Application of zinc chloride precipitation method for rapid isolation and concentration of infectious Pectobacterium spp. and Dickeya spp. lytic bacteriophages from surface water and plant and soil extracts

Czajkowski, Robert; Ozymko, Zofia; Łojkowska, Ewa

doi:10.1007/s12223-015-0411-1

Cited by 15 publications

(7 citation statements)

References 18 publications

(26 reference statements)

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“…For example, virus titers, including phage titers in sea water can be relatively low necessitating preparatory concentration of the sample [41] that is typically done by filtration, precipitation, or a combination of both [3,42]. Czajkowski and colleagues [43], for example, demonstrated that zinc chloride could be used to concentrate phages from water or plant or soil extracts sufficiently to detect phages by direct plating without enrichment culture. They suggested that this gave a more accurate sampling of the diversity of phages in their samples.…”

Section: Phage Isolation Methodsmentioning

confidence: 99%

Phages for Phage Therapy: Isolation, Characterization, and Host Range Breadth

2019

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For a bacteriophage to be useful for phage therapy it must be both isolated from the environment and shown to have certain characteristics beyond just killing strains of the target bacterial pathogen. These include desirable characteristics such as a relatively broad host range and a lack of other characteristics such as carrying toxin genes and the ability to form a lysogen. While phages are commonly isolated first and subsequently characterized, it is possible to alter isolation procedures to bias the isolation toward phages with desirable characteristics. Some of these variations are regularly used by some groups while others have only been shown in a few publications. In this review I will describe (1) isolation procedures and variations that are designed to isolate phages with broader host ranges, (2) characterization procedures used to show that a phage may have utility in phage therapy, including some of the limits of such characterization, and (3) results of a survey and discussion with phage researchers in industry and academia on the practice of characterization of phages.

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Section: Phage Isolation Methodsmentioning

confidence: 99%

Phages for Phage Therapy: Isolation, Characterization, and Host Range Breadth

2019

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“…This approach is better suited to non-faecal samples and is routinely used to study aquatic environments. Similarly, zinc chloride and ammonium acetate precipitation protocols to concentrate phages are more suited to non-faecal samples [ 42 , 43 ].…”

Section: Vlp Isolationmentioning

confidence: 99%

Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review

et al. 2021

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The human gut is colonised by a vast array of microbes that include bacteria, viruses, fungi, and archaea. While interest in these microbial entities has largely focused on the bacterial constituents, recently the viral component has attracted more attention. Metagenomic advances, compared to classical isolation procedures, have greatly enhanced our understanding of the composition, diversity, and function of viruses in the human microbiome (virome). We highlight that viral extraction methodologies are crucial in terms of identifying and characterising communities of viruses infecting eukaryotes and bacteria. Different viral extraction protocols, including those used in some of the most significant human virome publications to date, have introduced biases affecting their a overall conclusions. It is important that protocol variations should be clearly highlighted across studies, with the ultimate goal of identifying and acknowledging biases associated with different protocols and, perhaps, the generation of an unbiased and standardised method for examining this portion of the human microbiome.

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“…The supernatants were sterilized treated with 5% v/v chloroform which safely inactivates any bacteria as well as enveloped viruses but will generally leave most Caudovirales intact [16]. Subsequently, viral particles were precipitated by adding 1 ml of a 2 M ZnCl 2 solution per 50 ml of sample, mixing shortly by inversion, and incubating the suspension at 37°C without agitation for 15 minutes [129]. After precipitation, the samples were centrifuged again at 8'000 g for 15 minutes and the supernatant was discarded.…”

Section: Bacteriophage Isolation Basic Proceduresmentioning

confidence: 99%

Systematic exploration ofEscherichia coliphage-host interactions with the BASEL phage collection

Maffei

Shaidullina

Burkolter

et al. 2021

Preprint

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Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of molecular mechanisms underlying phage-host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage-host interactions by composing a well-assorted library of 66 newly isolated phages infecting the model organism Escherichia coli that we share with the community as the BASEL collection (BActeriophage SElection for your Laboratory). This collection is largely representative of natural E. coli phage diversity and was intensively characterized phenotypically and genomically alongside ten well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to eleven defense systems across different layers of bacterial immunity, and matched these results to the phages' host range across a panel of pathogenic enterobacterial strains. Our results reveal clear patterns in the distribution of phage phenotypes and genomic features that highlight systematic differences in the potency of different immunity systems and point towards the molecular basis of receptor specificity in several phage groups. Strong trade-offs were detected between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications.

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Application of zinc chloride precipitation method for rapid isolation and concentration of infectious Pectobacterium spp. and Dickeya spp. lytic bacteriophages from surface water and plant and soil extracts

Cited by 15 publications

References 18 publications

Phages for Phage Therapy: Isolation, Characterization, and Host Range Breadth

Phages for Phage Therapy: Isolation, Characterization, and Host Range Breadth

Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review

Systematic exploration ofEscherichia coliphage-host interactions with the BASEL phage collection

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