR (rep-PCR) using BOXA1R and BOXA2R as single primers was investigated for its potential to genotype bacteriophage. Previously, this technique has been...
BACKGROUND
Repetitive-PCR (rep-PCR) using BOXA1R and BOXA2R as single primers was investigated for its potential to genotype bacteriophage. Previously, this technique has been primarily used for the discrimination of bacterial strains. Reproducible DNA fingerprint patterns for various phage types were generated using either of the two primers.
RESULTS
The similarity index of replicates ranged from 89.4-100% for BOXA2R-PCR, and from 90 to 100% for BOXA1R-PCR. The method of DNA isolation (p = 0.08) and the phage propagation conditions at two different temperatures (p = 0.527) had no significant influence on generated patterns. Rep-PCR amplification products were generated from different templates including purified phage DNA, phage lysates and phage plaques. The use of this method enabled comparisons of phage genetic profiles to establish their similarity to related or unrelated phages and their bacterial hosts.
CONCLUSION
The findings suggest that repetitive-PCR could be used as a rapid and inexpensive method to preliminary screen phage isolates prior to their selection for more comprehensive studies. The adoption of this rapid, simple and reproducible technique could facilitate preliminary characterisation of a large number of phage isolates and the investigation of genetic relationship between phage genotypes.
Topics: Bacteriophages; DNA Primers; DNA, Viral; Genotyping Techniques; Phylogeny; Polymerase Chain Reaction; Temperature
PubMed: 32527227
DOI: 10.1186/s12866-020-01770-2 -
FEMS Microbiology Reviews Sep 2014Bacteria-phage coevolution, the reciprocal evolution between bacterial hosts and the phages that infect them, is an important driver of ecological and evolutionary... (Review)
Review
Bacteria-phage coevolution, the reciprocal evolution between bacterial hosts and the phages that infect them, is an important driver of ecological and evolutionary processes in microbial communities. There is growing evidence from both laboratory and natural populations that coevolution can maintain phenotypic and genetic diversity, increase the rate of bacterial and phage evolution and divergence, affect community structure, and shape the evolution of ecologically relevant bacterial traits. Although the study of bacteria-phage coevolution is still in its infancy, with open questions regarding the specificity of the interaction, the gene networks of coevolving partners, and the relative importance of the coevolving interaction in complex communities and environments, there have recently been major advancements in the field. In this review, we sum up our current understanding of bacteria-phage coevolution both in the laboratory and in nature, discuss recent findings on both the coevolutionary process itself and the impact of coevolution on bacterial phenotype, diversity and interactions with other species (particularly their eukaryotic hosts), and outline future directions for the field.
Topics: Bacteria; Bacteriophages; Biodiversity; Biological Evolution; Gene Regulatory Networks; Host-Pathogen Interactions
PubMed: 24617569
DOI: 10.1111/1574-6976.12072 -
Science Progress 2004There are several unusual features about phage when you first encounter them as a biologist. They are small, but conform to one of a few morphological types. Next their... (Review)
Review
There are several unusual features about phage when you first encounter them as a biologist. They are small, but conform to one of a few morphological types. Next their genomes can be composed of DNA or RNA and be single or double stranded. Finally they are numerically more abundant than prokaryotes and a significant proportion of them form an association in their microbial host populations termed lysogeny. The latter findings indicate that they are numerically significant in microbial populations. Since bacterial and phage abundance or lack of it is related in environments, this implies that the phage populations 'titrate' their hosts, and more probably the host's physiological status. Microbial populations wax and wane with nutritional inputs and there is a dynamic relationship between phage population sizes and host numbers and physiology. Overlay this with the different phage life cycle strategies, exemplified at the extremes by phage lambda (temperate) and phage T4 (virulent), then it becomes apparent that phage are a component in nutrient cycling in ecology. But their contribution does not stop there. Many are capable of transduction, moving DNA from one cell into another. So they can also aid the evolutionary progress of microbial populations by allowing them to share genes, just as gene exchange via plasmids and transformation does. Our perception of bacteria has been derived from pure culture studies and we are just being able to appreciate how subtle their ecological interactions are. This is no less true of the studies on bacteriophage, which are almost all based on laboratory experimentation, where the hosts are physiologically stressed by growing in 'high nutritional and optimum conditions'. The natural environment is naturally discontinuous and life evolved in this. Thus our perceptions of bacteriophage and their life cycle patterns derived from laboratory experimentation may be a little off the mark when we come to understand how they and their hosts interact in the niches available to them. It is worth just considering this as you read the article, as I suspect phage behaviours are more intimately involved in, and moderated by the physiological stresses in the life cycle of bacteria than we currently believe.
Topics: Bacteria; Bacteriophages; Genome, Viral; Transduction, Genetic; Water Microbiology
PubMed: 15884658
DOI: 10.3184/003685004783238526 -
Microbiological Research Jan 2020In the process of bacteriophage and bacteria struggle, adsorption is the key factor to determine who is the winner. In this paper, the molecular mechanism of tailed... (Review)
Review
In the process of bacteriophage and bacteria struggle, adsorption is the key factor to determine who is the winner. In this paper, the molecular mechanism of tailed bacteriophage recognition and adsorption to host and the strategy of "fighting wisdom and courage" between them are reviewed.
Topics: Adsorption; Bacteria; Bacteriophages; Virus Attachment
PubMed: 31561173
DOI: 10.1016/j.micres.2019.126344 -
Microbial Biotechnology Sep 2022A system consisting of a connected mixed and tubular bioreactor was designed to study bacterial biofilm formation and the effect of its exposure to bacteriophages under...
A system consisting of a connected mixed and tubular bioreactor was designed to study bacterial biofilm formation and the effect of its exposure to bacteriophages under different experimental conditions. The bacterial biofilm inside silicone tubular bioreactor was formed during the continuous pumping of bacterial cells at a constant physiological state for 2 h and subsequent washing with a buffer for 24 h. Monitoring bacterial and bacteriophage concentration along the tubular bioreactor was performed via a piercing method. The presence of biofilm and planktonic cells was demonstrated by combining the piercing method, measurement of planktonic cell concentration at the tubular bioreactor outlet, and optical microscopy. The planktonic cell formation rate was found to be 8.95 × 10 h and increased approximately four-fold (4×) after biofilm exposure to an LB medium. Exposure of bacterial biofilm to bacteriophages in the LB medium resulted in a rapid decrease of biofilm and planktonic cell concentration, to below the detection limit within < 2 h. When bacteriophages were supplied in the buffer, only a moderate decrease in the concentration of both bacterial cell types was observed. After biofilm washing with buffer to remove unadsorbed bacteriophages, its exposure to the LB medium (without bacteriophages) resulted in a rapid decrease in bacterial concentration: again below the detection limit in < 2 h.
Topics: Bacteria; Bacteriophage T4; Bacteriophages; Biofilms; Bioreactors; Escherichia coli; Plankton
PubMed: 35638465
DOI: 10.1111/1751-7915.14079