Bacteriophage-based tools: recent advances and novel applications

O’Sullivan, L.; Buttimer, Colin; McAuliffe, Olivia; Bolton, Declan; Coffey, Aidan

doi:10.12688/f1000research.9705.1

Cited by 30 publications

(16 citation statements)

References 48 publications

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“…For example, phages are now known to employ complex communication systems [93,94], and to play roles in health and disease that can lead to non-host-derived immunity in humans [5,[95][96][97]. As these knowledge gaps are filled in, it becomes critical to incorporate phages into ecosystem models [98] that will ultimately help advance phage-based biotechnological [99] and therapeutic applications [100]. Fundamental to this, however, is the need to understand strategies driving phage-host interaction biology and infection efficiency.…”

Section: Discussionmentioning

confidence: 99%

Multiple mechanisms drive phage infection efficiency in nearly identical hosts

et al. 2018

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Phage-host interactions are critical to ecology, evolution, and biotechnology. Central to those is infection efficiency, which remains poorly understood, particularly in nature. Here we apply genome-wide transcriptomics and proteomics to investigate infection efficiency in nature's own experiment: two nearly identical (genetically and physiologically) Bacteroidetes bacterial strains (host18 and host38) that are genetically intractable, but environmentally important, where phage infection efficiency varies. On host18, specialist phage phi18:3 infects efficiently, whereas generalist phi38:1 infects inefficiently. On host38, only phi38:1 infects, and efficiently. Overall, phi18:3 globally repressed host18's transcriptome and proteome, expressed genes that likely evaded host restriction/modification (R/M) defenses and controlled its metabolism, and synchronized phage transcription with translation. In contrast, phi38:1 failed to repress host18's transcriptome and proteome, did not evade host R/M defenses or express genes for metabolism control, did not synchronize transcripts with proteins and its protein abundances were likely targeted by host proteases. However, on host38, phi38:1 globally repressed host transcriptome and proteome, synchronized phage transcription with translation, and infected host38 efficiently. Together these findings reveal multiple infection inefficiencies. While this contrasts the single mechanisms often revealed in laboratory mutant studies, it likely better reflects the phage-host interaction dynamics that occur in nature.

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Section: Discussionmentioning

confidence: 99%

Multiple mechanisms drive phage infection efficiency in nearly identical hosts

et al. 2018

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“…The vast potential of bacteriophages (phages) and their component parts as diagnostic and antibacterial tools is being realized in medicine (e.g., phage therapy) (Schooley et al, 2017;Skurnik et al, 2007), biotechnology (Karimi et al, 2016;Lee et al, 2012;O'Sullivan et al, 2016), and the food industry (Guenther et al, 2009;Schmelcher and Loessner, 2014). The advantage of using phages as antibacterial agents is their natural ability to infect and kill a specific range of bacteria within highly complex microbial populations.…”

Section: Introductionmentioning

confidence: 99%

Salmonella Phage S16 Tail Fiber Adhesin Features a Rare Polyglycine Rich Domain for Host Recognition

et al. 2018

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The ability of phages to infect specific bacteria has led to their exploitation as bio-tools for bacterial remediation and detection. Many phages recognize bacterial hosts via adhesin tips of their long tail fibers (LTFs). Adhesin sequence plasticity modulates receptor specificity, and thus primarily defines a phage's host range. Here we present the crystal structure of an adhesin (gp38) attached to a trimeric b-helical tip (gp37) from the Salmonella phage S16 LTF. Gp38 contains rare polyglycine type II helices folded into a packed lattice, herein designated ''PG II sandwich.'' Sequence variability within the domain is limited to surface-exposed helices and distal loops that form putative receptor-binding sites. In silico analyses revealed a prevalence of the adhesin architecture among T-even phages, excluding the archetypal T4 phage. Overall, S16 LTF provides a valuable model for understanding binding mechanisms of phage adhesins, and for engineering of phage adhesins with expandable or modulated host ranges.

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“…The B. cereus group is genetically homogeneous [ 1 ]. Bacteriophages with narrow host specificity within the B. cereus group have shown utility for typing and possess potential for drug discovery and biocontrol [ 3 ]. Phages are also considered important mediators of microbial genetic exchange with potential to impact both the adaptation and virulence of their respective hosts in addition to influencing host ecology and evolution [ 4 , 5 ].…”

Section: Introductionmentioning

confidence: 99%

Genomic characterization of three novel Basilisk-like phages infecting Bacillus anthracis

et al. 2018

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BackgroundIn the present study, we sequenced the complete genomes of three novel bacteriophages v_B-Bak1, v_B-Bak6, v_B-Bak10 previously isolated from historical anthrax burial sites in the South Caucasus country of Georgia. We report here major trends in the molecular evolution of these phages, which we designate as “Basilisk-Like-Phages” (BLPs), and illustrate patterns in their evolution, genomic plasticity and core genome architecture.ResultsComparative whole genome sequence analysis revealed a close evolutionary relationship between our phages and two unclassified Bacillus cereus group phages, phage Basilisk, a broad host range phage (Grose JH et al., J Vir. 2014;88(20):11846-11860) and phage PBC4, a highly host-restricted phage and close relative of Basilisk (Na H. et al. FEMS Microbiol. letters. 2016;363(12)). Genome comparisons of phages v_B-Bak1, v_B-Bak6, and v_B-Bak10 revealed significant similarity in sequence, gene content, and synteny with both Basilisk and PBC4. Transmission electron microscopy (TEM) confirmed the three phages belong to the Siphoviridae family. In contrast to the broad host range of phage Basilisk and the single-strain specificity of PBC4, our three phages displayed host specificity for Bacillus anthracis. Bacillus species including Bacillus cereus, Bacillus subtilis, Bacillus anthracoides, and Bacillus megaterium were refractory to infection.ConclusionsData reported here provide further insight into the shared genomic architecture, host range specificity, and molecular evolution of these rare B. cereus group phages. To date, the three phages represent the only known close relatives of the Basilisk and PBC4 phages and their shared genetic attributes and unique host specificity for B. anthracis provides additional insight into candidate host range determinants.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5056-4) contains supplementary material, which is available to authorized users.

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Bacteriophage-based tools: recent advances and novel applications

Cited by 30 publications

References 48 publications

Multiple mechanisms drive phage infection efficiency in nearly identical hosts

Multiple mechanisms drive phage infection efficiency in nearly identical hosts

Salmonella Phage S16 Tail Fiber Adhesin Features a Rare Polyglycine Rich Domain for Host Recognition

Genomic characterization of three novel Basilisk-like phages infecting Bacillus anthracis

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