Representational Difference Analysis (RDA) of bacteriophage genomes

Lammens, Elke; Ceyssens, Pieter‐Jan; Voet, Maria-Helena; Hertveldt, Kirsten; Lavigne, Rob; Volckaert, Guido

doi:10.1016/j.mimet.2009.02.006

Cited by 32 publications

(17 citation statements)

References 19 publications

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“…10 7 cfu/mL at −80°C. Of the six bacteriophage strains used (Table S1), four (LKD16, PEV2, LUZ19, and LUZ7) were from the Podoviridae, and two (14/1 and LMA2) were from the Myoviridae (64)(65)(66). LUZ7 and PEV2 have 70-nm icosahedral capsids and short tails, typical of the Podoviridae.…”

Section: Methodsmentioning

confidence: 99%

Contrasted coevolutionary dynamics between a bacterial pathogen and its bacteriophages

Betts

Kaltz

Hochberg

2014

Proc. Natl. Acad. Sci. U.S.A.

100

101

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Significance Scientists have long debated the dynamic form of perpetual reciprocal adaptations, or coevolution, between hosts and their parasites. The two main types of antagonistic coevolution described to date are arms race dynamics, in which interaction traits escalate through time, and fluctuating selection dynamics, in which traits cycle through time. We used experimental evolution between Pseudomonas aeruginosa and a panel of its lytic phages and found the full known range of coevolutionary dynamics. We argue that the coevolutionary pattern is determined by whether phages typically adsorb directly to receptors on the bacterial outer membrane or instead use retractable type IV pili as a primary or alternative site. Our results have applications in the use of phages as therapeutics or disinfectants to control bacterial pathogens.

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Section: Methodsmentioning

confidence: 99%

Contrasted coevolutionary dynamics between a bacterial pathogen and its bacteriophages

Betts

Kaltz

Hochberg

2014

Proc. Natl. Acad. Sci. U.S.A.

100

101

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“…The majority of genes, 50 (70.4%), are found in the positive strand, and 21 (29.6%) are found in the negative strand. The search using the blastn algorithm in the NCBI database showed that phage DL62 is closely related to phiKMV‐like phages (> 95%), such as phiKMV and LUZ19 (Lavigne et al ., ; Lammens et al ., ) and these phages are grouped into the T7‐like phage genus in the subfamily of the Autographivirinae . Genomes of T7‐type phage have been previously sequenced for phages of Klebsiella pneumonia , for example (Drulis‐Kawa et al ., ), where genes are arranged into three clusters: early genes (cluster I), DNA metabolism (class II) and structural proteins for phage assembly and for host lysis (class III) (Lavigne et al ., ).…”

Section: Resultsmentioning

confidence: 99%

A novel bacteriophage cocktail reduces and disperses Pseudomonas aeruginosa biofilms under static and flow conditions

Alves

Esteban

Kot

et al. 2015

Microbial Biotechnology

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Summary P seudomonas aeruginosa is an opportunistic human pathogen that forms highly stable communities – biofilms, which contribute to the establishment and maintenance of infections. The biofilm state and intrinsic/acquired bacterial resistance mechanisms contribute to resistance/tolerance to antibiotics that is frequently observed in P . aeruginosa isolates. Here we describe the isolation and characterization of six novel lytic bacteriophages: viruses that infect bacteria, which together efficiently infect and kill a wide range of P . aeruginosa clinical isolates. The phages were used to formulate a cocktail with the potential to eliminate P . aeruginosa PAO1 planktonic cultures. Two biofilm models were studied, one static and one dynamic, and the phage cocktail was assessed for its ability to reduce and disperse the biofilm biomass. For the static model, after 4 h of contact with the phage suspension (MOI 10) more than 95% of biofilm biomass was eliminated. In the flow biofilm model, a slower rate of activity by the phage was observed, but 48 h after addition of the phage cocktail the biofilm was dispersed, with most cells eliminated (> 4 logs) comparing with the control. This cocktail has the potential for development as a therapeutic to control P . aeruginosa infections, which are predominantly biofilm centred.

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“…The genus was extended with other Pseudomonas phages (PT2, PT5, phikF77, and LUZ19) (30,31,32), Vibrio phage VP93 (5), and Ralstonia phage RSB1 (25). Recently, Pseudomonas fluorescens phage phi-2 has been proposed as a member of this genus (46).…”

Section: Resultsmentioning

confidence: 99%

“…This recently established phage genus is classified within the Autographivirinae subfamily of the Podoviridae along with the "T7-like viruses" and "SP6-like viruses." It groups phages with a common transcriptional scheme, able to infect a wide range of environmentally important bacteria, such as Vibrio spp., Pseudomonas spp., and Ralstonia solanacearum (5,8,25,30,31,32,33,46).…”

mentioning

confidence: 99%

Bacteriophages LIMElight and LIMEzero of Pantoea agglomerans, Belonging to the “phiKMV-Like Viruses”

Adriaenssens

Ceyssens

Dunon

et al. 2011

Appl Environ Microbiol

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Pantoea agglomerans is a common soil bacterium used in the biocontrol of fungi and bacteria but is also an opportunistic human pathogen. It has been described extensively in this context, but knowledge of bacteriophages infecting this species is limited. Bacteriophages LIMEzero and LIMElight of P. agglomerans are lytic phages, isolated from soil samples, belonging to the Podoviridae and are the first Pantoea phages of this family to be described. The double-stranded DNA ( Pantoea agglomerans bacteria are Gram-negative, nonsporulating, facultatively anaerobic rods that belong to the family of the Enterobacteriaceae. Synonyms of this species name are Enterobacter agglomerans, Erwinia herbicola, and Erwinia milletiae (6, 19). The genus name Pantoea is derived from the Greek word pantoios, which means "of all sorts and sources," a descriptor well reflected in the habitat, since species of the genus have been isolated from plant surfaces, seeds, water, soil, and even humans and animals (3,19,41). Pantoea agglomerans is known in plant production as a biocontrol agent. It is used in postharvest control of a number of fungi (for instance, Penicillium expansum, Rhizopus stolonifer, Monilinia laxa, and Botrytis cinerea) on a wide variety of fruits (18,44,45,54).

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Representational Difference Analysis (RDA) of bacteriophage genomes

Cited by 32 publications

References 19 publications

Contrasted coevolutionary dynamics between a bacterial pathogen and its bacteriophages

Contrasted coevolutionary dynamics between a bacterial pathogen and its bacteriophages

A novel bacteriophage cocktail reduces and disperses Pseudomonas aeruginosa biofilms under static and flow conditions

Bacteriophages LIMElight and LIMEzero of Pantoea agglomerans, Belonging to the “phiKMV-Like Viruses”

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